Starting phenix.real_space_refine on Mon Jun 9 01:31:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8bpr_16164/06_2025/8bpr_16164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8bpr_16164/06_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_16164/06_2025/8bpr_16164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8bpr_16164/06_2025/8bpr_16164.map" model { file = "/net/cci-nas-00/data/ceres_data/8bpr_16164/06_2025/8bpr_16164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8bpr_16164/06_2025/8bpr_16164.cif" } resolution = 3.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 1, 'GLU:plan': 6, 'ARG:plan': 3, 'PHE:plan': 1, 'HIS:plan': 2} 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: {'GLN:plan1': 2, 'ASP:plan': 4, 'TYR:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 21, 'ARG:plan': 15} 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: {'GLN:plan1': 2, 'ASP:plan': 2, 'TYR:plan': 5, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 24, 'ARG:plan': 15} 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: {'GLN:plan1': 2, 'ASN:plan1': 1, 'HIS:plan': 2, 'PHE:plan': 1, 'GLU:plan': 9, 'ARG:plan': 5} 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: {'GLN:plan1': 4, 'ASP:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 1, 'TRP:plan': 2, 'HIS:plan': 6, 'PHE:plan': 5, 'GLU:plan': 17, 'ARG:plan': 19} 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: 11.61, per 1000 atoms: 1.15 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: 2.87 Conformation dependent library (CDL) restraints added in 2.5 seconds 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: 3.65 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: 3.31 Time building geometry restraints manager: 3.35 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 341 or resid 901 through 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 341 or resid 901 through 902)) } ncs_group { reference = (chain 'D' and (resid 9 through 18 or resid 22 through 71 or resid 77 through 19 \ 4 or resid 201)) selection = (chain 'E' and (resid 9 through 48 or resid 54 through 102 or resid 122 through \ 153 or resid 162 through 194 or resid 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: 128.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 38.360 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.070 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 171.400 ------------------------------------------------------------------------------- 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 : 3.39 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.006 0.001 TRP A 105 HIS 0.003 0.001 HIS A 277 PHE 0.007 0.001 PHE B 6 TYR 0.004 0.001 TYR B 178 ARG 0.003 0.000 ARG A 335 Details of bonding type rmsd hydrogen bonds : bond 0.19107 ( 594) hydrogen bonds : angle 5.79913 ( 1652) metal coordination : bond 0.01055 ( 12) metal coordination : angle 22.64220 ( 18) covalent geometry : bond 0.00394 (10250) covalent geometry : angle 0.50885 (14146) *********************** 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 : 1.058 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: 0.3499 time to fit residues: 77.0270 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 : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 50.0000 chunk 107 optimal weight: 8.9990 chunk 59 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 72 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 128 optimal weight: 40.0000 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4287 r_free = 0.4287 target = 0.150537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.108199 restraints weight = 41430.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.105981 restraints weight = 18823.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.107366 restraints weight = 13099.507| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3619 r_free = 0.3619 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10262 Z= 0.182 Angle : 0.685 23.137 14164 Z= 0.318 Chirality : 0.040 0.160 1677 Planarity : 0.004 0.035 1745 Dihedral : 16.964 89.057 2012 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.98 % Allowed : 10.93 % Favored : 86.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.23), residues: 1359 helix: 2.40 (0.21), residues: 655 sheet: 0.76 (0.37), residues: 195 loop : -0.94 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 171 HIS 0.006 0.002 HIS A 257 PHE 0.018 0.002 PHE A 259 TYR 0.018 0.002 TYR F 102 ARG 0.007 0.001 ARG F 94 Details of bonding type rmsd hydrogen bonds : bond 0.04770 ( 594) hydrogen bonds : angle 4.20394 ( 1652) metal coordination : bond 0.00764 ( 12) metal coordination : angle 8.90087 ( 18) covalent geometry : bond 0.00414 (10250) covalent geometry : angle 0.60693 (14146) *********************** 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 108 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 231 GLU cc_start: 0.8729 (mp0) cc_final: 0.8337 (mp0) REVERT: B 131 TYR cc_start: 0.8696 (t80) cc_final: 0.8445 (t80) REVERT: F 90 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7469 (m-80) REVERT: F 129 LEU cc_start: 0.8946 (mm) cc_final: 0.8505 (tt) outliers start: 15 outliers final: 11 residues processed: 101 average time/residue: 0.2477 time to fit residues: 34.4464 Evaluate side-chains 85 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 116 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 248 VAL Chi-restraints excluded: chain B residue 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain F residue 90 TYR Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 74 optimal weight: 7.9990 chunk 120 optimal weight: 20.0000 chunk 87 optimal weight: 0.3980 chunk 83 optimal weight: 50.0000 chunk 58 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 93 optimal weight: 8.9990 chunk 80 optimal weight: 0.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN ** A 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.143323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.087809 restraints weight = 40537.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.091081 restraints weight = 16253.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.093209 restraints weight = 9558.913| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3361 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3361 r_free = 0.3361 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 10262 Z= 0.249 Angle : 0.710 14.829 14164 Z= 0.345 Chirality : 0.042 0.143 1677 Planarity : 0.005 0.055 1745 Dihedral : 17.061 86.509 2012 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.14 % Allowed : 13.08 % Favored : 82.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.23), residues: 1359 helix: 2.48 (0.21), residues: 651 sheet: 0.70 (0.36), residues: 192 loop : -1.13 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 295 HIS 0.009 0.003 HIS B 277 PHE 0.031 0.003 PHE A 259 TYR 0.020 0.002 TYR F 102 ARG 0.007 0.001 ARG B 335 Details of bonding type rmsd hydrogen bonds : bond 0.05580 ( 594) hydrogen bonds : angle 4.14029 ( 1652) metal coordination : bond 0.00838 ( 12) metal coordination : angle 6.29933 ( 18) covalent geometry : bond 0.00579 (10250) covalent geometry : angle 0.67357 (14146) *********************** 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 93 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 1.068 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8508 (mm-40) cc_final: 0.7899 (mp10) REVERT: B 131 TYR cc_start: 0.8972 (t80) cc_final: 0.8452 (t80) REVERT: F 90 TYR cc_start: 0.7894 (OUTLIER) cc_final: 0.7358 (m-80) REVERT: F 115 ILE cc_start: 0.9169 (mp) cc_final: 0.8698 (tt) REVERT: F 127 ARG cc_start: 0.9043 (ppt170) cc_final: 0.8693 (ppt170) REVERT: F 129 LEU cc_start: 0.8911 (mm) cc_final: 0.8441 (tp) outliers start: 22 outliers final: 16 residues processed: 84 average time/residue: 0.2445 time to fit residues: 28.5391 Evaluate side-chains 82 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 65 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 307 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 121 ASN Chi-restraints excluded: chain F residue 152 LEU Chi-restraints excluded: chain F residue 156 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 42 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 chunk 63 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 66 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 chunk 99 optimal weight: 20.0000 chunk 15 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 chunk 80 optimal weight: 30.0000 chunk 41 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4222 r_free = 0.4222 target = 0.147125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.104706 restraints weight = 42147.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.099780 restraints weight = 21047.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.100767 restraints weight = 16047.155| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3470 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3470 r_free = 0.3470 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3470 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10262 Z= 0.114 Angle : 0.558 12.025 14164 Z= 0.271 Chirality : 0.037 0.155 1677 Planarity : 0.004 0.046 1745 Dihedral : 16.624 89.035 2012 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.32 % Allowed : 16.56 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.23), residues: 1359 helix: 2.83 (0.20), residues: 658 sheet: 0.91 (0.37), residues: 187 loop : -0.90 (0.26), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 105 HIS 0.005 0.001 HIS B 284 PHE 0.008 0.001 PHE A 259 TYR 0.020 0.001 TYR A 19 ARG 0.018 0.001 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.03474 ( 594) hydrogen bonds : angle 3.69271 ( 1652) metal coordination : bond 0.00311 ( 12) metal coordination : angle 4.79749 ( 18) covalent geometry : bond 0.00250 (10250) covalent geometry : angle 0.53140 (14146) *********************** 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 85 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.224 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8450 (mm-40) cc_final: 0.7825 (mp10) REVERT: A 119 GLU cc_start: 0.8535 (tm-30) cc_final: 0.8228 (tp30) REVERT: A 231 GLU cc_start: 0.8691 (mp0) cc_final: 0.8463 (mp0) REVERT: A 232 GLU cc_start: 0.8888 (tp30) cc_final: 0.8655 (tp30) REVERT: A 237 GLN cc_start: 0.9264 (mt0) cc_final: 0.8659 (mt0) REVERT: B 131 TYR cc_start: 0.8900 (t80) cc_final: 0.8358 (t80) REVERT: B 312 GLN cc_start: 0.9068 (tm-30) cc_final: 0.8702 (tp40) REVERT: F 90 TYR cc_start: 0.8007 (OUTLIER) cc_final: 0.7503 (m-80) REVERT: F 115 ILE cc_start: 0.9186 (mp) cc_final: 0.8670 (tt) REVERT: F 129 LEU cc_start: 0.9048 (mm) cc_final: 0.8597 (tt) outliers start: 11 outliers final: 8 residues processed: 81 average time/residue: 0.2871 time to fit residues: 33.2728 Evaluate side-chains 74 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 1.398 ------------------------------------------------------------------------------- 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 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 75 optimal weight: 0.9980 chunk 3 optimal weight: 0.0770 chunk 62 optimal weight: 1.9990 chunk 37 optimal weight: 0.0870 chunk 1 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 103 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 95 optimal weight: 50.0000 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 284 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.145737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.101761 restraints weight = 47151.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.101865 restraints weight = 22142.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.102469 restraints weight = 14253.016| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- 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 = 0.26 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 = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10262 Z= 0.126 Angle : 0.532 9.974 14164 Z= 0.262 Chirality : 0.037 0.138 1677 Planarity : 0.004 0.046 1745 Dihedral : 16.501 89.308 2012 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.48 % Allowed : 16.39 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.23), residues: 1359 helix: 2.97 (0.20), residues: 659 sheet: 0.90 (0.36), residues: 195 loop : -0.83 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 105 HIS 0.004 0.001 HIS B 277 PHE 0.013 0.001 PHE A 259 TYR 0.008 0.001 TYR F 102 ARG 0.010 0.001 ARG B 223 Details of bonding type rmsd hydrogen bonds : bond 0.03616 ( 594) hydrogen bonds : angle 3.59047 ( 1652) metal coordination : bond 0.00324 ( 12) metal coordination : angle 3.90894 ( 18) covalent geometry : bond 0.00286 (10250) covalent geometry : angle 0.51361 (14146) *********************** 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 80 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8517 (mm-40) cc_final: 0.7859 (mp10) REVERT: A 237 GLN cc_start: 0.9174 (mt0) cc_final: 0.8303 (mt0) REVERT: B 131 TYR cc_start: 0.8937 (t80) cc_final: 0.8408 (t80) REVERT: B 312 GLN cc_start: 0.9063 (tm-30) cc_final: 0.8638 (tm-30) REVERT: F 90 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7239 (m-80) REVERT: F 115 ILE cc_start: 0.9173 (mp) cc_final: 0.8730 (tt) REVERT: F 129 LEU cc_start: 0.8804 (mm) cc_final: 0.8396 (tt) outliers start: 12 outliers final: 10 residues processed: 74 average time/residue: 0.2622 time to fit residues: 27.0693 Evaluate side-chains 76 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 65 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 50.0000 chunk 55 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 81 optimal weight: 20.0000 chunk 74 optimal weight: 7.9990 chunk 75 optimal weight: 7.9990 chunk 107 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.141892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090797 restraints weight = 26680.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.091881 restraints weight = 14292.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.092873 restraints weight = 10021.000| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3343 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3343 r_free = 0.3343 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3343 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8049 moved from start: 0.4352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10262 Z= 0.251 Angle : 0.660 9.355 14164 Z= 0.330 Chirality : 0.041 0.143 1677 Planarity : 0.005 0.043 1745 Dihedral : 16.814 92.429 2012 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.64 % Allowed : 16.56 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.23), residues: 1359 helix: 2.69 (0.20), residues: 662 sheet: 0.53 (0.36), residues: 204 loop : -0.91 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 295 HIS 0.009 0.003 HIS B 277 PHE 0.029 0.002 PHE A 259 TYR 0.013 0.002 TYR A 150 ARG 0.008 0.001 ARG A 102 Details of bonding type rmsd hydrogen bonds : bond 0.05256 ( 594) hydrogen bonds : angle 3.93182 ( 1652) metal coordination : bond 0.00720 ( 12) metal coordination : angle 4.35587 ( 18) covalent geometry : bond 0.00585 (10250) covalent geometry : angle 0.64173 (14146) *********************** 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 83 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 1.013 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8554 (mm-40) cc_final: 0.7966 (mp10) REVERT: A 237 GLN cc_start: 0.9090 (mt0) cc_final: 0.8789 (mt0) REVERT: B 39 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8652 (tt) REVERT: B 131 TYR cc_start: 0.8987 (t80) cc_final: 0.8380 (t80) REVERT: B 279 LEU cc_start: 0.9217 (tp) cc_final: 0.8998 (tt) REVERT: B 312 GLN cc_start: 0.9017 (tm-30) cc_final: 0.8552 (tm-30) REVERT: F 90 TYR cc_start: 0.8097 (OUTLIER) cc_final: 0.7558 (m-80) REVERT: F 115 ILE cc_start: 0.9124 (mp) cc_final: 0.8618 (tt) REVERT: F 118 LYS cc_start: 0.9104 (mmtm) cc_final: 0.8326 (ptmm) REVERT: F 129 LEU cc_start: 0.9122 (mm) cc_final: 0.8683 (tp) outliers start: 19 outliers final: 12 residues processed: 78 average time/residue: 0.2338 time to fit residues: 25.7075 Evaluate side-chains 73 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 59 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 214 GLU Chi-restraints excluded: chain A residue 284 HIS Chi-restraints excluded: chain B residue 39 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 307 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 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 15 optimal weight: 0.9980 chunk 64 optimal weight: 0.5980 chunk 98 optimal weight: 30.0000 chunk 128 optimal weight: 40.0000 chunk 102 optimal weight: 50.0000 chunk 0 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 120 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 116 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 = 0.4175 r_free = 0.4175 target = 0.143418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.098492 restraints weight = 35922.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.095567 restraints weight = 20412.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.096290 restraints weight = 15803.077| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3399 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3399 r_free = 0.3399 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3399 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10262 Z= 0.173 Angle : 0.579 10.465 14164 Z= 0.290 Chirality : 0.039 0.178 1677 Planarity : 0.004 0.045 1745 Dihedral : 16.723 90.003 2012 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 3.64 % Allowed : 17.05 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.24), residues: 1359 helix: 2.83 (0.20), residues: 663 sheet: 0.49 (0.36), residues: 207 loop : -0.84 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 105 HIS 0.006 0.002 HIS B 277 PHE 0.018 0.002 PHE A 259 TYR 0.008 0.001 TYR F 102 ARG 0.009 0.001 ARG F 94 Details of bonding type rmsd hydrogen bonds : bond 0.04167 ( 594) hydrogen bonds : angle 3.70786 ( 1652) metal coordination : bond 0.00505 ( 12) metal coordination : angle 3.62445 ( 18) covalent geometry : bond 0.00399 (10250) covalent geometry : angle 0.56468 (14146) *********************** 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 87 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8547 (mm-40) cc_final: 0.7875 (mp10) REVERT: A 119 GLU cc_start: 0.8596 (tm-30) cc_final: 0.8115 (tm-30) REVERT: B 39 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8721 (tt) REVERT: B 131 TYR cc_start: 0.8956 (t80) cc_final: 0.8333 (t80) REVERT: B 312 GLN cc_start: 0.9121 (tm-30) cc_final: 0.8647 (tm-30) REVERT: F 90 TYR cc_start: 0.8089 (OUTLIER) cc_final: 0.7539 (m-80) REVERT: F 115 ILE cc_start: 0.9140 (mp) cc_final: 0.8655 (tt) REVERT: F 118 LYS cc_start: 0.9158 (mmtm) cc_final: 0.8383 (ptmm) REVERT: F 129 LEU cc_start: 0.9077 (mm) cc_final: 0.8639 (tp) outliers start: 19 outliers final: 15 residues processed: 80 average time/residue: 0.2583 time to fit residues: 30.3821 Evaluate side-chains 77 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 1.934 ------------------------------------------------------------------------------- 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 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 175 LEU Chi-restraints excluded: chain B residue 307 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 121 ASN 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 58 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 123 optimal weight: 30.0000 chunk 23 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 90 optimal weight: 8.9990 chunk 35 optimal weight: 0.0870 chunk 63 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 44 optimal weight: 0.7980 chunk 116 optimal weight: 0.9990 overall best weight: 0.6160 ------------------------------------------------------------------------------- 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 = 0.4193 r_free = 0.4193 target = 0.145033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.093978 restraints weight = 30426.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.096171 restraints weight = 15162.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.097322 restraints weight = 9202.563| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3418 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3418 r_free = 0.3418 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3418 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10262 Z= 0.114 Angle : 0.546 11.151 14164 Z= 0.269 Chirality : 0.037 0.199 1677 Planarity : 0.004 0.048 1745 Dihedral : 16.550 89.362 2012 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 2.98 % Allowed : 18.21 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.24), residues: 1359 helix: 2.98 (0.21), residues: 664 sheet: 0.72 (0.36), residues: 208 loop : -0.74 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 105 HIS 0.005 0.001 HIS B 284 PHE 0.010 0.001 PHE A 259 TYR 0.007 0.001 TYR F 102 ARG 0.009 0.001 ARG F 94 Details of bonding type rmsd hydrogen bonds : bond 0.03341 ( 594) hydrogen bonds : angle 3.51629 ( 1652) metal coordination : bond 0.00286 ( 12) metal coordination : angle 2.85955 ( 18) covalent geometry : bond 0.00253 (10250) covalent geometry : angle 0.53674 (14146) *********************** 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 78 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 63 time to evaluate : 1.042 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8506 (mm-40) cc_final: 0.7761 (mp10) REVERT: B 131 TYR cc_start: 0.8926 (t80) cc_final: 0.8267 (t80) REVERT: B 312 GLN cc_start: 0.9007 (tm-30) cc_final: 0.8536 (tm-30) REVERT: F 90 TYR cc_start: 0.8106 (OUTLIER) cc_final: 0.7536 (m-80) REVERT: F 118 LYS cc_start: 0.9081 (mmtm) cc_final: 0.8370 (ptmm) REVERT: F 129 LEU cc_start: 0.9130 (mm) cc_final: 0.8711 (tp) outliers start: 15 outliers final: 12 residues processed: 72 average time/residue: 0.3059 time to fit residues: 30.7829 Evaluate side-chains 75 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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 148 SER 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 101 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 123 optimal weight: 40.0000 chunk 32 optimal weight: 0.3980 chunk 133 optimal weight: 20.0000 chunk 139 optimal weight: 4.9990 chunk 11 optimal weight: 0.0060 chunk 23 optimal weight: 0.2980 overall best weight: 0.5400 ------------------------------------------------------------------------------- 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 = 0.4199 r_free = 0.4199 target = 0.145502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.103556 restraints weight = 39907.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097905 restraints weight = 22841.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.099791 restraints weight = 15237.869| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3461 r_free = 0.3461 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4650 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= 0.109 Angle : 0.534 11.360 14164 Z= 0.264 Chirality : 0.037 0.192 1677 Planarity : 0.004 0.051 1745 Dihedral : 16.490 88.224 2012 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.48 % Allowed : 18.87 % Favored : 78.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.24), residues: 1359 helix: 3.07 (0.20), residues: 664 sheet: 0.82 (0.36), residues: 210 loop : -0.65 (0.28), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 105 HIS 0.006 0.001 HIS B 284 PHE 0.009 0.001 PHE A 259 TYR 0.006 0.001 TYR A 310 ARG 0.009 0.000 ARG F 94 Details of bonding type rmsd hydrogen bonds : bond 0.03182 ( 594) hydrogen bonds : angle 3.41812 ( 1652) metal coordination : bond 0.00268 ( 12) metal coordination : angle 2.39258 ( 18) covalent geometry : bond 0.00243 (10250) covalent geometry : angle 0.52759 (14146) *********************** 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 80 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 68 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7643 (mp10) REVERT: A 232 GLU cc_start: 0.8895 (tp30) cc_final: 0.8570 (tp30) REVERT: A 312 GLN cc_start: 0.8690 (tm-30) cc_final: 0.8484 (tm-30) REVERT: B 131 TYR cc_start: 0.8914 (t80) cc_final: 0.8296 (t80) REVERT: B 312 GLN cc_start: 0.9008 (tm-30) cc_final: 0.8530 (tm-30) REVERT: F 115 ILE cc_start: 0.9129 (mp) cc_final: 0.8818 (mp) REVERT: F 118 LYS cc_start: 0.9162 (mmtm) cc_final: 0.8414 (ptmm) REVERT: F 129 LEU cc_start: 0.9070 (mm) cc_final: 0.8630 (tp) outliers start: 12 outliers final: 11 residues processed: 76 average time/residue: 0.3477 time to fit residues: 37.9143 Evaluate side-chains 75 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 1.313 ------------------------------------------------------------------------------- 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 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 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 11 optimal weight: 0.0270 chunk 111 optimal weight: 0.9980 chunk 49 optimal weight: 0.0070 chunk 45 optimal weight: 0.3980 chunk 52 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 83 optimal weight: 20.0000 chunk 26 optimal weight: 0.8980 chunk 131 optimal weight: 50.0000 chunk 86 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- 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 = 0.4209 r_free = 0.4209 target = 0.146310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.104197 restraints weight = 42795.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.100857 restraints weight = 20404.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.102374 restraints weight = 15108.595| |-----------------------------------------------------------------------------| r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3486 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3486 r_free = 0.3486 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3486 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.4739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10262 Z= 0.100 Angle : 0.527 11.410 14164 Z= 0.259 Chirality : 0.037 0.212 1677 Planarity : 0.004 0.053 1745 Dihedral : 16.414 86.628 2012 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.48 % Allowed : 19.04 % Favored : 78.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.28 (0.24), residues: 1359 helix: 3.11 (0.20), residues: 665 sheet: 0.94 (0.37), residues: 206 loop : -0.57 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 105 HIS 0.008 0.001 HIS B 284 PHE 0.007 0.001 PHE B 6 TYR 0.006 0.001 TYR B 131 ARG 0.011 0.000 ARG F 94 Details of bonding type rmsd hydrogen bonds : bond 0.02862 ( 594) hydrogen bonds : angle 3.33263 ( 1652) metal coordination : bond 0.00203 ( 12) metal coordination : angle 2.05793 ( 18) covalent geometry : bond 0.00222 (10250) covalent geometry : angle 0.52224 (14146) ********************** 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: 12 poor density : 70 time to evaluate : 0.932 Fit side-chains revert: symmetry clash REVERT: A 34 GLN cc_start: 0.8497 (mm-40) cc_final: 0.7703 (mp10) REVERT: A 232 GLU cc_start: 0.8857 (tp30) cc_final: 0.8544 (tp30) REVERT: A 237 GLN cc_start: 0.8840 (mt0) cc_final: 0.8077 (mt0) REVERT: B 131 TYR cc_start: 0.8916 (t80) cc_final: 0.8302 (t80) REVERT: B 312 GLN cc_start: 0.9014 (tm-30) cc_final: 0.8527 (tm-30) REVERT: F 118 LYS cc_start: 0.9156 (mmtm) cc_final: 0.8446 (ptmm) REVERT: F 127 ARG cc_start: 0.9206 (ppt170) cc_final: 0.8846 (ppt170) REVERT: F 129 LEU cc_start: 0.9065 (mm) cc_final: 0.8649 (tp) REVERT: F 157 LYS cc_start: 0.9397 (pttm) cc_final: 0.9144 (tppt) outliers start: 12 outliers final: 10 residues processed: 77 average time/residue: 0.2789 time to fit residues: 30.1421 Evaluate side-chains 76 residues out of total 1081 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 328 VAL Chi-restraints excluded: chain B residue 332 SER Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain F residue 152 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 116 optimal weight: 0.0050 chunk 89 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 97 optimal weight: 30.0000 chunk 133 optimal weight: 8.9990 chunk 28 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.0198 ------------------------------------------------------------------------------- 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 = 0.4181 r_free = 0.4181 target = 0.144235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.100725 restraints weight = 36085.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.095996 restraints weight = 21109.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.097819 restraints weight = 15388.700| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3435 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3435 r_free = 0.3435 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3435 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10262 Z= 0.146 Angle : 0.567 11.078 14164 Z= 0.280 Chirality : 0.038 0.196 1677 Planarity : 0.004 0.050 1745 Dihedral : 16.506 89.027 2012 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.65 % Allowed : 19.37 % Favored : 77.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.24), residues: 1359 helix: 3.08 (0.20), residues: 665 sheet: 0.88 (0.37), residues: 203 loop : -0.60 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 105 HIS 0.008 0.002 HIS B 284 PHE 0.018 0.002 PHE F 98 TYR 0.007 0.001 TYR A 178 ARG 0.010 0.000 ARG F 94 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 594) hydrogen bonds : angle 3.42975 ( 1652) metal coordination : bond 0.00392 ( 12) metal coordination : angle 2.22106 ( 18) covalent geometry : bond 0.00339 (10250) covalent geometry : angle 0.56176 (14146) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4389.01 seconds wall clock time: 79 minutes 17.31 seconds (4757.31 seconds total)