Starting phenix.real_space_refine on Wed Aug 5 14:01:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8bpr_16164/08_2026/8bpr_16164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpr_16164/08_2026/8bpr_16164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8bpr_16164/08_2026/8bpr_16164.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8bpr_16164/08_2026/8bpr_16164.cif" model { file = "/net/cci-nas-00/data/ceres_data/8bpr_16164/08_2026/8bpr_16164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpr_16164/08_2026/8bpr_16164.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8bpr_16164/08_2026/8bpr_16164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpr_16164/08_2026/8bpr_16164.map" } resolution = 3.65 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= 0.002 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 48 5.49 5 Mg 2 5.21 5 S 19 5.16 5 C 6066 2.51 5 N 1944 2.21 5 O 1973 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10055 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 2660 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 Conformer: "B" Number of residues, atoms: 341, 2652 Classifications: {'peptide': 341} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 322} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'GLU:plan': 2} Unresolved non-hydrogen planarities: 8 bond proxies already assigned to first conformer: 2692 Chain: "B" Number of atoms: 2643 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 340, 2635 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 340, 2635 Classifications: {'peptide': 340} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 17, 'TRANS': 322} Chain breaks: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 2673 Chain: "C" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 203 Classifications: {'peptide': 41} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 774 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 774 Classifications: {'peptide': 157} Incomplete info: {'truncation_to_alanine': 118} Link IDs: {'PTRANS': 6, 'TRANS': 150} Chain breaks: 4 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 558 Unresolved non-hydrogen dihedrals: 346 Unresolved non-hydrogen chiralities: 47 Planarities with less than four sites: {'GLU:plan': 21, 'ARG:plan': 15, 'GLN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 245 Chain: "E" Number of atoms: 861 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 861 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 132} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 3 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 488 Unresolved non-hydrogen angles: 622 Unresolved non-hydrogen dihedrals: 389 Unresolved non-hydrogen chiralities: 53 Planarities with less than four sites: {'ARG:plan': 15, 'GLN:plan1': 2, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 24, 'ASN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 5} Unresolved non-hydrogen planarities: 262 Chain: "F" Number of atoms: 1005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1005 Classifications: {'peptide': 154} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 6, 'TRANS': 147} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 170 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 136 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'GLU:plan': 9, 'ARG:plan': 5, 'GLN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "G" Number of atoms: 945 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 945 Classifications: {'peptide': 193} Incomplete info: {'truncation_to_alanine': 148} Link IDs: {'PTRANS': 14, 'TRANS': 178} Chain breaks: 4 Unresolved chain link angles: 14 Unresolved non-hydrogen bonds: 578 Unresolved non-hydrogen angles: 741 Unresolved non-hydrogen dihedrals: 477 Unresolved non-hydrogen chiralities: 62 Planarities with less than four sites: {'GLU:plan': 17, 'ARG:plan': 19, 'GLN:plan1': 4, 'ASP:plan': 2, 'PHE:plan': 5, 'HIS:plan': 6, 'TYR:plan': 4, 'TRP:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 294 Chain: "X" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 426 Classifications: {'DNA': 21} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 20} Chain: "Y" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" 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 5739 SG CYS D 55 43.572 87.803 58.251 1.00187.00 S ATOM 5755 SG CYS D 58 40.684 86.789 56.482 1.00186.50 S ATOM 5799 SG CYS D 67 43.623 86.075 55.256 1.00198.45 S ATOM 5815 SG CYS D 70 41.299 88.973 54.452 1.00194.96 S ATOM 6485 SG CYS E 55 18.226 31.458 61.849 1.00388.72 S ATOM 6501 SG CYS E 58 19.386 34.024 62.778 1.00384.50 S ATOM 6545 SG CYS E 67 17.483 33.088 65.781 1.00324.74 S ATOM 6561 SG CYS E 70 15.165 33.476 63.024 1.00332.08 S ATOM 7380 SG CYS F 55 68.613 12.947 73.407 1.00115.77 S ATOM 7396 SG CYS F 58 68.887 15.480 74.630 1.00 97.49 S ATOM 7440 SG CYS F 67 69.461 16.970 72.486 1.00131.47 S ATOM 7456 SG CYS F 70 72.318 14.522 72.967 1.00134.38 S Time building chain proxies: 3.47, per 1000 atoms: 0.35 Number of scatterers: 10055 At special positions: 0 Unit cell: (96.32, 100.62, 165.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 19 16.00 P 48 15.00 Mg 2 11.99 O 1973 8.00 N 1944 7.00 C 6066 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=0, symmetry=0 Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 768.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 201 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 70 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 67 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 55 " pdb="ZN ZN D 201 " - pdb=" SG CYS D 58 " pdb=" ZN E 201 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 67 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 70 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 55 " pdb="ZN ZN E 201 " - pdb=" SG CYS E 58 " pdb=" ZN F 201 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 67 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 70 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 58 " pdb="ZN ZN F 201 " - pdb=" SG CYS F 55 " Number of angles added : 18 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2540 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 13 sheets defined 52.5% alpha, 14.1% beta 11 base pairs and 42 stacking pairs defined. Time for finding SS restraints: 1.33 Creating SS restraints... Processing helix chain 'A' and resid 35 through 47 Processing helix chain 'A' and resid 54 through 58 Processing helix chain 'A' and resid 100 through 107 Processing helix chain 'A' and resid 114 through 122 removed outlier: 4.173A pdb=" N LEU A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 138 removed outlier: 3.680A pdb=" N ARG A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 163 removed outlier: 3.976A pdb=" N ALA A 163 " --> pdb=" O ALA A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 202 removed outlier: 3.896A pdb=" N TYR A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N GLU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) Proline residue: A 195 - end of helix Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 241 through 245 removed outlier: 3.512A pdb=" N ASP A 245 " --> pdb=" O PRO A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 285 Processing helix chain 'A' and resid 300 through 312 Processing helix chain 'B' and resid 35 through 47 removed outlier: 3.541A pdb=" N LEU B 47 " --> pdb=" O ILE B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 105 removed outlier: 3.876A pdb=" N LEU B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 117 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 124 through 138 Processing helix chain 'B' and resid 141 through 163 removed outlier: 3.947A pdb=" N ALA B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA B 163 " --> pdb=" O ALA B 159 " (cutoff:3.500A) Processing helix chain 'B' and resid 169 through 205 removed outlier: 4.061A pdb=" N GLU B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ALA B 184 " --> pdb=" O ASP B 180 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ARG B 192 " --> pdb=" O ARG B 188 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALA B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Proline residue: B 195 - end of helix Processing helix chain 'B' and resid 220 through 227 Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 241 through 245 removed outlier: 3.530A pdb=" N ASP B 245 " --> pdb=" O PRO B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 256 through 260 Processing helix chain 'B' and resid 261 through 285 Processing helix chain 'B' and resid 300 through 312 Processing helix chain 'C' and resid 5 through 16 Processing helix chain 'C' and resid 22 through 35 Processing helix chain 'C' and resid 35 through 48 Processing helix chain 'D' and resid 5 through 17 removed outlier: 4.300A pdb=" N LYS D 9 " --> pdb=" O GLU D 5 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N LEU D 10 " --> pdb=" O SER D 6 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 17 " --> pdb=" O ALA D 13 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 34 removed outlier: 3.852A pdb=" N PHE D 34 " --> pdb=" O LEU D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 47 removed outlier: 4.503A pdb=" N GLU D 47 " --> pdb=" O ALA D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 96 Processing helix chain 'D' and resid 125 through 129 Processing helix chain 'D' and resid 142 through 153 Processing helix chain 'D' and resid 175 through 179 removed outlier: 3.767A pdb=" N ALA D 179 " --> pdb=" O LEU D 176 " (cutoff:3.500A) Processing helix chain 'D' and resid 180 through 190 Processing helix chain 'E' and resid 10 through 17 removed outlier: 3.615A pdb=" N LEU E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 23 through 35 Processing helix chain 'E' and resid 35 through 50 Processing helix chain 'E' and resid 85 through 96 Processing helix chain 'E' and resid 110 through 114 Processing helix chain 'E' and resid 121 through 127 Processing helix chain 'E' and resid 142 through 159 Processing helix chain 'E' and resid 180 through 190 Processing helix chain 'F' and resid 5 through 17 Processing helix chain 'F' and resid 21 through 35 Processing helix chain 'F' and resid 36 through 47 removed outlier: 3.836A pdb=" N GLU F 40 " --> pdb=" O LYS F 36 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLU F 47 " --> pdb=" O ALA F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 96 removed outlier: 3.772A pdb=" N SER F 95 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N GLY F 96 " --> pdb=" O LEU F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 126 Processing helix chain 'F' and resid 127 through 129 No H-bonds generated for 'chain 'F' and resid 127 through 129' Processing helix chain 'F' and resid 142 through 160 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.925A pdb=" N GLU G 91 " --> pdb=" O HIS G 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 109 Processing helix chain 'G' and resid 114 through 132 Proline residue: G 120 - end of helix Processing helix chain 'G' and resid 135 through 150 removed outlier: 3.516A pdb=" N ARG G 145 " --> pdb=" O TRP G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 189 removed outlier: 3.545A pdb=" N GLY G 179 " --> pdb=" O LEU G 175 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 199 Proline residue: G 196 - end of helix Processing helix chain 'G' and resid 206 through 219 Processing helix chain 'G' and resid 221 through 226 removed outlier: 3.941A pdb=" N GLU G 225 " --> pdb=" O ARG G 222 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 9 removed outlier: 5.337A pdb=" N LEU A 3 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLU A 73 " --> pdb=" O LEU A 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 113 removed outlier: 3.600A pdb=" N LEU A 319 " --> pdb=" O SER A 26 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N CYS A 331 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA A 27 " --> pdb=" O CYS A 331 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N VAL A 333 " --> pdb=" O ALA A 27 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL A 29 " --> pdb=" O VAL A 333 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 92 through 94 removed outlier: 4.400A pdb=" N VAL A 92 " --> pdb=" O VAL A 99 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS A 97 " --> pdb=" O LEU A 94 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 209 through 214 removed outlier: 3.613A pdb=" N ASP A 246 " --> pdb=" O GLU A 214 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 9 removed outlier: 6.137A pdb=" N LEU B 3 " --> pdb=" O GLU B 73 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N GLU B 73 " --> pdb=" O LEU B 3 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU B 93 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 113 removed outlier: 6.186A pdb=" N VAL B 111 " --> pdb=" O LEU B 291 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ASP B 293 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL B 113 " --> pdb=" O ASP B 293 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N LEU B 290 " --> pdb=" O GLN B 316 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N GLY B 24 " --> pdb=" O ALA B 317 " (cutoff:3.500A) removed outlier: 7.719A pdb=" N LEU B 319 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N SER B 26 " --> pdb=" O LEU B 319 " (cutoff:3.500A) removed outlier: 8.340A pdb=" N GLY B 321 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LEU B 28 " --> pdb=" O GLY B 321 " (cutoff:3.500A) removed outlier: 9.037A pdb=" N CYS B 331 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA B 27 " --> pdb=" O CYS B 331 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL B 333 " --> pdb=" O ALA B 27 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N VAL B 29 " --> pdb=" O VAL B 333 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 209 through 214 removed outlier: 3.533A pdb=" N ASP B 246 " --> pdb=" O GLU B 214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 100 through 101 removed outlier: 7.166A pdb=" N ASP D 76 " --> pdb=" O LEU D 101 " (cutoff:3.500A) removed outlier: 10.564A pdb=" N GLU D 134 " --> pdb=" O ASP D 76 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N SER D 78 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N VAL D 136 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU D 80 " --> pdb=" O VAL D 136 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N VAL D 135 " --> pdb=" O THR D 164 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 192 through 193 removed outlier: 6.046A pdb=" N VAL E 135 " --> pdb=" O THR E 164 " (cutoff:3.500A) removed outlier: 7.539A pdb=" N LEU E 80 " --> pdb=" O VAL E 136 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N ALA E 138 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL E 82 " --> pdb=" O ALA E 138 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N HIS E 103 " --> pdb=" O ALA E 81 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N VAL E 83 " --> pdb=" O HIS E 103 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.673A pdb=" N ARG F 53 " --> pdb=" O ALA F 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 101 through 104 removed outlier: 6.135A pdb=" N ALA F 81 " --> pdb=" O HIS F 103 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU F 80 " --> pdb=" O VAL F 136 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'G' and resid 15 through 24 removed outlier: 6.362A pdb=" N VAL G 19 " --> pdb=" O VAL G 35 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL G 35 " --> pdb=" O VAL G 19 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N LEU G 78 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N VAL G 44 " --> pdb=" O LEU G 78 " (cutoff:3.500A) removed outlier: 8.554A pdb=" N GLN G 80 " --> pdb=" O VAL G 44 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N GLN G 67 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N ALA G 81 " --> pdb=" O ARG G 65 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ARG G 65 " --> pdb=" O ALA G 81 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N LEU G 83 " --> pdb=" O HIS G 63 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N HIS G 63 " --> pdb=" O LEU G 83 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 167 through 169 removed outlier: 3.560A pdb=" N LEU G 163 " --> pdb=" O VAL G 173 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL G 173 " --> pdb=" O LEU G 163 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1598 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 42 stacking parallelities Total time for adding SS restraints: 1.51 Time building geometry restraints manager: 0.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3129 1.34 - 1.45: 1455 1.45 - 1.57: 5550 1.57 - 1.69: 94 1.69 - 1.81: 22 Bond restraints: 10250 Sorted by residual: bond pdb=" N3B ANP B 901 " pdb=" PG ANP B 901 " ideal model delta sigma weight residual 1.795 1.629 0.166 2.00e-02 2.50e+03 6.86e+01 bond pdb=" N3B ANP A 901 " pdb=" PG ANP A 901 " ideal model delta sigma weight residual 1.795 1.631 0.164 2.00e-02 2.50e+03 6.73e+01 bond pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.54e+01 bond pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 1.700 1.622 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C3' DT X 19 " pdb=" C2' DT X 19 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.75e+00 ... (remaining 10245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 13996 2.20 - 4.40: 130 4.40 - 6.60: 13 6.60 - 8.80: 5 8.80 - 11.01: 2 Bond angle restraints: 14146 Sorted by residual: angle pdb=" N3 DT X 10 " pdb=" C4 DT X 10 " pdb=" O4 DT X 10 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" N3 DT X 19 " pdb=" C4 DT X 19 " pdb=" O4 DT X 19 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT Y 19 " pdb=" C4 DT Y 19 " pdb=" O4 DT Y 19 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT Y 21 " pdb=" C4 DT Y 21 " pdb=" O4 DT Y 21 " ideal model delta sigma weight residual 119.90 122.34 -2.44 6.00e-01 2.78e+00 1.66e+01 angle pdb=" N3 DT X 8 " pdb=" C4 DT X 8 " pdb=" O4 DT X 8 " ideal model delta sigma weight residual 119.90 122.33 -2.43 6.00e-01 2.78e+00 1.63e+01 ... (remaining 14141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5264 17.95 - 35.89: 427 35.89 - 53.84: 229 53.84 - 71.79: 20 71.79 - 89.73: 4 Dihedral angle restraints: 5944 sinusoidal: 2004 harmonic: 3940 Sorted by residual: dihedral pdb=" CA ALA E 167 " pdb=" C ALA E 167 " pdb=" N TYR E 168 " pdb=" CA TYR E 168 " ideal model delta harmonic sigma weight residual 180.00 161.80 18.20 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA GLU D 133 " pdb=" C GLU D 133 " pdb=" N GLU D 134 " pdb=" CA GLU D 134 " ideal model delta harmonic sigma weight residual 180.00 162.17 17.83 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ARG D 127 " pdb=" C ARG D 127 " pdb=" N ARG D 128 " pdb=" CA ARG D 128 " ideal model delta harmonic sigma weight residual 180.00 162.86 17.14 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1463 0.057 - 0.113: 208 0.113 - 0.170: 4 0.170 - 0.227: 0 0.227 - 0.283: 2 Chirality restraints: 1677 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP A 901 " pdb=" C2' ANP A 901 " pdb=" C4' ANP A 901 " pdb=" O3' ANP A 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA VAL F 161 " pdb=" N VAL F 161 " pdb=" C VAL F 161 " pdb=" CB VAL F 161 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.15 2.00e-01 2.50e+01 5.98e-01 ... (remaining 1674 not shown) Planarity restraints: 1745 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP E 88 " -0.006 2.00e-02 2.50e+03 1.28e-02 1.63e+00 pdb=" C ASP E 88 " 0.022 2.00e-02 2.50e+03 pdb=" O ASP E 88 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU E 89 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER A 114 " 0.021 5.00e-02 4.00e+02 3.14e-02 1.57e+00 pdb=" N PRO A 115 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 115 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 115 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 123 " 0.021 5.00e-02 4.00e+02 3.12e-02 1.56e+00 pdb=" N PRO A 124 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO A 124 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 124 " 0.017 5.00e-02 4.00e+02 ... (remaining 1742 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 60 2.64 - 3.20: 8305 3.20 - 3.77: 14384 3.77 - 4.33: 17909 4.33 - 4.90: 29849 Nonbonded interactions: 70507 Sorted by model distance: nonbonded pdb=" O2G ANP B 901 " pdb="MG MG B 902 " model vdw 2.072 2.170 nonbonded pdb=" OG1 THR B 37 " pdb="MG MG B 902 " model vdw 2.078 2.170 nonbonded pdb=" O1B ANP B 901 " pdb="MG MG B 902 " model vdw 2.115 2.170 nonbonded pdb=" O1B ANP A 901 " pdb="MG MG A 902 " model vdw 2.132 2.170 nonbonded pdb=" O2G ANP A 901 " pdb="MG MG A 902 " model vdw 2.145 2.170 ... (remaining 70502 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 51 or resid 53 through 72 or (resid 73 and (name \ N or name CA or name C or name O or name CB )) or resid 74 through 96 or (resid \ 97 and (name N or name CA or name C or name O or name CB )) or resid 98 through \ 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) or r \ esid 142 through 165 or (resid 166 and (name N or name CA or name C or name O or \ name CB )) or resid 167 through 191 or resid 193 through 197 or resid 199 throu \ gh 902)) selection = (chain 'B' and (resid 1 through 49 or (resid 50 and (name N or name CA or name C \ or name O or name CB )) or resid 51 through 191 or resid 193 through 197 or res \ id 199 through 285 or (resid 286 and (name N or name CA or name C or name O or n \ ame CB )) or resid 287 through 902)) } ncs_group { reference = (chain 'D' and (resid 9 through 18 or resid 22 through 71 or resid 77 through 20 \ 1)) selection = (chain 'E' and (resid 9 through 48 or resid 54 through 102 or resid 122 through \ 153 or resid 162 through 201)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.920 Find NCS groups from input model: 0.140 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:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 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 : 0.004 0.166 10262 Z= 0.282 Angle : 0.974 46.607 14164 Z= 0.364 Chirality : 0.039 0.283 1677 Planarity : 0.003 0.031 1745 Dihedral : 16.792 89.732 3404 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.66 % Allowed : 0.00 % Favored : 99.34 % 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 are not related in a simple way. whole: 0.86 (0.23), residues: 1359 helix: 1.80 (0.21), residues: 638 sheet: 0.54 (0.37), residues: 193 loop : -0.96 (0.26), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 335 TYR 0.004 0.001 TYR B 178 PHE 0.007 0.001 PHE B 6 TRP 0.006 0.001 TRP A 105 HIS 0.003 0.001 HIS A 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.28 (10250) covalent geometry : angle 0.54547 / 0.33 (14146) hydrogen bonds : bond 0.19107 / 12.28 ( 594) hydrogen bonds : angle 5.79913 / 4.15 ( 1652) metal coordination : bond 0.01055 / 0.62 ( 12) metal coordination : angle 22.64220 / 13.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 174 time to evaluate : 0.292 Fit side-chains revert: symmetry clash REVERT: A 32 ASN cc_start: 0.7231 (m-40) cc_final: 0.6879 (t0) REVERT: A 34 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7380 (mp10) REVERT: A 55 LEU cc_start: 0.8863 (tp) cc_final: 0.8516 (tp) REVERT: B 131 TYR cc_start: 0.8732 (t80) cc_final: 0.8480 (t80) REVERT: F 129 LEU cc_start: 0.8463 (mm) cc_final: 0.8256 (tp) outliers start: 1 outliers final: 0 residues processed: 174 average time/residue: 0.1283 time to fit residues: 28.7858 Evaluate side-chains 96 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 98 optimal weight: 0.0980 chunk 107 optimal weight: 8.9990 chunk 10 optimal weight: 0.3980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 40.0000 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 20.0000 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.147930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.097309 restraints weight = 30242.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.100136 restraints weight = 16559.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.101861 restraints weight = 8796.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.101969 restraints weight = 7511.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.101637 restraints weight = 6233.361| |-----------------------------------------------------------------------------| r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 10262 Z= 0.285 Angle : 0.858 26.980 14164 Z= 0.405 Chirality : 0.047 0.253 1677 Planarity : 0.006 0.053 1745 Dihedral : 16.672 76.850 1956 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.64 % Allowed : 10.60 % Favored : 85.76 % 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 are not related in a simple way. whole: 0.97 (0.23), residues: 1359 helix: 2.07 (0.20), residues: 655 sheet: 0.21 (0.36), residues: 201 loop : -1.12 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 94 TYR 0.022 0.003 TYR F 102 PHE 0.030 0.003 PHE A 259 TRP 0.018 0.003 TRP B 171 HIS 0.012 0.003 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00651 / 0.29 (10250) covalent geometry : angle 0.78285 / 0.40 (14146) hydrogen bonds : bond 0.05794 / 3.90 ( 594) hydrogen bonds : angle 4.46622 / 3.18 ( 1652) metal coordination : bond 0.01001 / 0.64 ( 12) metal coordination : angle 9.87274 / 5.53 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 90 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8369 (mp0) cc_final: 0.8119 (mp0) REVERT: B 131 TYR cc_start: 0.8786 (t80) cc_final: 0.8471 (t80) REVERT: B 245 ASP cc_start: 0.8878 (m-30) cc_final: 0.8659 (m-30) REVERT: F 90 TYR cc_start: 0.8147 (OUTLIER) cc_final: 0.7617 (m-80) REVERT: F 129 LEU cc_start: 0.9062 (mm) cc_final: 0.8629 (tt) REVERT: F 144 GLU cc_start: 0.8557 (mp0) cc_final: 0.8314 (mt-10) outliers start: 19 outliers final: 14 residues processed: 102 average time/residue: 0.1062 time to fit residues: 15.1919 Evaluate side-chains 91 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 LEU Chi-restraints excluded: chain F residue 161 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 89 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 131 optimal weight: 50.0000 chunk 71 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 141 optimal weight: 9.9990 chunk 85 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 34 GLN B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.147298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.093662 restraints weight = 29809.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.096700 restraints weight = 13629.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.098700 restraints weight = 8519.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.099934 restraints weight = 6377.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.100635 restraints weight = 5355.712| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3499 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3499 r_free = 0.3499 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3499 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10262 Z= 0.139 Angle : 0.617 19.724 14164 Z= 0.292 Chirality : 0.040 0.160 1677 Planarity : 0.004 0.041 1745 Dihedral : 16.614 73.156 1956 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.98 % Allowed : 13.25 % Favored : 83.77 % 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 are not related in a simple way. whole: 1.49 (0.23), residues: 1359 helix: 2.57 (0.21), residues: 657 sheet: 0.52 (0.36), residues: 197 loop : -1.03 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 98 TYR 0.018 0.001 TYR F 102 PHE 0.015 0.001 PHE A 259 TRP 0.008 0.001 TRP B 105 HIS 0.004 0.002 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.14 (10250) covalent geometry : angle 0.55935 / 0.29 (14146) hydrogen bonds : bond 0.04490 / 2.99 ( 594) hydrogen bonds : angle 3.94757 / 2.77 ( 1652) metal coordination : bond 0.00538 / 0.36 ( 12) metal coordination : angle 7.32330 / 3.99 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 83 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8566 (mm-40) cc_final: 0.8356 (mm110) REVERT: A 102 ARG cc_start: 0.8609 (mmt90) cc_final: 0.8399 (mmt90) REVERT: B 131 TYR cc_start: 0.8860 (t80) cc_final: 0.8513 (t80) REVERT: B 245 ASP cc_start: 0.8938 (m-30) cc_final: 0.8616 (m-30) REVERT: F 90 TYR cc_start: 0.7813 (OUTLIER) cc_final: 0.7316 (m-80) REVERT: F 115 ILE cc_start: 0.9324 (mt) cc_final: 0.8787 (tt) REVERT: F 127 ARG cc_start: 0.9107 (ppt170) cc_final: 0.8338 (ppt170) REVERT: F 129 LEU cc_start: 0.8867 (mm) cc_final: 0.8473 (tt) REVERT: F 144 GLU cc_start: 0.8547 (mp0) cc_final: 0.8336 (mt-10) outliers start: 15 outliers final: 11 residues processed: 89 average time/residue: 0.1076 time to fit residues: 13.3778 Evaluate side-chains 88 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 0.0010 chunk 81 optimal weight: 20.0000 chunk 23 optimal weight: 0.5980 chunk 30 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 131 optimal weight: 50.0000 chunk 140 optimal weight: 9.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.147630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.096835 restraints weight = 26138.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.098494 restraints weight = 15022.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.100460 restraints weight = 8785.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.100437 restraints weight = 7003.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.100372 restraints weight = 5801.780| |-----------------------------------------------------------------------------| r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10262 Z= 0.115 Angle : 0.560 14.147 14164 Z= 0.274 Chirality : 0.038 0.150 1677 Planarity : 0.004 0.043 1745 Dihedral : 16.590 75.401 1956 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.15 % Allowed : 14.90 % Favored : 81.95 % 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 are not related in a simple way. whole: 1.82 (0.23), residues: 1359 helix: 2.82 (0.20), residues: 658 sheet: 0.93 (0.36), residues: 187 loop : -0.92 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 128 TYR 0.007 0.001 TYR A 310 PHE 0.009 0.001 PHE A 259 TRP 0.008 0.001 TRP B 105 HIS 0.004 0.001 HIS B 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00241 / 0.11 (10250) covalent geometry : angle 0.52559 / 0.27 (14146) hydrogen bonds : bond 0.03660 / 2.44 ( 594) hydrogen bonds : angle 3.72513 / 2.61 ( 1652) metal coordination : bond 0.00359 / 0.23 ( 12) metal coordination : angle 5.41482 / 2.89 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.393 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8415 (mm-40) cc_final: 0.7887 (mp10) REVERT: A 102 ARG cc_start: 0.8681 (mmt90) cc_final: 0.8412 (mmt90) REVERT: B 131 TYR cc_start: 0.8877 (t80) cc_final: 0.8496 (t80) REVERT: B 245 ASP cc_start: 0.9013 (m-30) cc_final: 0.8590 (m-30) REVERT: B 312 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8595 (tp40) REVERT: F 90 TYR cc_start: 0.8017 (OUTLIER) cc_final: 0.7504 (m-80) REVERT: F 115 ILE cc_start: 0.9313 (mt) cc_final: 0.8771 (tt) REVERT: F 129 LEU cc_start: 0.9094 (mm) cc_final: 0.8661 (tt) REVERT: F 144 GLU cc_start: 0.8533 (mp0) cc_final: 0.8319 (mt-10) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.1019 time to fit residues: 12.3657 Evaluate side-chains 91 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 80 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 78 optimal weight: 40.0000 chunk 56 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 106 optimal weight: 7.9990 chunk 105 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 119 optimal weight: 50.0000 chunk 139 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.147746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.104365 restraints weight = 38396.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.100454 restraints weight = 20591.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.101381 restraints weight = 14777.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101667 restraints weight = 11726.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.101909 restraints weight = 9539.458| |-----------------------------------------------------------------------------| r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3527 r_free = 0.3527 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10262 Z= 0.169 Angle : 0.604 10.894 14164 Z= 0.302 Chirality : 0.040 0.168 1677 Planarity : 0.004 0.038 1745 Dihedral : 16.635 79.609 1956 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.15 % Allowed : 15.56 % Favored : 81.29 % 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 are not related in a simple way. whole: 1.81 (0.23), residues: 1359 helix: 2.81 (0.20), residues: 658 sheet: 0.77 (0.36), residues: 193 loop : -0.87 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 162 TYR 0.009 0.001 TYR A 143 PHE 0.019 0.002 PHE A 259 TRP 0.009 0.001 TRP B 105 HIS 0.007 0.002 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (10250) covalent geometry : angle 0.58105 / 0.30 (14146) hydrogen bonds : bond 0.04409 / 2.95 ( 594) hydrogen bonds : angle 3.80851 / 2.68 ( 1652) metal coordination : bond 0.00470 / 0.30 ( 12) metal coordination : angle 4.63511 / 2.51 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 70 time to evaluate : 0.377 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8545 (mm-40) cc_final: 0.7959 (mp10) REVERT: A 102 ARG cc_start: 0.8680 (mmt90) cc_final: 0.8467 (mmt90) REVERT: A 231 GLU cc_start: 0.8669 (mp0) cc_final: 0.8174 (mp0) REVERT: B 131 TYR cc_start: 0.8815 (t80) cc_final: 0.8408 (t80) REVERT: B 245 ASP cc_start: 0.9035 (m-30) cc_final: 0.8832 (m-30) REVERT: B 312 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8632 (tm-30) REVERT: F 90 TYR cc_start: 0.7931 (OUTLIER) cc_final: 0.7396 (m-80) REVERT: F 115 ILE cc_start: 0.9267 (mt) cc_final: 0.8838 (tt) REVERT: F 129 LEU cc_start: 0.9029 (mm) cc_final: 0.8607 (tt) REVERT: F 144 GLU cc_start: 0.8513 (mp0) cc_final: 0.8282 (mt-10) outliers start: 16 outliers final: 13 residues processed: 80 average time/residue: 0.1155 time to fit residues: 12.8313 Evaluate side-chains 83 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 122 optimal weight: 50.0000 chunk 34 optimal weight: 3.9990 chunk 131 optimal weight: 50.0000 chunk 78 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 87 optimal weight: 9.9990 chunk 74 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 HIS ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 243 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.141266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.093180 restraints weight = 35910.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.090314 restraints weight = 21710.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.092362 restraints weight = 16351.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.093164 restraints weight = 10389.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.093218 restraints weight = 9077.023| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.4305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.072 10262 Z= 0.452 Angle : 0.975 13.816 14164 Z= 0.474 Chirality : 0.050 0.180 1677 Planarity : 0.007 0.086 1745 Dihedral : 17.190 85.209 1956 Min Nonbonded Distance : 1.780 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 4.30 % Allowed : 15.73 % Favored : 79.97 % 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 are not related in a simple way. whole: 0.84 (0.23), residues: 1359 helix: 1.98 (0.20), residues: 656 sheet: 0.19 (0.36), residues: 186 loop : -1.21 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG F 162 TYR 0.024 0.003 TYR A 150 PHE 0.050 0.004 PHE A 259 TRP 0.019 0.003 TRP A 295 HIS 0.019 0.004 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.01047 / 0.45 (10250) covalent geometry : angle 0.95150 / 0.47 (14146) hydrogen bonds : bond 0.07354 / 4.98 ( 594) hydrogen bonds : angle 4.71844 / 3.33 ( 1652) metal coordination : bond 0.01378 / 0.91 ( 12) metal coordination : angle 6.10425 / 3.35 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 65 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8633 (mm-40) cc_final: 0.8238 (mp10) REVERT: B 39 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8820 (tt) REVERT: B 312 GLN cc_start: 0.9020 (tm-30) cc_final: 0.8641 (tm-30) REVERT: F 90 TYR cc_start: 0.8175 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: F 115 ILE cc_start: 0.9260 (mt) cc_final: 0.8833 (tt) REVERT: F 129 LEU cc_start: 0.9141 (mm) cc_final: 0.8663 (tp) outliers start: 23 outliers final: 18 residues processed: 83 average time/residue: 0.1133 time to fit residues: 13.2060 Evaluate side-chains 81 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 322 LEU Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 39 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 42 optimal weight: 0.3980 chunk 65 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 125 optimal weight: 20.0000 chunk 136 optimal weight: 9.9990 chunk 74 optimal weight: 5.9990 chunk 92 optimal weight: 3.9990 chunk 129 optimal weight: 5.9990 chunk 36 optimal weight: 0.0010 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.145966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.102968 restraints weight = 49322.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.099214 restraints weight = 24073.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.100971 restraints weight = 15997.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.100535 restraints weight = 12402.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101136 restraints weight = 10558.688| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 10262 Z= 0.142 Angle : 0.640 11.704 14164 Z= 0.317 Chirality : 0.040 0.202 1677 Planarity : 0.004 0.046 1745 Dihedral : 16.851 79.181 1956 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.48 % Allowed : 19.87 % Favored : 77.65 % 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 are not related in a simple way. whole: 1.54 (0.23), residues: 1359 helix: 2.63 (0.20), residues: 658 sheet: 0.42 (0.35), residues: 207 loop : -1.01 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 162 TYR 0.016 0.001 TYR B 131 PHE 0.015 0.001 PHE A 259 TRP 0.011 0.001 TRP B 105 HIS 0.004 0.002 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.14 (10250) covalent geometry : angle 0.61923 / 0.32 (14146) hydrogen bonds : bond 0.04558 / 3.03 ( 594) hydrogen bonds : angle 3.92163 / 2.74 ( 1652) metal coordination : bond 0.00426 / 0.26 ( 12) metal coordination : angle 4.53207 / 2.37 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.245 Fit side-chains REVERT: A 34 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8159 (mp10) REVERT: A 119 GLU cc_start: 0.8533 (tm-30) cc_final: 0.8093 (tm-30) REVERT: B 131 TYR cc_start: 0.8837 (t80) cc_final: 0.8460 (t80) REVERT: B 312 GLN cc_start: 0.9034 (tm-30) cc_final: 0.8650 (tm-30) REVERT: F 90 TYR cc_start: 0.8104 (OUTLIER) cc_final: 0.7561 (m-80) REVERT: F 115 ILE cc_start: 0.9228 (mt) cc_final: 0.8782 (tt) REVERT: F 129 LEU cc_start: 0.9044 (mm) cc_final: 0.8582 (tp) outliers start: 12 outliers final: 10 residues processed: 79 average time/residue: 0.1053 time to fit residues: 11.7400 Evaluate side-chains 78 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 9.9990 chunk 83 optimal weight: 50.0000 chunk 24 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 125 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 91 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.145350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.102123 restraints weight = 42674.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.097804 restraints weight = 21764.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.099650 restraints weight = 14357.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.099534 restraints weight = 10623.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.099932 restraints weight = 9436.502| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10262 Z= 0.167 Angle : 0.631 10.717 14164 Z= 0.311 Chirality : 0.040 0.184 1677 Planarity : 0.004 0.042 1745 Dihedral : 16.802 83.402 1956 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.65 % Allowed : 19.70 % Favored : 77.65 % 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 are not related in a simple way. whole: 1.68 (0.23), residues: 1359 helix: 2.77 (0.20), residues: 662 sheet: 0.38 (0.35), residues: 204 loop : -0.93 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 162 TYR 0.013 0.001 TYR B 131 PHE 0.017 0.002 PHE A 259 TRP 0.011 0.001 TRP B 105 HIS 0.007 0.002 HIS B 277 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (10250) covalent geometry : angle 0.61420 / 0.31 (14146) hydrogen bonds : bond 0.04471 / 2.98 ( 594) hydrogen bonds : angle 3.83641 / 2.68 ( 1652) metal coordination : bond 0.00454 / 0.28 ( 12) metal coordination : angle 4.04373 / 2.15 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 66 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8562 (mm-40) cc_final: 0.8075 (mp10) REVERT: A 102 ARG cc_start: 0.8562 (mmt90) cc_final: 0.8325 (mmt90) REVERT: A 119 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7948 (tm-30) REVERT: B 39 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8771 (tt) REVERT: B 131 TYR cc_start: 0.8854 (t80) cc_final: 0.8444 (t80) REVERT: B 312 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8646 (tm-30) REVERT: F 90 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7541 (m-80) REVERT: F 115 ILE cc_start: 0.9201 (mt) cc_final: 0.8769 (tt) REVERT: F 127 ARG cc_start: 0.9195 (ppt170) cc_final: 0.8814 (ppt170) REVERT: F 129 LEU cc_start: 0.9090 (mm) cc_final: 0.8637 (tp) outliers start: 13 outliers final: 11 residues processed: 74 average time/residue: 0.1117 time to fit residues: 11.7619 Evaluate side-chains 78 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 65 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 53 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 109 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 91 optimal weight: 10.0000 chunk 117 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.146928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.094649 restraints weight = 32657.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.099086 restraints weight = 15979.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.100220 restraints weight = 8019.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.100158 restraints weight = 6678.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.100490 restraints weight = 6978.108| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3495 r_free = 0.3495 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10262 Z= 0.117 Angle : 0.587 11.601 14164 Z= 0.290 Chirality : 0.038 0.204 1677 Planarity : 0.004 0.044 1745 Dihedral : 16.672 80.359 1956 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.48 % Allowed : 20.03 % Favored : 77.48 % 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 are not related in a simple way. whole: 1.91 (0.24), residues: 1359 helix: 2.94 (0.20), residues: 663 sheet: 0.55 (0.36), residues: 206 loop : -0.83 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 223 TYR 0.014 0.001 TYR B 131 PHE 0.010 0.001 PHE A 259 TRP 0.012 0.001 TRP B 105 HIS 0.008 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.12 (10250) covalent geometry : angle 0.57510 / 0.29 (14146) hydrogen bonds : bond 0.03737 / 2.47 ( 594) hydrogen bonds : angle 3.67173 / 2.56 ( 1652) metal coordination : bond 0.00282 / 0.16 ( 12) metal coordination : angle 3.31506 / 1.72 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.375 Fit side-chains REVERT: A 34 GLN cc_start: 0.8564 (mm-40) cc_final: 0.8043 (mp10) REVERT: B 131 TYR cc_start: 0.8895 (t80) cc_final: 0.8486 (t80) REVERT: B 312 GLN cc_start: 0.9035 (tm-30) cc_final: 0.8610 (tm-30) REVERT: F 90 TYR cc_start: 0.8129 (OUTLIER) cc_final: 0.7618 (m-80) REVERT: F 115 ILE cc_start: 0.9207 (mt) cc_final: 0.8707 (tt) REVERT: F 129 LEU cc_start: 0.9147 (mm) cc_final: 0.8700 (tp) outliers start: 12 outliers final: 10 residues processed: 77 average time/residue: 0.1098 time to fit residues: 11.9688 Evaluate side-chains 76 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 16 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 0.4980 chunk 103 optimal weight: 30.0000 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 75 optimal weight: 0.6980 chunk 124 optimal weight: 30.0000 chunk 100 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.143504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.101390 restraints weight = 47297.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.097547 restraints weight = 23505.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.098722 restraints weight = 16350.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.099722 restraints weight = 10936.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099796 restraints weight = 9700.327| |-----------------------------------------------------------------------------| r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10262 Z= 0.144 Angle : 0.598 10.606 14164 Z= 0.297 Chirality : 0.039 0.191 1677 Planarity : 0.004 0.043 1745 Dihedral : 16.696 81.241 1956 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.98 % Allowed : 19.70 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.24), residues: 1359 helix: 2.97 (0.20), residues: 663 sheet: 0.61 (0.36), residues: 205 loop : -0.78 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 162 TYR 0.013 0.001 TYR B 131 PHE 0.014 0.001 PHE A 259 TRP 0.010 0.001 TRP B 105 HIS 0.007 0.002 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (10250) covalent geometry : angle 0.58759 / 0.30 (14146) hydrogen bonds : bond 0.03968 / 2.64 ( 594) hydrogen bonds : angle 3.66796 / 2.56 ( 1652) metal coordination : bond 0.00369 / 0.22 ( 12) metal coordination : angle 3.21356 / 1.69 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.364 Fit side-chains REVERT: A 34 GLN cc_start: 0.8609 (mm-40) cc_final: 0.8025 (mp10) REVERT: B 131 TYR cc_start: 0.8903 (t80) cc_final: 0.8478 (t80) REVERT: B 312 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8632 (tm-30) REVERT: F 90 TYR cc_start: 0.7981 (OUTLIER) cc_final: 0.7454 (m-80) REVERT: F 115 ILE cc_start: 0.9186 (mt) cc_final: 0.8682 (tt) REVERT: F 129 LEU cc_start: 0.9023 (mm) cc_final: 0.8560 (tp) outliers start: 15 outliers final: 11 residues processed: 75 average time/residue: 0.1030 time to fit residues: 11.0836 Evaluate side-chains 77 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 136 VAL Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 99 optimal weight: 20.0000 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 74 optimal weight: 5.9990 chunk 40 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 29 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 33 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.147181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.097925 restraints weight = 28939.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.099925 restraints weight = 18166.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.103605 restraints weight = 9699.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.102259 restraints weight = 7190.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.101963 restraints weight = 5863.843| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3518 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3518 r_free = 0.3518 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3518 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.4540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10262 Z= 0.118 Angle : 0.582 10.878 14164 Z= 0.289 Chirality : 0.038 0.196 1677 Planarity : 0.004 0.044 1745 Dihedral : 16.655 79.825 1956 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 2.48 % Allowed : 20.03 % Favored : 77.48 % 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 are not related in a simple way. whole: 2.06 (0.24), residues: 1359 helix: 3.04 (0.20), residues: 663 sheet: 0.66 (0.36), residues: 208 loop : -0.74 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 223 TYR 0.013 0.001 TYR B 131 PHE 0.010 0.001 PHE A 259 TRP 0.011 0.001 TRP B 105 HIS 0.008 0.001 HIS B 284 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (10250) covalent geometry : angle 0.57345 / 0.29 (14146) hydrogen bonds : bond 0.03662 / 2.41 ( 594) hydrogen bonds : angle 3.58505 / 2.50 ( 1652) metal coordination : bond 0.00275 / 0.15 ( 12) metal coordination : angle 2.87469 / 1.48 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1990.81 seconds wall clock time: 34 minutes 46.27 seconds (2086.27 seconds total)