Starting phenix.real_space_refine on Sat Aug 23 05:59:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bpr_16164/08_2025/8bpr_16164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpr_16164/08_2025/8bpr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8bpr_16164/08_2025/8bpr_16164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpr_16164/08_2025/8bpr_16164.map" model { file = "/net/cci-nas-00/data/ceres_data/8bpr_16164/08_2025/8bpr_16164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpr_16164/08_2025/8bpr_16164.cif" } 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-2.0-5787/lib/python3.9/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: 3.34, per 1000 atoms: 0.33 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: 0.72 Conformation dependent library (CDL) restraints added in 515.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.90 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: 1.47 Time building geometry restraints manager: 0.96 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=" O5' ANP B 901 " pdb=" PA ANP B 901 " ideal model delta sigma weight residual 1.655 1.593 0.062 2.00e-02 2.50e+03 9.63e+00 ... (remaining 10245 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 14022 2.20 - 4.40: 104 4.40 - 6.60: 13 6.60 - 8.80: 5 8.80 - 11.01: 2 Bond angle restraints: 14146 Sorted by residual: angle pdb=" O1B ANP A 901 " pdb=" PB ANP A 901 " pdb=" O3A ANP A 901 " ideal model delta sigma weight residual 103.40 114.41 -11.01 3.00e+00 1.11e-01 1.35e+01 angle pdb=" O1B ANP B 901 " pdb=" PB ANP B 901 " pdb=" O3A ANP B 901 " ideal model delta sigma weight residual 103.40 114.37 -10.97 3.00e+00 1.11e-01 1.34e+01 angle pdb=" PA ANP A 901 " pdb=" O3A ANP A 901 " pdb=" PB ANP A 901 " ideal model delta sigma weight residual 125.41 133.35 -7.94 3.00e+00 1.11e-01 7.01e+00 angle pdb=" PA ANP B 901 " pdb=" O3A ANP B 901 " pdb=" PB ANP B 901 " ideal model delta sigma weight residual 125.41 133.13 -7.72 3.00e+00 1.11e-01 6.61e+00 angle pdb=" CB LYS F 118 " pdb=" CG LYS F 118 " pdb=" CD LYS F 118 " ideal model delta sigma weight residual 111.30 117.18 -5.88 2.30e+00 1.89e-01 6.53e+00 ... (remaining 14141 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 5287 17.95 - 35.89: 440 35.89 - 53.84: 235 53.84 - 71.79: 28 71.79 - 89.73: 10 Dihedral angle restraints: 6000 sinusoidal: 2060 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 5997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1505 0.057 - 0.113: 166 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: 5.170 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.790 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 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:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 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= 0.196 Angle : 0.954 46.607 14164 Z= 0.293 Chirality : 0.036 0.283 1677 Planarity : 0.003 0.031 1745 Dihedral : 17.505 89.732 3460 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 aren 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 covalent geometry : bond 0.00394 (10250) covalent geometry : angle 0.50885 (14146) hydrogen bonds : bond 0.19107 ( 594) hydrogen bonds : angle 5.79913 ( 1652) metal coordination : bond 0.01055 ( 12) metal coordination : angle 22.64220 ( 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 : 0.318 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: 0.1471 time to fit residues: 31.9762 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 : 0.451 ------------------------------------------------------------------------------- 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: 0.8980 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: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.4240 r_free = 0.4240 target = 0.146476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.093326 restraints weight = 30176.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.096437 restraints weight = 13737.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.098445 restraints weight = 8565.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.099722 restraints weight = 6404.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.100383 restraints weight = 5402.519| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3512 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3512 r_free = 0.3512 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 = 0.3512 r_free = 0.3512 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3512 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 10262 Z= 0.316 Angle : 0.835 24.453 14164 Z= 0.399 Chirality : 0.045 0.161 1677 Planarity : 0.006 0.051 1745 Dihedral : 17.260 84.936 2012 Min Nonbonded Distance : 1.775 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.31 % Allowed : 11.42 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.23), residues: 1359 helix: 2.07 (0.20), residues: 652 sheet: 0.60 (0.38), residues: 180 loop : -1.17 (0.25), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 129 TYR 0.021 0.002 TYR F 102 PHE 0.036 0.003 PHE A 259 TRP 0.018 0.003 TRP B 171 HIS 0.011 0.003 HIS A 277 Details of bonding type rmsd covalent geometry : bond 0.00732 (10250) covalent geometry : angle 0.76917 (14146) hydrogen bonds : bond 0.05901 ( 594) hydrogen bonds : angle 4.43241 ( 1652) metal coordination : bond 0.01105 ( 12) metal coordination : angle 9.16328 ( 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 99 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 82 time to evaluate : 0.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 131 TYR cc_start: 0.8861 (t80) cc_final: 0.8443 (t80) REVERT: B 245 ASP cc_start: 0.8928 (m-30) cc_final: 0.8619 (m-30) REVERT: F 90 TYR cc_start: 0.7891 (OUTLIER) cc_final: 0.7290 (m-80) REVERT: F 129 LEU cc_start: 0.8775 (mm) cc_final: 0.8355 (tt) REVERT: F 144 GLU cc_start: 0.8587 (mp0) cc_final: 0.8352 (mt-10) outliers start: 17 outliers final: 12 residues processed: 94 average time/residue: 0.1180 time to fit residues: 15.1332 Evaluate side-chains 80 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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: 0.0870 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 141 optimal weight: 2.9990 chunk 85 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.146964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095594 restraints weight = 29714.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.097937 restraints weight = 14965.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.098615 restraints weight = 10209.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.099556 restraints weight = 7073.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.099874 restraints weight = 6045.088| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10262 Z= 0.123 Angle : 0.581 16.496 14164 Z= 0.276 Chirality : 0.038 0.145 1677 Planarity : 0.004 0.039 1745 Dihedral : 16.797 84.027 2012 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.31 % Allowed : 13.58 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.23), residues: 1359 helix: 2.65 (0.21), residues: 658 sheet: 0.77 (0.37), residues: 187 loop : -1.02 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 94 TYR 0.015 0.001 TYR F 102 PHE 0.010 0.001 PHE A 259 TRP 0.010 0.001 TRP B 105 HIS 0.004 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00270 (10250) covalent geometry : angle 0.53645 (14146) hydrogen bonds : bond 0.03837 ( 594) hydrogen bonds : angle 3.83977 ( 1652) metal coordination : bond 0.00482 ( 12) metal coordination : angle 6.29521 ( 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 95 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 131 TYR cc_start: 0.8881 (t80) cc_final: 0.8376 (t80) REVERT: B 245 ASP cc_start: 0.9055 (m-30) cc_final: 0.8690 (m-30) REVERT: B 312 GLN cc_start: 0.9011 (tm-30) cc_final: 0.8583 (tp40) REVERT: F 90 TYR cc_start: 0.8069 (OUTLIER) cc_final: 0.7578 (m-80) REVERT: F 115 ILE cc_start: 0.9205 (mp) cc_final: 0.8661 (tt) REVERT: F 127 ARG cc_start: 0.9217 (ppt170) cc_final: 0.8936 (ppt170) REVERT: F 129 LEU cc_start: 0.9082 (mm) cc_final: 0.8672 (tt) REVERT: F 144 GLU cc_start: 0.8529 (mp0) cc_final: 0.8289 (mt-10) outliers start: 17 outliers final: 11 residues processed: 86 average time/residue: 0.1132 time to fit residues: 13.4099 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 : 0.349 ------------------------------------------------------------------------------- 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 169 SER 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 31 optimal weight: 0.7980 chunk 32 optimal weight: 0.0020 chunk 81 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 104 optimal weight: 20.0000 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 chunk 131 optimal weight: 50.0000 chunk 140 optimal weight: 3.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 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 = 0.4201 r_free = 0.4201 target = 0.145610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.095493 restraints weight = 26318.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.097228 restraints weight = 14964.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.099414 restraints weight = 8623.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.099193 restraints weight = 7910.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.098642 restraints weight = 6096.446| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10262 Z= 0.143 Angle : 0.551 10.981 14164 Z= 0.271 Chirality : 0.038 0.143 1677 Planarity : 0.004 0.042 1745 Dihedral : 16.568 88.075 2012 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.32 % Allowed : 16.72 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.23), residues: 1359 helix: 2.84 (0.20), residues: 658 sheet: 0.68 (0.36), residues: 194 loop : -0.88 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 102 TYR 0.011 0.001 TYR A 19 PHE 0.015 0.001 PHE A 259 TRP 0.009 0.001 TRP B 105 HIS 0.005 0.001 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00326 (10250) covalent geometry : angle 0.52574 (14146) hydrogen bonds : bond 0.03930 ( 594) hydrogen bonds : angle 3.67443 ( 1652) metal coordination : bond 0.00359 ( 12) metal coordination : angle 4.68797 ( 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 86 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 237 GLN cc_start: 0.9288 (mt0) cc_final: 0.8696 (mt0) REVERT: B 131 TYR cc_start: 0.8914 (t80) cc_final: 0.8360 (t80) REVERT: B 245 ASP cc_start: 0.9128 (m-30) cc_final: 0.8846 (m-30) REVERT: B 312 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8638 (tm-30) REVERT: F 90 TYR cc_start: 0.8035 (OUTLIER) cc_final: 0.7523 (m-80) REVERT: F 115 ILE cc_start: 0.9193 (mp) cc_final: 0.8686 (tt) REVERT: F 129 LEU cc_start: 0.9169 (mm) cc_final: 0.8736 (tt) REVERT: F 144 GLU cc_start: 0.8584 (mp0) cc_final: 0.8246 (mt-10) outliers start: 11 outliers final: 8 residues processed: 82 average time/residue: 0.1252 time to fit residues: 14.2570 Evaluate side-chains 81 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.475 ------------------------------------------------------------------------------- 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 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: 30.0000 chunk 56 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 7 optimal weight: 0.0570 chunk 106 optimal weight: 5.9990 chunk 105 optimal weight: 8.9990 chunk 44 optimal weight: 0.0970 chunk 119 optimal weight: 50.0000 chunk 139 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4219 r_free = 0.4219 target = 0.147189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.103304 restraints weight = 39325.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.100236 restraints weight = 19093.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.101858 restraints weight = 14290.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.101683 restraints weight = 10084.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.103666 restraints weight = 8892.194| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.3743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10262 Z= 0.105 Angle : 0.506 9.851 14164 Z= 0.248 Chirality : 0.036 0.138 1677 Planarity : 0.003 0.045 1745 Dihedral : 16.417 86.923 2012 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.15 % Allowed : 17.72 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.00 (0.23), residues: 1359 helix: 2.94 (0.20), residues: 659 sheet: 0.86 (0.36), residues: 195 loop : -0.76 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 94 TYR 0.006 0.001 TYR F 102 PHE 0.008 0.001 PHE A 259 TRP 0.008 0.001 TRP B 105 HIS 0.003 0.001 HIS A 257 Details of bonding type rmsd covalent geometry : bond 0.00231 (10250) covalent geometry : angle 0.49206 (14146) hydrogen bonds : bond 0.03112 ( 594) hydrogen bonds : angle 3.50711 ( 1652) metal coordination : bond 0.00263 ( 12) metal coordination : angle 3.39744 ( 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 87 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 GLU cc_start: 0.8766 (tp30) cc_final: 0.8538 (tp30) REVERT: A 237 GLN cc_start: 0.9062 (mt0) cc_final: 0.8392 (mt0) REVERT: B 131 TYR cc_start: 0.8907 (t80) cc_final: 0.8316 (t80) REVERT: B 245 ASP cc_start: 0.9085 (m-30) cc_final: 0.8778 (m-30) REVERT: B 312 GLN cc_start: 0.9051 (tm-30) cc_final: 0.8635 (tm-30) REVERT: F 90 TYR cc_start: 0.7928 (OUTLIER) cc_final: 0.7408 (m-80) REVERT: F 115 ILE cc_start: 0.9161 (mp) cc_final: 0.8685 (tt) REVERT: F 129 LEU cc_start: 0.9011 (mm) cc_final: 0.8598 (tt) REVERT: F 144 GLU cc_start: 0.8533 (mp0) cc_final: 0.8305 (mt-10) outliers start: 10 outliers final: 6 residues processed: 83 average time/residue: 0.1196 time to fit residues: 13.7409 Evaluate side-chains 76 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 69 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 214 GLU 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 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: 4.9990 chunk 131 optimal weight: 40.0000 chunk 78 optimal weight: 40.0000 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 115 optimal weight: 0.9980 chunk 3 optimal weight: 0.2980 chunk 87 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 127 optimal weight: 30.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 83 HIS ** 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 = 0.4126 r_free = 0.4126 target = 0.139739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.094720 restraints weight = 35739.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.090645 restraints weight = 21312.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.091817 restraints weight = 16335.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.091804 restraints weight = 12619.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.092212 restraints weight = 10472.871| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3338 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3338 r_free = 0.3338 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3338 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 10262 Z= 0.391 Angle : 0.815 12.158 14164 Z= 0.404 Chirality : 0.045 0.152 1677 Planarity : 0.006 0.048 1745 Dihedral : 16.933 95.755 2012 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 4.30 % Allowed : 16.39 % Favored : 79.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.23), residues: 1359 helix: 2.43 (0.21), residues: 660 sheet: 0.33 (0.36), residues: 196 loop : -1.00 (0.27), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 129 TYR 0.020 0.002 TYR A 150 PHE 0.042 0.004 PHE A 259 TRP 0.015 0.002 TRP A 295 HIS 0.015 0.004 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00908 (10250) covalent geometry : angle 0.79780 (14146) hydrogen bonds : bond 0.06184 ( 594) hydrogen bonds : angle 4.25467 ( 1652) metal coordination : bond 0.01043 ( 12) metal coordination : angle 4.72423 ( 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 : 0.370 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8725 (mm110) cc_final: 0.7999 (mp10) REVERT: A 119 GLU cc_start: 0.8684 (tm-30) cc_final: 0.8281 (tm-30) REVERT: A 161 LEU cc_start: 0.8508 (tt) cc_final: 0.8260 (tt) REVERT: A 231 GLU cc_start: 0.8523 (pm20) cc_final: 0.8298 (pm20) REVERT: B 39 LEU cc_start: 0.9037 (OUTLIER) cc_final: 0.8746 (tt) REVERT: B 312 GLN cc_start: 0.9059 (tm-30) cc_final: 0.8590 (tm-30) REVERT: F 90 TYR cc_start: 0.8042 (OUTLIER) cc_final: 0.7497 (m-80) REVERT: F 115 ILE cc_start: 0.9110 (mp) cc_final: 0.8639 (tt) REVERT: F 129 LEU cc_start: 0.9122 (mm) cc_final: 0.8639 (tp) REVERT: F 152 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8623 (tp) outliers start: 23 outliers final: 15 residues processed: 80 average time/residue: 0.1156 time to fit residues: 12.9683 Evaluate side-chains 74 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL 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 148 SER 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 74 THR Chi-restraints excluded: chain B residue 156 GLN 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 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: 0.9990 chunk 67 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 chunk 125 optimal weight: 30.0000 chunk 136 optimal weight: 20.0000 chunk 74 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4176 r_free = 0.4176 target = 0.143636 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.090154 restraints weight = 49292.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.094025 restraints weight = 20197.779| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.094966 restraints weight = 10632.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.095861 restraints weight = 7373.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.095933 restraints weight = 6921.085| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10262 Z= 0.132 Angle : 0.582 10.406 14164 Z= 0.287 Chirality : 0.038 0.188 1677 Planarity : 0.004 0.047 1745 Dihedral : 16.686 88.853 2012 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.98 % Allowed : 18.87 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.24), residues: 1359 helix: 2.76 (0.21), residues: 663 sheet: 0.42 (0.36), residues: 206 loop : -0.83 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 94 TYR 0.008 0.001 TYR F 151 PHE 0.013 0.001 PHE A 259 TRP 0.010 0.001 TRP B 105 HIS 0.005 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00296 (10250) covalent geometry : angle 0.56871 (14146) hydrogen bonds : bond 0.03971 ( 594) hydrogen bonds : angle 3.70687 ( 1652) metal coordination : bond 0.00382 ( 12) metal coordination : angle 3.47129 ( 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: 15 poor density : 68 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8378 (tm-30) cc_final: 0.7924 (tm-30) REVERT: B 39 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8649 (tt) REVERT: B 131 TYR cc_start: 0.8907 (t80) cc_final: 0.8516 (t80) REVERT: B 312 GLN cc_start: 0.8981 (tm-30) cc_final: 0.8527 (tm-30) REVERT: F 90 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7527 (m-80) REVERT: F 115 ILE cc_start: 0.9118 (mp) cc_final: 0.8607 (tt) REVERT: F 118 LYS cc_start: 0.9051 (mmtm) cc_final: 0.8307 (ptmm) REVERT: F 129 LEU cc_start: 0.9116 (mm) cc_final: 0.8685 (tp) outliers start: 15 outliers final: 10 residues processed: 80 average time/residue: 0.1160 time to fit residues: 13.0150 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 : 0.371 ------------------------------------------------------------------------------- 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 39 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 175 LEU 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 152 LEU Chi-restraints excluded: chain F residue 156 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 121 optimal weight: 50.0000 chunk 83 optimal weight: 40.0000 chunk 24 optimal weight: 0.5980 chunk 56 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.3980 chunk 88 optimal weight: 10.0000 chunk 125 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 137 optimal weight: 50.0000 chunk 91 optimal weight: 10.0000 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 HIS B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.140971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.088016 restraints weight = 42766.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.091899 restraints weight = 19188.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092096 restraints weight = 10114.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.092767 restraints weight = 7707.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.092792 restraints weight = 6918.246| |-----------------------------------------------------------------------------| r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3332 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3332 r_free = 0.3332 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3332 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 10262 Z= 0.247 Angle : 0.663 10.295 14164 Z= 0.329 Chirality : 0.041 0.164 1677 Planarity : 0.005 0.045 1745 Dihedral : 16.786 94.082 2012 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 4.14 % Allowed : 18.38 % 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 aren not related in a simple way. whole: 1.64 (0.24), residues: 1359 helix: 2.66 (0.21), residues: 661 sheet: 0.39 (0.37), residues: 204 loop : -0.83 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 94 TYR 0.012 0.002 TYR A 150 PHE 0.026 0.002 PHE A 259 TRP 0.009 0.002 TRP B 105 HIS 0.009 0.002 HIS B 277 Details of bonding type rmsd covalent geometry : bond 0.00576 (10250) covalent geometry : angle 0.65001 (14146) hydrogen bonds : bond 0.04980 ( 594) hydrogen bonds : angle 3.95790 ( 1652) metal coordination : bond 0.00700 ( 12) metal coordination : angle 3.71243 ( 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 85 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8782 (mm110) cc_final: 0.8093 (mp10) REVERT: B 39 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8680 (tt) REVERT: B 180 ASP cc_start: 0.7757 (m-30) cc_final: 0.7546 (t0) REVERT: B 312 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8550 (tm-30) REVERT: F 90 TYR cc_start: 0.8202 (OUTLIER) cc_final: 0.7632 (m-80) REVERT: F 115 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8896 (mp) REVERT: F 129 LEU cc_start: 0.9174 (mm) cc_final: 0.8705 (tp) outliers start: 22 outliers final: 16 residues processed: 78 average time/residue: 0.1176 time to fit residues: 12.7486 Evaluate side-chains 81 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 62 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL 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 148 SER 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 169 SER 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 115 ILE Chi-restraints excluded: chain F residue 121 ASN Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 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: 0.9990 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 91 optimal weight: 0.0030 chunk 117 optimal weight: 2.9990 overall best weight: 0.5592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 HIS B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.144172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.099242 restraints weight = 32658.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.096160 restraints weight = 19977.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.097114 restraints weight = 14409.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.097496 restraints weight = 10832.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097616 restraints weight = 9096.222| |-----------------------------------------------------------------------------| r_work (final): 0.3427 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3427 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3427 r_free = 0.3427 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3427 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4693 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= 0.114 Angle : 0.562 10.725 14164 Z= 0.275 Chirality : 0.038 0.198 1677 Planarity : 0.004 0.048 1745 Dihedral : 16.584 89.226 2012 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 2.81 % Allowed : 19.87 % 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 aren not related in a simple way. whole: 1.92 (0.24), residues: 1359 helix: 2.92 (0.21), residues: 657 sheet: 0.47 (0.36), residues: 208 loop : -0.71 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 94 TYR 0.007 0.001 TYR A 310 PHE 0.008 0.001 PHE A 259 TRP 0.010 0.001 TRP B 105 HIS 0.009 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00251 (10250) covalent geometry : angle 0.55292 (14146) hydrogen bonds : bond 0.03392 ( 594) hydrogen bonds : angle 3.62252 ( 1652) metal coordination : bond 0.00291 ( 12) metal coordination : angle 2.84575 ( 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 88 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 74 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.6933 (mtp85) cc_final: 0.6584 (ttm110) REVERT: A 119 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8128 (tp30) REVERT: B 39 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8708 (tt) REVERT: B 131 TYR cc_start: 0.8891 (t80) cc_final: 0.8495 (t80) REVERT: B 312 GLN cc_start: 0.9001 (tm-30) cc_final: 0.8531 (tm-30) REVERT: F 90 TYR cc_start: 0.8085 (OUTLIER) cc_final: 0.7505 (m-80) REVERT: F 115 ILE cc_start: 0.9120 (OUTLIER) cc_final: 0.8816 (mp) REVERT: F 118 LYS cc_start: 0.9090 (mmtm) cc_final: 0.8331 (ptmm) REVERT: F 129 LEU cc_start: 0.9144 (mm) cc_final: 0.8704 (tp) outliers start: 14 outliers final: 10 residues processed: 84 average time/residue: 0.1243 time to fit residues: 14.4444 Evaluate side-chains 80 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 67 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL 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 169 SER Chi-restraints excluded: chain B residue 175 LEU 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 115 ILE 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 16 optimal weight: 0.0060 chunk 64 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 103 optimal weight: 30.0000 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 130 optimal weight: 9.9990 chunk 75 optimal weight: 0.8980 chunk 124 optimal weight: 50.0000 chunk 100 optimal weight: 5.9990 overall best weight: 0.8798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 83 HIS B 284 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.143349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.089952 restraints weight = 47095.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.094150 restraints weight = 18791.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.095390 restraints weight = 8762.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.095798 restraints weight = 6793.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.095859 restraints weight = 6580.071| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3403 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3403 r_free = 0.3403 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3403 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10262 Z= 0.139 Angle : 0.589 11.283 14164 Z= 0.289 Chirality : 0.038 0.181 1677 Planarity : 0.004 0.050 1745 Dihedral : 16.563 90.876 2012 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.81 % Allowed : 20.20 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.98 (0.24), residues: 1359 helix: 2.97 (0.21), residues: 657 sheet: 0.55 (0.37), residues: 207 loop : -0.69 (0.28), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 94 TYR 0.006 0.001 TYR A 310 PHE 0.019 0.002 PHE F 98 TRP 0.009 0.001 TRP B 105 HIS 0.008 0.002 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00320 (10250) covalent geometry : angle 0.58167 (14146) hydrogen bonds : bond 0.03736 ( 594) hydrogen bonds : angle 3.63293 ( 1652) metal coordination : bond 0.00370 ( 12) metal coordination : angle 2.69095 ( 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 82 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 7 ARG cc_start: 0.6828 (mtp85) cc_final: 0.6587 (ttp-110) REVERT: B 39 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8638 (tt) REVERT: B 131 TYR cc_start: 0.8919 (t80) cc_final: 0.8524 (t80) REVERT: B 312 GLN cc_start: 0.8985 (tm-30) cc_final: 0.8517 (tm-30) REVERT: F 115 ILE cc_start: 0.9128 (OUTLIER) cc_final: 0.8813 (mp) REVERT: F 129 LEU cc_start: 0.9157 (mm) cc_final: 0.8709 (tp) outliers start: 14 outliers final: 10 residues processed: 79 average time/residue: 0.1209 time to fit residues: 13.2114 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 : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL 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 169 SER Chi-restraints excluded: chain B residue 175 LEU 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 115 ILE 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: 0.7980 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 74 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 115 optimal weight: 0.0000 chunk 29 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4183 r_free = 0.4183 target = 0.144372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.094883 restraints weight = 29400.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.096970 restraints weight = 16592.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.100120 restraints weight = 9121.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.099536 restraints weight = 7291.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.099046 restraints weight = 5585.159| |-----------------------------------------------------------------------------| r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3460 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3460 r_free = 0.3460 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3460 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.4851 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= 0.116 Angle : 0.567 10.336 14164 Z= 0.278 Chirality : 0.037 0.209 1677 Planarity : 0.004 0.047 1745 Dihedral : 16.506 88.614 2012 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.65 % Allowed : 20.03 % 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 aren not related in a simple way. whole: 2.05 (0.24), residues: 1359 helix: 2.99 (0.21), residues: 662 sheet: 0.63 (0.37), residues: 208 loop : -0.67 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 94 TYR 0.006 0.001 TYR A 310 PHE 0.009 0.001 PHE A 193 TRP 0.009 0.001 TRP B 105 HIS 0.009 0.001 HIS B 284 Details of bonding type rmsd covalent geometry : bond 0.00263 (10250) covalent geometry : angle 0.56126 (14146) hydrogen bonds : bond 0.03297 ( 594) hydrogen bonds : angle 3.54621 ( 1652) metal coordination : bond 0.00265 ( 12) metal coordination : angle 2.35982 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2140.85 seconds wall clock time: 37 minutes 19.76 seconds (2239.76 seconds total)