Starting phenix.real_space_refine on Tue Aug 26 06:40:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8y82_39030/08_2025/8y82_39030_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8y82_39030/08_2025/8y82_39030.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8y82_39030/08_2025/8y82_39030_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8y82_39030/08_2025/8y82_39030_neut_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8y82_39030/08_2025/8y82_39030.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8y82_39030/08_2025/8y82_39030.map" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.058 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: 6 Type Number sf(0) Gaussians P 166 5.49 5 Mg 4 5.21 5 S 124 5.16 5 C 21510 2.51 5 N 5934 2.21 5 O 6776 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 34514 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3659 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 443} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 Chain: "C" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "D" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "E" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4609 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "F" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 Chain: "G" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "H" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "I" Number of atoms: 3659 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3659 Classifications: {'peptide': 463} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 443} Chain breaks: 5 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "J" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 Chain: "K" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "L" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "M" Number of atoms: 4609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 576, 4609 Classifications: {'peptide': 576} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 552} Chain breaks: 2 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 3629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 3629 Classifications: {'peptide': 456} Link IDs: {'PTRANS': 27, 'TRANS': 428} Chain breaks: 2 Chain: "O" Number of atoms: 442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 442 Classifications: {'RNA': 21} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 2, 'rna3p': 18} Chain: "P" Number of atoms: 411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 411 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.22, per 1000 atoms: 0.21 Number of scatterers: 34514 At special positions: 0 Unit cell: (110.818, 151.341, 212.539, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 124 16.00 P 166 15.00 Mg 4 11.99 O 6776 8.00 N 5934 7.00 C 21510 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 476.8 nanoseconds 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7320 Finding SS restraints... Secondary structure from input PDB file: 156 helices and 50 sheets defined 42.1% alpha, 18.8% beta 60 base pairs and 104 stacking pairs defined. Time for finding SS restraints: 4.61 Creating SS restraints... Processing helix chain 'A' and resid 5 through 16 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.599A pdb=" N THR A 149 " --> pdb=" O ASP A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 168 through 176 Processing helix chain 'A' and resid 207 through 219 removed outlier: 4.111A pdb=" N CYS A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 242 removed outlier: 3.763A pdb=" N ASP A 242 " --> pdb=" O ARG A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 276 removed outlier: 3.784A pdb=" N GLN A 266 " --> pdb=" O GLU A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 296 Processing helix chain 'A' and resid 302 through 310 Processing helix chain 'A' and resid 355 through 367 Processing helix chain 'A' and resid 383 through 391 Processing helix chain 'A' and resid 406 through 414 Processing helix chain 'A' and resid 414 through 430 Processing helix chain 'A' and resid 458 through 466 Processing helix chain 'A' and resid 513 through 519 removed outlier: 3.883A pdb=" N ARG A 517 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N GLU A 518 " --> pdb=" O ASP A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 520 through 529 Processing helix chain 'A' and resid 532 through 549 Processing helix chain 'B' and resid 21 through 25 Processing helix chain 'B' and resid 29 through 37 Processing helix chain 'B' and resid 39 through 43 removed outlier: 3.900A pdb=" N CYS B 43 " --> pdb=" O TYR B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 59 No H-bonds generated for 'chain 'B' and resid 57 through 59' Processing helix chain 'B' and resid 60 through 72 removed outlier: 3.703A pdb=" N LEU B 64 " --> pdb=" O HIS B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 89 through 94 Processing helix chain 'B' and resid 111 through 120 removed outlier: 3.646A pdb=" N GLY B 115 " --> pdb=" O ASP B 111 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ALA B 118 " --> pdb=" O HIS B 114 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASN B 119 " --> pdb=" O GLY B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 151 through 157 removed outlier: 4.515A pdb=" N LYS B 156 " --> pdb=" O SER B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 174 Processing helix chain 'B' and resid 175 through 177 No H-bonds generated for 'chain 'B' and resid 175 through 177' Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 192 through 209 removed outlier: 3.788A pdb=" N VAL B 196 " --> pdb=" O CYS B 192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 295 removed outlier: 3.607A pdb=" N SER B 294 " --> pdb=" O LEU B 290 " (cutoff:3.500A) Processing helix chain 'B' and resid 312 through 322 removed outlier: 3.528A pdb=" N GLN B 317 " --> pdb=" O GLU B 313 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER B 322 " --> pdb=" O GLY B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 429 removed outlier: 4.437A pdb=" N THR B 421 " --> pdb=" O GLY B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 459 Processing helix chain 'B' and resid 469 through 473 Processing helix chain 'E' and resid 5 through 16 Processing helix chain 'E' and resid 27 through 33 removed outlier: 3.508A pdb=" N ARG E 30 " --> pdb=" O GLY E 27 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLY E 33 " --> pdb=" O ARG E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 64 through 78 Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 100 through 112 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 168 through 176 removed outlier: 3.505A pdb=" N SER E 172 " --> pdb=" O TYR E 168 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 203 removed outlier: 3.787A pdb=" N GLN E 202 " --> pdb=" O PRO E 199 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR E 203 " --> pdb=" O ASP E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 205 through 219 removed outlier: 3.910A pdb=" N ILE E 217 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG E 218 " --> pdb=" O ALA E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 230 through 242 Processing helix chain 'E' and resid 262 through 275 removed outlier: 3.651A pdb=" N GLN E 266 " --> pdb=" O GLU E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 297 Processing helix chain 'E' and resid 302 through 310 removed outlier: 4.130A pdb=" N LYS E 308 " --> pdb=" O ALA E 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 355 through 367 Processing helix chain 'E' and resid 383 through 391 removed outlier: 3.597A pdb=" N ILE E 387 " --> pdb=" O GLY E 383 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 414 Processing helix chain 'E' and resid 414 through 430 Processing helix chain 'E' and resid 455 through 457 No H-bonds generated for 'chain 'E' and resid 455 through 457' Processing helix chain 'E' and resid 458 through 466 Processing helix chain 'E' and resid 517 through 519 No H-bonds generated for 'chain 'E' and resid 517 through 519' Processing helix chain 'E' and resid 520 through 529 Processing helix chain 'E' and resid 532 through 549 Processing helix chain 'F' and resid 21 through 25 Processing helix chain 'F' and resid 29 through 37 Processing helix chain 'F' and resid 39 through 44 Processing helix chain 'F' and resid 57 through 59 No H-bonds generated for 'chain 'F' and resid 57 through 59' Processing helix chain 'F' and resid 60 through 73 removed outlier: 3.727A pdb=" N LEU F 64 " --> pdb=" O HIS F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 95 Processing helix chain 'F' and resid 111 through 120 removed outlier: 3.563A pdb=" N GLY F 115 " --> pdb=" O ASP F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'F' and resid 133 through 138 Processing helix chain 'F' and resid 151 through 157 removed outlier: 4.597A pdb=" N LYS F 156 " --> pdb=" O SER F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 174 Processing helix chain 'F' and resid 185 through 190 Processing helix chain 'F' and resid 193 through 208 Processing helix chain 'F' and resid 276 through 295 Processing helix chain 'F' and resid 312 through 323 removed outlier: 3.726A pdb=" N PHE F 323 " --> pdb=" O ALA F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 417 through 429 removed outlier: 4.073A pdb=" N THR F 421 " --> pdb=" O GLY F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 443 through 459 Processing helix chain 'F' and resid 469 through 473 Processing helix chain 'I' and resid 5 through 16 Processing helix chain 'I' and resid 121 through 132 Processing helix chain 'I' and resid 145 through 156 removed outlier: 3.599A pdb=" N THR I 149 " --> pdb=" O ASP I 145 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 176 Processing helix chain 'I' and resid 207 through 219 removed outlier: 4.133A pdb=" N CYS I 211 " --> pdb=" O GLU I 207 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 242 Processing helix chain 'I' and resid 262 through 275 removed outlier: 3.809A pdb=" N GLN I 266 " --> pdb=" O GLU I 262 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 296 Processing helix chain 'I' and resid 302 through 310 Processing helix chain 'I' and resid 355 through 367 Processing helix chain 'I' and resid 383 through 391 Processing helix chain 'I' and resid 406 through 414 Processing helix chain 'I' and resid 414 through 430 Processing helix chain 'I' and resid 458 through 466 Processing helix chain 'I' and resid 513 through 519 removed outlier: 3.883A pdb=" N ARG I 517 " --> pdb=" O LEU I 514 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N GLU I 518 " --> pdb=" O ASP I 515 " (cutoff:3.500A) Processing helix chain 'I' and resid 520 through 529 Processing helix chain 'I' and resid 532 through 549 Processing helix chain 'J' and resid 21 through 25 Processing helix chain 'J' and resid 29 through 37 Processing helix chain 'J' and resid 39 through 43 removed outlier: 3.889A pdb=" N CYS J 43 " --> pdb=" O TYR J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 59 No H-bonds generated for 'chain 'J' and resid 57 through 59' Processing helix chain 'J' and resid 60 through 72 removed outlier: 3.704A pdb=" N LEU J 64 " --> pdb=" O HIS J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 94 Processing helix chain 'J' and resid 111 through 120 removed outlier: 3.647A pdb=" N GLY J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA J 118 " --> pdb=" O HIS J 114 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN J 119 " --> pdb=" O GLY J 115 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 134 Processing helix chain 'J' and resid 135 through 137 No H-bonds generated for 'chain 'J' and resid 135 through 137' Processing helix chain 'J' and resid 151 through 157 removed outlier: 4.515A pdb=" N LYS J 156 " --> pdb=" O SER J 153 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 174 Processing helix chain 'J' and resid 175 through 177 No H-bonds generated for 'chain 'J' and resid 175 through 177' Processing helix chain 'J' and resid 186 through 189 Processing helix chain 'J' and resid 192 through 209 removed outlier: 3.789A pdb=" N VAL J 196 " --> pdb=" O CYS J 192 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY J 209 " --> pdb=" O TYR J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 276 through 295 removed outlier: 3.608A pdb=" N SER J 294 " --> pdb=" O LEU J 290 " (cutoff:3.500A) Processing helix chain 'J' and resid 312 through 322 removed outlier: 3.529A pdb=" N GLN J 317 " --> pdb=" O GLU J 313 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER J 322 " --> pdb=" O GLY J 318 " (cutoff:3.500A) Processing helix chain 'J' and resid 417 through 429 removed outlier: 4.438A pdb=" N THR J 421 " --> pdb=" O GLY J 417 " (cutoff:3.500A) Processing helix chain 'J' and resid 443 through 459 Processing helix chain 'J' and resid 469 through 473 Processing helix chain 'M' and resid 5 through 16 Processing helix chain 'M' and resid 27 through 31 Processing helix chain 'M' and resid 36 through 53 Processing helix chain 'M' and resid 64 through 78 Processing helix chain 'M' and resid 88 through 98 Processing helix chain 'M' and resid 100 through 112 Processing helix chain 'M' and resid 120 through 132 Processing helix chain 'M' and resid 145 through 155 removed outlier: 3.651A pdb=" N ALA M 150 " --> pdb=" O VAL M 146 " (cutoff:3.500A) Processing helix chain 'M' and resid 168 through 176 Processing helix chain 'M' and resid 198 through 203 removed outlier: 3.787A pdb=" N GLN M 202 " --> pdb=" O PRO M 199 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR M 203 " --> pdb=" O ASP M 200 " (cutoff:3.500A) Processing helix chain 'M' and resid 205 through 219 removed outlier: 3.598A pdb=" N ILE M 217 " --> pdb=" O LEU M 213 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG M 218 " --> pdb=" O ALA M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 230 through 242 Processing helix chain 'M' and resid 262 through 275 removed outlier: 3.652A pdb=" N GLN M 266 " --> pdb=" O GLU M 262 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 297 Processing helix chain 'M' and resid 302 through 310 removed outlier: 4.130A pdb=" N LYS M 308 " --> pdb=" O ALA M 304 " (cutoff:3.500A) Processing helix chain 'M' and resid 355 through 367 Processing helix chain 'M' and resid 383 through 391 removed outlier: 3.597A pdb=" N ILE M 387 " --> pdb=" O GLY M 383 " (cutoff:3.500A) Processing helix chain 'M' and resid 406 through 414 Processing helix chain 'M' and resid 414 through 430 Processing helix chain 'M' and resid 455 through 457 No H-bonds generated for 'chain 'M' and resid 455 through 457' Processing helix chain 'M' and resid 458 through 466 Processing helix chain 'M' and resid 517 through 519 No H-bonds generated for 'chain 'M' and resid 517 through 519' Processing helix chain 'M' and resid 520 through 529 Processing helix chain 'M' and resid 532 through 549 Processing helix chain 'N' and resid 21 through 25 Processing helix chain 'N' and resid 29 through 37 Processing helix chain 'N' and resid 39 through 44 Processing helix chain 'N' and resid 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 60 through 73 removed outlier: 3.727A pdb=" N LEU N 64 " --> pdb=" O HIS N 60 " (cutoff:3.500A) Processing helix chain 'N' and resid 89 through 95 Processing helix chain 'N' and resid 111 through 120 removed outlier: 3.563A pdb=" N GLY N 115 " --> pdb=" O ASP N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 132 Processing helix chain 'N' and resid 133 through 138 Processing helix chain 'N' and resid 151 through 157 removed outlier: 4.596A pdb=" N LYS N 156 " --> pdb=" O SER N 153 " (cutoff:3.500A) Processing helix chain 'N' and resid 165 through 174 Processing helix chain 'N' and resid 184 through 190 removed outlier: 4.194A pdb=" N LEU N 188 " --> pdb=" O ASN N 184 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 208 removed outlier: 3.563A pdb=" N VAL N 196 " --> pdb=" O CYS N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 276 through 295 Processing helix chain 'N' and resid 312 through 323 removed outlier: 3.726A pdb=" N PHE N 323 " --> pdb=" O ALA N 319 " (cutoff:3.500A) Processing helix chain 'N' and resid 417 through 429 removed outlier: 4.074A pdb=" N THR N 421 " --> pdb=" O GLY N 417 " (cutoff:3.500A) Processing helix chain 'N' and resid 443 through 459 Processing helix chain 'N' and resid 469 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 137 through 140 Processing sheet with id=AA2, first strand: chain 'A' and resid 221 through 224 removed outlier: 6.098A pdb=" N LEU A 251 " --> pdb=" O TYR A 280 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL A 282 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TRP A 253 " --> pdb=" O VAL A 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 579 through 580 Processing sheet with id=AA4, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.528A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS A 444 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 335 through 338 removed outlier: 4.528A pdb=" N LEU A 501 " --> pdb=" O VAL A 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 371 through 373 removed outlier: 6.899A pdb=" N ILE A 343 " --> pdb=" O TYR A 403 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR A 403 " --> pdb=" O ILE A 343 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS A 345 " --> pdb=" O GLN A 401 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N GLN A 401 " --> pdb=" O CYS A 345 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 347 " --> pdb=" O ILE A 399 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE A 399 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR A 349 " --> pdb=" O ASN A 397 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 561 removed outlier: 3.528A pdb=" N ALA A 569 " --> pdb=" O CYS A 561 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 13 removed outlier: 6.812A pdb=" N GLU B 373 " --> pdb=" O LEU B 369 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 19 through 20 Processing sheet with id=AB1, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.113A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N CYS B 107 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR B 54 " --> pdb=" O CYS B 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 98 through 99 removed outlier: 7.113A pdb=" N VAL B 50 " --> pdb=" O VAL B 99 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ILE B 183 " --> pdb=" O LEU B 146 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL B 148 " --> pdb=" O ILE B 183 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 159 through 160 Processing sheet with id=AB4, first strand: chain 'E' and resid 138 through 139 removed outlier: 8.041A pdb=" N PHE E 139 " --> pdb=" O MET E 20 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TRP E 22 " --> pdb=" O PHE E 139 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET E 21 " --> pdb=" O VAL E 222 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER E 224 " --> pdb=" O MET E 21 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N PHE E 23 " --> pdb=" O SER E 224 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU E 221 " --> pdb=" O TYR E 252 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR E 254 " --> pdb=" O LEU E 221 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL E 223 " --> pdb=" O THR E 254 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TRP E 253 " --> pdb=" O VAL E 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'E' and resid 161 through 162 Processing sheet with id=AB6, first strand: chain 'E' and resid 330 through 332 removed outlier: 3.910A pdb=" N LEU E 331 " --> pdb=" O SER E 580 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER E 580 " --> pdb=" O LEU E 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'E' and resid 335 through 338 removed outlier: 4.631A pdb=" N LEU E 501 " --> pdb=" O VAL E 338 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N HIS E 444 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 335 through 338 removed outlier: 4.631A pdb=" N LEU E 501 " --> pdb=" O VAL E 338 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 371 through 373 removed outlier: 6.625A pdb=" N ILE E 343 " --> pdb=" O TYR E 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR E 403 " --> pdb=" O ILE E 343 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N CYS E 345 " --> pdb=" O GLN E 401 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN E 401 " --> pdb=" O CYS E 345 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL E 347 " --> pdb=" O ILE E 399 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE E 399 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N THR E 349 " --> pdb=" O ASN E 397 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 558 through 561 removed outlier: 3.615A pdb=" N ALA E 569 " --> pdb=" O CYS E 561 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 12 through 13 removed outlier: 3.989A pdb=" N SER F 12 " --> pdb=" O TYR F 366 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR F 366 " --> pdb=" O SER F 12 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU F 375 " --> pdb=" O PRO F 368 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU F 331 " --> pdb=" O PHE F 412 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE F 303 " --> pdb=" O GLU F 330 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL F 332 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N ILE F 305 " --> pdb=" O VAL F 332 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ILE F 334 " --> pdb=" O ILE F 305 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS F 307 " --> pdb=" O ILE F 334 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 19 through 20 Processing sheet with id=AC4, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.602A pdb=" N VAL F 50 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N CYS F 107 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR F 54 " --> pdb=" O CYS F 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'F' and resid 98 through 99 removed outlier: 6.602A pdb=" N VAL F 50 " --> pdb=" O VAL F 99 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG F 51 " --> pdb=" O VAL F 145 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU F 147 " --> pdb=" O ARG F 51 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA F 53 " --> pdb=" O LEU F 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'F' and resid 159 through 160 removed outlier: 3.927A pdb=" N TYR F 160 " --> pdb=" O PHE F 163 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 381 through 382 Processing sheet with id=AC8, first strand: chain 'I' and resid 137 through 140 Processing sheet with id=AC9, first strand: chain 'I' and resid 221 through 224 removed outlier: 6.098A pdb=" N LEU I 251 " --> pdb=" O TYR I 280 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N VAL I 282 " --> pdb=" O LEU I 251 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N TRP I 253 " --> pdb=" O VAL I 282 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 579 through 580 Processing sheet with id=AD2, first strand: chain 'I' and resid 335 through 338 removed outlier: 4.529A pdb=" N LEU I 501 " --> pdb=" O VAL I 338 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N HIS I 444 " --> pdb=" O ILE I 492 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'I' and resid 335 through 338 removed outlier: 4.529A pdb=" N LEU I 501 " --> pdb=" O VAL I 338 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'I' and resid 371 through 373 removed outlier: 6.899A pdb=" N ILE I 343 " --> pdb=" O TYR I 403 " (cutoff:3.500A) removed outlier: 4.891A pdb=" N TYR I 403 " --> pdb=" O ILE I 343 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N CYS I 345 " --> pdb=" O GLN I 401 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N GLN I 401 " --> pdb=" O CYS I 345 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL I 347 " --> pdb=" O ILE I 399 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ILE I 399 " --> pdb=" O VAL I 347 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N THR I 349 " --> pdb=" O ASN I 397 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 558 through 561 removed outlier: 3.528A pdb=" N ALA I 569 " --> pdb=" O CYS I 561 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'J' and resid 12 through 13 removed outlier: 6.812A pdb=" N GLU J 373 " --> pdb=" O LEU J 369 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA J 223 " --> pdb=" O LYS J 302 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'J' and resid 19 through 20 Processing sheet with id=AD8, first strand: chain 'J' and resid 98 through 99 removed outlier: 7.114A pdb=" N VAL J 50 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 8.466A pdb=" N CYS J 107 " --> pdb=" O LEU J 52 " (cutoff:3.500A) removed outlier: 5.872A pdb=" N TYR J 54 " --> pdb=" O CYS J 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'J' and resid 98 through 99 removed outlier: 7.114A pdb=" N VAL J 50 " --> pdb=" O VAL J 99 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N ILE J 183 " --> pdb=" O LEU J 146 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N VAL J 148 " --> pdb=" O ILE J 183 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'J' and resid 159 through 160 Processing sheet with id=AE2, first strand: chain 'M' and resid 138 through 140 removed outlier: 8.041A pdb=" N PHE M 139 " --> pdb=" O MET M 20 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N TRP M 22 " --> pdb=" O PHE M 139 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N MET M 21 " --> pdb=" O VAL M 222 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N SER M 224 " --> pdb=" O MET M 21 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE M 23 " --> pdb=" O SER M 224 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N LEU M 221 " --> pdb=" O TYR M 252 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N THR M 254 " --> pdb=" O LEU M 221 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL M 223 " --> pdb=" O THR M 254 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N TRP M 253 " --> pdb=" O VAL M 282 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE2 Processing sheet with id=AE3, first strand: chain 'M' and resid 161 through 162 Processing sheet with id=AE4, first strand: chain 'M' and resid 330 through 332 removed outlier: 3.910A pdb=" N LEU M 331 " --> pdb=" O SER M 580 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER M 580 " --> pdb=" O LEU M 331 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'M' and resid 335 through 338 removed outlier: 4.631A pdb=" N LEU M 501 " --> pdb=" O VAL M 338 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N HIS M 444 " --> pdb=" O ILE M 492 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 335 through 338 removed outlier: 4.631A pdb=" N LEU M 501 " --> pdb=" O VAL M 338 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 371 through 373 removed outlier: 6.625A pdb=" N ILE M 343 " --> pdb=" O TYR M 403 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N TYR M 403 " --> pdb=" O ILE M 343 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N CYS M 345 " --> pdb=" O GLN M 401 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N GLN M 401 " --> pdb=" O CYS M 345 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL M 347 " --> pdb=" O ILE M 399 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ILE M 399 " --> pdb=" O VAL M 347 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N THR M 349 " --> pdb=" O ASN M 397 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 558 through 561 removed outlier: 3.616A pdb=" N ALA M 569 " --> pdb=" O CYS M 561 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'N' and resid 12 through 13 removed outlier: 3.990A pdb=" N SER N 12 " --> pdb=" O TYR N 366 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N TYR N 366 " --> pdb=" O SER N 12 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N LEU N 375 " --> pdb=" O PRO N 368 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N LEU N 331 " --> pdb=" O PHE N 412 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ILE N 303 " --> pdb=" O GLU N 330 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL N 332 " --> pdb=" O ILE N 303 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N ILE N 305 " --> pdb=" O VAL N 332 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ILE N 334 " --> pdb=" O ILE N 305 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LYS N 307 " --> pdb=" O ILE N 334 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N CYS N 244 " --> pdb=" O TYR N 260 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'N' and resid 19 through 20 Processing sheet with id=AF2, first strand: chain 'N' and resid 98 through 99 removed outlier: 6.602A pdb=" N VAL N 50 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N CYS N 107 " --> pdb=" O LEU N 52 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N TYR N 54 " --> pdb=" O CYS N 107 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'N' and resid 98 through 99 removed outlier: 6.602A pdb=" N VAL N 50 " --> pdb=" O VAL N 99 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N ARG N 51 " --> pdb=" O VAL N 145 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N LEU N 147 " --> pdb=" O ARG N 51 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA N 53 " --> pdb=" O LEU N 147 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'N' and resid 159 through 160 removed outlier: 3.927A pdb=" N TYR N 160 " --> pdb=" O PHE N 163 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 381 through 382 1385 hydrogen bonds defined for protein. 3870 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 144 hydrogen bonds 272 hydrogen bond angles 0 basepair planarities 60 basepair parallelities 104 stacking parallelities Total time for adding SS restraints: 6.66 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 5309 1.32 - 1.44: 10697 1.44 - 1.57: 19148 1.57 - 1.69: 324 1.69 - 1.82: 190 Bond restraints: 35668 Sorted by residual: bond pdb=" N PHE I 247 " pdb=" CA PHE I 247 " ideal model delta sigma weight residual 1.458 1.485 -0.028 7.40e-03 1.83e+04 1.39e+01 bond pdb=" CA SER M 167 " pdb=" CB SER M 167 " ideal model delta sigma weight residual 1.541 1.503 0.038 1.20e-02 6.94e+03 1.00e+01 bond pdb=" C PRO M 35 " pdb=" O PRO M 35 " ideal model delta sigma weight residual 1.233 1.199 0.035 1.10e-02 8.26e+03 9.91e+00 bond pdb=" C THR N 189 " pdb=" O THR N 189 " ideal model delta sigma weight residual 1.236 1.195 0.041 1.32e-02 5.74e+03 9.75e+00 bond pdb=" N THR J 401 " pdb=" CA THR J 401 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.04e-02 9.25e+03 9.45e+00 ... (remaining 35663 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 48026 2.27 - 4.54: 921 4.54 - 6.81: 104 6.81 - 9.09: 20 9.09 - 11.36: 9 Bond angle restraints: 49080 Sorted by residual: angle pdb=" N GLN N 191 " pdb=" CA GLN N 191 " pdb=" C GLN N 191 " ideal model delta sigma weight residual 110.80 122.16 -11.36 2.13e+00 2.20e-01 2.84e+01 angle pdb=" N ILE N 462 " pdb=" CA ILE N 462 " pdb=" C ILE N 462 " ideal model delta sigma weight residual 113.20 108.09 5.11 9.60e-01 1.09e+00 2.83e+01 angle pdb=" N ILE F 462 " pdb=" CA ILE F 462 " pdb=" C ILE F 462 " ideal model delta sigma weight residual 113.20 108.11 5.09 9.60e-01 1.09e+00 2.81e+01 angle pdb=" C GLN I 15 " pdb=" N ASN I 16 " pdb=" CA ASN I 16 " ideal model delta sigma weight residual 123.03 116.09 6.94 1.34e+00 5.57e-01 2.69e+01 angle pdb=" N LEU M 14 " pdb=" CA LEU M 14 " pdb=" C LEU M 14 " ideal model delta sigma weight residual 111.28 105.67 5.61 1.09e+00 8.42e-01 2.65e+01 ... (remaining 49075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.84: 19914 35.84 - 71.68: 1210 71.68 - 107.52: 63 107.52 - 143.36: 0 143.36 - 179.20: 9 Dihedral angle restraints: 21196 sinusoidal: 9828 harmonic: 11368 Sorted by residual: dihedral pdb=" C5' AMP E 601 " pdb=" O5' AMP E 601 " pdb=" P AMP E 601 " pdb=" O3P AMP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 119.20 -179.20 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" N SER E 167 " pdb=" C SER E 167 " pdb=" CA SER E 167 " pdb=" CB SER E 167 " ideal model delta harmonic sigma weight residual 122.80 133.95 -11.15 0 2.50e+00 1.60e-01 1.99e+01 dihedral pdb=" C2' AMP M 601 " pdb=" C1' AMP M 601 " pdb=" N9 AMP M 601 " pdb=" C4 AMP M 601 " ideal model delta sinusoidal sigma weight residual 91.55 168.06 -76.50 1 2.00e+01 2.50e-03 1.84e+01 ... (remaining 21193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5178 0.095 - 0.190: 281 0.190 - 0.284: 19 0.284 - 0.379: 5 0.379 - 0.474: 3 Chirality restraints: 5486 Sorted by residual: chirality pdb=" CA ALA N 187 " pdb=" N ALA N 187 " pdb=" C ALA N 187 " pdb=" CB ALA N 187 " both_signs ideal model delta sigma weight residual False 2.48 2.01 0.47 2.00e-01 2.50e+01 5.62e+00 chirality pdb=" CA SER E 167 " pdb=" N SER E 167 " pdb=" C SER E 167 " pdb=" CB SER E 167 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.41e+00 chirality pdb=" CA ARG J 190 " pdb=" N ARG J 190 " pdb=" C ARG J 190 " pdb=" CB ARG J 190 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.46 2.00e-01 2.50e+01 5.18e+00 ... (remaining 5483 not shown) Planarity restraints: 5684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU I 14 " -0.020 2.00e-02 2.50e+03 4.16e-02 1.73e+01 pdb=" C LEU I 14 " 0.072 2.00e-02 2.50e+03 pdb=" O LEU I 14 " -0.027 2.00e-02 2.50e+03 pdb=" N GLN I 15 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER M 31 " 0.017 2.00e-02 2.50e+03 3.40e-02 1.16e+01 pdb=" C SER M 31 " -0.059 2.00e-02 2.50e+03 pdb=" O SER M 31 " 0.022 2.00e-02 2.50e+03 pdb=" N ALA M 32 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS I 315 " 0.051 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO I 316 " -0.129 5.00e-02 4.00e+02 pdb=" CA PRO I 316 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO I 316 " 0.041 5.00e-02 4.00e+02 ... (remaining 5681 not shown) Histogram of nonbonded interaction distances: 1.53 - 2.20: 45 2.20 - 2.88: 13477 2.88 - 3.55: 50725 3.55 - 4.23: 85171 4.23 - 4.90: 144233 Nonbonded interactions: 293651 Sorted by model distance: nonbonded pdb=" OH TYR E 168 " pdb=" CB GLN M 192 " model vdw 1.526 3.440 nonbonded pdb=" OE1 GLU J 330 " pdb=" CA GLY J 414 " model vdw 1.815 3.440 nonbonded pdb=" OD2 ASP F 261 " pdb=" CG1 VAL F 463 " model vdw 1.885 3.460 nonbonded pdb=" CB GLN E 192 " pdb=" OH TYR M 168 " model vdw 1.898 3.440 nonbonded pdb=" OD2 ASP E 188 " pdb=" NH1 ARG E 190 " model vdw 1.909 3.120 ... (remaining 293646 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'I' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 5 through 473) selection = chain 'J' selection = (chain 'N' and resid 5 through 473) } ncs_group { reference = (chain 'C' and resid 1 through 21) selection = chain 'G' selection = (chain 'K' and resid 1 through 21) selection = chain 'O' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'E' selection = chain 'M' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.000 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: 0.030 Extract box with map and model: 0.530 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 32.410 Find NCS groups from input model: 0.580 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 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 : 0.005 0.410 35670 Z= 0.315 Angle : 0.714 11.358 49080 Z= 0.410 Chirality : 0.047 0.474 5486 Planarity : 0.005 0.076 5684 Dihedral : 20.404 179.197 13876 Min Nonbonded Distance : 1.526 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.63 % Favored : 95.21 % Rotamer: Outliers : 1.83 % Allowed : 30.62 % Favored : 67.56 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.14), residues: 3842 helix: 0.73 (0.14), residues: 1476 sheet: -0.67 (0.20), residues: 758 loop : -0.64 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 411 TYR 0.019 0.001 TYR N 274 PHE 0.016 0.001 PHE M 287 TRP 0.015 0.001 TRP M 502 HIS 0.011 0.001 HIS M 52 Details of bonding type rmsd covalent geometry : bond 0.00388 (35668) covalent geometry : angle 0.71429 (49080) hydrogen bonds : bond 0.15270 ( 1469) hydrogen bonds : angle 6.39042 ( 4142) Misc. bond : bond 0.30703 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 761 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 379 LEU cc_start: 0.7792 (mm) cc_final: 0.7539 (tt) REVERT: B 100 MET cc_start: 0.6540 (mmm) cc_final: 0.5933 (tpt) REVERT: E 93 PHE cc_start: 0.8950 (OUTLIER) cc_final: 0.8169 (m-80) REVERT: I 15 GLN cc_start: 0.8242 (OUTLIER) cc_final: 0.7772 (tt0) REVERT: I 390 ILE cc_start: 0.3550 (tp) cc_final: 0.3291 (tp) REVERT: J 302 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8313 (tttt) REVERT: M 30 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7571 (ttm170) REVERT: M 48 TYR cc_start: 0.6424 (t80) cc_final: 0.6076 (t80) REVERT: M 133 ASN cc_start: 0.7722 (t0) cc_final: 0.7071 (t0) REVERT: M 165 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.7218 (mm-30) REVERT: M 198 THR cc_start: 0.7157 (m) cc_final: 0.6936 (m) REVERT: M 332 ARG cc_start: 0.7614 (ttp-170) cc_final: 0.7088 (ttt180) REVERT: M 461 LEU cc_start: 0.6202 (tp) cc_final: 0.5810 (mp) REVERT: M 546 ILE cc_start: 0.7237 (mt) cc_final: 0.6661 (mt) REVERT: M 566 GLU cc_start: 0.3991 (mp0) cc_final: 0.3252 (tt0) REVERT: M 579 PHE cc_start: 0.6685 (p90) cc_final: 0.6305 (p90) REVERT: N 40 TYR cc_start: 0.7166 (t80) cc_final: 0.6874 (t80) REVERT: N 70 GLU cc_start: 0.6773 (mt-10) cc_final: 0.6511 (tt0) REVERT: N 276 SER cc_start: 0.8212 (p) cc_final: 0.8007 (m) REVERT: N 280 MET cc_start: 0.8263 (tpp) cc_final: 0.8054 (tpt) REVERT: N 376 LEU cc_start: 0.7331 (tp) cc_final: 0.7018 (tp) outliers start: 61 outliers final: 27 residues processed: 815 average time/residue: 0.2271 time to fit residues: 290.6154 Evaluate side-chains 520 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 488 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain B residue 189 THR Chi-restraints excluded: chain B residue 190 ARG Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 265 VAL Chi-restraints excluded: chain I residue 266 GLN Chi-restraints excluded: chain I residue 269 ILE Chi-restraints excluded: chain I residue 326 LYS Chi-restraints excluded: chain I residue 329 PRO Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain J residue 41 SER Chi-restraints excluded: chain J residue 190 ARG Chi-restraints excluded: chain J residue 302 LYS Chi-restraints excluded: chain J residue 303 ILE Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 147 ILE Chi-restraints excluded: chain M residue 149 THR Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 165 GLU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 209 HIS Chi-restraints excluded: chain M residue 211 CYS Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 270 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 4.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.0980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 9.9990 chunk 401 optimal weight: 7.9990 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 20.0000 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 60 HIS ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 83 GLN ** E 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 114 HIS F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 ASN F 379 GLN ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 18 GLN I 120 ASN I 123 HIS I 244 ASN J 60 HIS J 166 HIS ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN M 83 GLN ** M 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 HIS ** M 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 533 ASN ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 296 ASN ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 450 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.153243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.121261 restraints weight = 58319.272| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.66 r_work: 0.3500 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 35670 Z= 0.233 Angle : 0.699 9.448 49080 Z= 0.357 Chirality : 0.044 0.211 5486 Planarity : 0.005 0.052 5684 Dihedral : 18.029 171.680 6558 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 6.44 % Allowed : 27.80 % Favored : 65.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.14), residues: 3842 helix: 0.79 (0.13), residues: 1464 sheet: -0.69 (0.19), residues: 784 loop : -0.75 (0.16), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG I 462 TYR 0.024 0.002 TYR N 87 PHE 0.023 0.002 PHE N 21 TRP 0.018 0.002 TRP N 418 HIS 0.017 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00537 (35668) covalent geometry : angle 0.69879 (49080) hydrogen bonds : bond 0.05166 ( 1469) hydrogen bonds : angle 5.12979 ( 4142) Misc. bond : bond 0.00449 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 215 poor density : 517 time to evaluate : 1.443 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 16 ASN cc_start: 0.9010 (OUTLIER) cc_final: 0.8671 (p0) REVERT: A 21 MET cc_start: 0.7407 (ttm) cc_final: 0.7206 (ttm) REVERT: A 22 TRP cc_start: 0.8368 (m100) cc_final: 0.8035 (m100) REVERT: A 136 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7787 (mptp) REVERT: A 289 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8427 (tm-30) REVERT: A 379 LEU cc_start: 0.7859 (mm) cc_final: 0.7634 (tt) REVERT: B 100 MET cc_start: 0.7089 (mmm) cc_final: 0.6549 (mmm) REVERT: B 441 LYS cc_start: 0.8222 (tttt) cc_final: 0.8021 (tptm) REVERT: E 93 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8319 (m-80) REVERT: E 132 MET cc_start: 0.8769 (ttp) cc_final: 0.8545 (ttt) REVERT: E 572 GLU cc_start: 0.7862 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: I 181 ILE cc_start: 0.8232 (OUTLIER) cc_final: 0.8029 (pt) REVERT: I 206 ARG cc_start: 0.5914 (tpt90) cc_final: 0.5524 (ptt-90) REVERT: I 463 LYS cc_start: 0.8046 (tppt) cc_final: 0.7671 (tppt) REVERT: I 537 TYR cc_start: 0.7754 (t80) cc_final: 0.7527 (t80) REVERT: I 547 LEU cc_start: 0.8134 (mm) cc_final: 0.7924 (mm) REVERT: J 40 TYR cc_start: 0.8633 (t80) cc_final: 0.8397 (t80) REVERT: J 72 GLN cc_start: 0.7359 (mt0) cc_final: 0.6845 (tm-30) REVERT: J 133 MET cc_start: 0.8547 (ptp) cc_final: 0.8226 (ptp) REVERT: J 154 TRP cc_start: 0.7633 (m-10) cc_final: 0.7351 (m-10) REVERT: J 426 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8230 (mt) REVERT: M 30 ARG cc_start: 0.7827 (OUTLIER) cc_final: 0.7489 (ttm170) REVERT: M 43 ASP cc_start: 0.8510 (t0) cc_final: 0.8229 (t0) REVERT: M 61 ASP cc_start: 0.7930 (p0) cc_final: 0.7692 (p0) REVERT: M 133 ASN cc_start: 0.8659 (t0) cc_final: 0.7900 (t0) REVERT: M 153 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7414 (t0) REVERT: M 332 ARG cc_start: 0.7839 (ttp-170) cc_final: 0.6988 (ptm-80) REVERT: M 461 LEU cc_start: 0.6198 (tp) cc_final: 0.5951 (mp) REVERT: M 497 ARG cc_start: 0.7018 (tpp-160) cc_final: 0.5054 (tpp-160) REVERT: M 531 ARG cc_start: 0.6330 (mtt180) cc_final: 0.6071 (ttp-170) REVERT: M 546 ILE cc_start: 0.7281 (mt) cc_final: 0.6987 (mt) REVERT: M 566 GLU cc_start: 0.4765 (mp0) cc_final: 0.3955 (tt0) REVERT: M 579 PHE cc_start: 0.7160 (p90) cc_final: 0.6751 (p90) REVERT: N 133 MET cc_start: 0.8608 (mtt) cc_final: 0.8181 (mtt) REVERT: N 190 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7006 (ttt-90) REVERT: N 197 MET cc_start: 0.7446 (mmp) cc_final: 0.7029 (mmp) REVERT: N 270 LYS cc_start: 0.8456 (OUTLIER) cc_final: 0.7999 (mmmm) REVERT: N 276 SER cc_start: 0.8576 (p) cc_final: 0.8369 (m) REVERT: N 302 LYS cc_start: 0.7949 (tttm) cc_final: 0.6795 (ttmm) outliers start: 215 outliers final: 115 residues processed: 675 average time/residue: 0.1931 time to fit residues: 212.4844 Evaluate side-chains 568 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 442 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 65 ASP Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 19 HIS Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 173 VAL Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 327 THR Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 120 ASN Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 181 ILE Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 257 SER Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 319 ILE Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 23 ASP Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 35 SER Chi-restraints excluded: chain J residue 58 THR Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 424 SER Chi-restraints excluded: chain J residue 426 LEU Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 30 ARG Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 157 LYS Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 125 LEU Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 245 SER Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 270 LYS Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 329 ILE Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 343 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 351 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 chunk 373 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 122 optimal weight: 0.4980 chunk 98 optimal weight: 0.9990 chunk 218 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 266 GLN ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 281 GLN ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN I 133 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 119 ASN ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 389 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.156314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.124196 restraints weight = 57890.117| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 2.76 r_work: 0.3538 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35670 Z= 0.140 Angle : 0.611 8.957 49080 Z= 0.310 Chirality : 0.041 0.333 5486 Planarity : 0.004 0.038 5684 Dihedral : 17.841 171.320 6514 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.97 % Allowed : 28.28 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.14), residues: 3842 helix: 1.00 (0.14), residues: 1476 sheet: -0.56 (0.19), residues: 800 loop : -0.70 (0.16), residues: 1566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 47 TYR 0.023 0.001 TYR N 291 PHE 0.021 0.001 PHE M 287 TRP 0.020 0.001 TRP M 510 HIS 0.013 0.001 HIS M 52 Details of bonding type rmsd covalent geometry : bond 0.00308 (35668) covalent geometry : angle 0.61104 (49080) hydrogen bonds : bond 0.04730 ( 1469) hydrogen bonds : angle 4.83032 ( 4142) Misc. bond : bond 0.00027 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 166 poor density : 495 time to evaluate : 1.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7818 (mm) REVERT: A 289 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8363 (tm-30) REVERT: B 100 MET cc_start: 0.7170 (mmm) cc_final: 0.6652 (mmm) REVERT: E 16 ASN cc_start: 0.8205 (OUTLIER) cc_final: 0.7914 (p0) REVERT: E 93 PHE cc_start: 0.9023 (OUTLIER) cc_final: 0.8209 (m-80) REVERT: E 210 LYS cc_start: 0.8275 (tppt) cc_final: 0.7806 (mtmm) REVERT: E 234 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.8089 (tpp) REVERT: E 492 ILE cc_start: 0.8975 (mt) cc_final: 0.8712 (mt) REVERT: E 572 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7375 (pt0) REVERT: F 249 ASP cc_start: 0.7637 (t0) cc_final: 0.7410 (t0) REVERT: F 256 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7743 (tt0) REVERT: I 206 ARG cc_start: 0.5895 (tpt90) cc_final: 0.5556 (ptt-90) REVERT: I 374 TYR cc_start: 0.5694 (t80) cc_final: 0.5463 (t80) REVERT: I 397 ASN cc_start: 0.6185 (m-40) cc_final: 0.5901 (t0) REVERT: I 463 LYS cc_start: 0.8118 (tppt) cc_final: 0.7711 (tppt) REVERT: I 522 ASP cc_start: 0.8525 (m-30) cc_final: 0.8084 (t0) REVERT: I 547 LEU cc_start: 0.8188 (mm) cc_final: 0.7952 (mm) REVERT: J 72 GLN cc_start: 0.7251 (mt0) cc_final: 0.6862 (tm-30) REVERT: J 128 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8221 (ptpp) REVERT: J 133 MET cc_start: 0.8611 (ptp) cc_final: 0.8275 (ptp) REVERT: J 192 CYS cc_start: 0.6958 (t) cc_final: 0.6631 (t) REVERT: J 288 LEU cc_start: 0.8574 (mt) cc_final: 0.8352 (mt) REVERT: M 43 ASP cc_start: 0.8479 (t0) cc_final: 0.8205 (t0) REVERT: M 131 GLU cc_start: 0.8439 (tm-30) cc_final: 0.8191 (tm-30) REVERT: M 133 ASN cc_start: 0.8621 (t0) cc_final: 0.7671 (t0) REVERT: M 155 SER cc_start: 0.8220 (m) cc_final: 0.7828 (p) REVERT: M 332 ARG cc_start: 0.7835 (ttp-170) cc_final: 0.6944 (ptm-80) REVERT: M 462 ARG cc_start: 0.4825 (mtp85) cc_final: 0.4338 (mtt-85) REVERT: M 497 ARG cc_start: 0.6926 (tpp-160) cc_final: 0.4821 (tpp-160) REVERT: M 508 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6827 (pm20) REVERT: M 566 GLU cc_start: 0.4844 (mp0) cc_final: 0.4086 (tt0) REVERT: N 49 GLN cc_start: 0.7748 (pm20) cc_final: 0.7541 (pm20) REVERT: N 190 ARG cc_start: 0.7622 (OUTLIER) cc_final: 0.6920 (ttt-90) REVERT: N 276 SER cc_start: 0.8648 (p) cc_final: 0.8369 (m) REVERT: N 278 GLN cc_start: 0.8085 (tp40) cc_final: 0.7808 (tp40) REVERT: N 302 LYS cc_start: 0.7831 (tttm) cc_final: 0.7502 (mtpp) outliers start: 166 outliers final: 94 residues processed: 622 average time/residue: 0.1991 time to fit residues: 203.0990 Evaluate side-chains 539 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 436 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 236 MET Chi-restraints excluded: chain I residue 237 LEU Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 319 ILE Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 180 ILE Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 466 ILE Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 153 ASP Chi-restraints excluded: chain M residue 157 LYS Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 251 LEU Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 230 optimal weight: 5.9990 chunk 370 optimal weight: 1.9990 chunk 254 optimal weight: 9.9990 chunk 165 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 307 optimal weight: 6.9990 chunk 154 optimal weight: 2.9990 chunk 225 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 194 optimal weight: 0.0030 overall best weight: 1.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 387 GLN F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 GLN I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 296 ASN J 367 GLN ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 389 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.153207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.119919 restraints weight = 57442.921| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 2.76 r_work: 0.3457 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 35670 Z= 0.164 Angle : 0.614 8.834 49080 Z= 0.312 Chirality : 0.041 0.214 5486 Planarity : 0.004 0.039 5684 Dihedral : 17.746 171.657 6501 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 6.53 % Allowed : 27.56 % Favored : 65.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.14), residues: 3842 helix: 1.00 (0.14), residues: 1474 sheet: -0.51 (0.19), residues: 800 loop : -0.73 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 47 TYR 0.022 0.002 TYR J 40 PHE 0.021 0.001 PHE N 90 TRP 0.017 0.001 TRP M 510 HIS 0.013 0.001 HIS M 52 Details of bonding type rmsd covalent geometry : bond 0.00376 (35668) covalent geometry : angle 0.61397 (49080) hydrogen bonds : bond 0.04643 ( 1469) hydrogen bonds : angle 4.74769 ( 4142) Misc. bond : bond 0.00020 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 218 poor density : 463 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8964 (OUTLIER) cc_final: 0.8371 (p90) REVERT: A 22 TRP cc_start: 0.8433 (m100) cc_final: 0.7996 (m100) REVERT: A 213 LEU cc_start: 0.8300 (OUTLIER) cc_final: 0.7929 (mm) REVERT: A 289 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8399 (tm-30) REVERT: A 318 SER cc_start: 0.8771 (OUTLIER) cc_final: 0.8507 (m) REVERT: A 319 ILE cc_start: 0.8492 (pt) cc_final: 0.8290 (pt) REVERT: B 34 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8141 (mp) REVERT: B 100 MET cc_start: 0.6899 (mmm) cc_final: 0.6501 (mmm) REVERT: B 302 LYS cc_start: 0.8978 (ttpt) cc_final: 0.8504 (ttmm) REVERT: E 16 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7915 (p0) REVERT: E 61 ASP cc_start: 0.8099 (p0) cc_final: 0.6059 (m-30) REVERT: E 93 PHE cc_start: 0.9066 (OUTLIER) cc_final: 0.8291 (m-80) REVERT: E 210 LYS cc_start: 0.8340 (tppt) cc_final: 0.7868 (mtmm) REVERT: E 234 MET cc_start: 0.8447 (OUTLIER) cc_final: 0.7906 (mpp) REVERT: E 492 ILE cc_start: 0.8988 (mt) cc_final: 0.8716 (mt) REVERT: E 572 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7261 (pt0) REVERT: F 249 ASP cc_start: 0.7682 (t0) cc_final: 0.7425 (t0) REVERT: F 256 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7722 (tt0) REVERT: I 206 ARG cc_start: 0.5848 (tpt90) cc_final: 0.5544 (ptt-90) REVERT: I 397 ASN cc_start: 0.6175 (m-40) cc_final: 0.5769 (t0) REVERT: I 463 LYS cc_start: 0.8143 (tppt) cc_final: 0.7680 (tppt) REVERT: I 547 LEU cc_start: 0.8272 (mm) cc_final: 0.7992 (mm) REVERT: J 72 GLN cc_start: 0.7317 (mt0) cc_final: 0.6804 (tm-30) REVERT: J 100 MET cc_start: 0.6356 (ppp) cc_final: 0.6113 (ppp) REVERT: J 133 MET cc_start: 0.8593 (ptp) cc_final: 0.8278 (ptp) REVERT: J 192 CYS cc_start: 0.7132 (t) cc_final: 0.6780 (t) REVERT: J 215 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8130 (mm) REVERT: M 47 ARG cc_start: 0.8113 (mtt-85) cc_final: 0.7858 (mtt-85) REVERT: M 131 GLU cc_start: 0.8523 (tm-30) cc_final: 0.8115 (tt0) REVERT: M 133 ASN cc_start: 0.8632 (t0) cc_final: 0.7516 (t0) REVERT: M 332 ARG cc_start: 0.7819 (ttp-170) cc_final: 0.7201 (ptm-80) REVERT: M 462 ARG cc_start: 0.5178 (mtp85) cc_final: 0.4618 (mpt-90) REVERT: M 497 ARG cc_start: 0.6941 (tpp-160) cc_final: 0.4355 (tpp-160) REVERT: M 508 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6892 (pm20) REVERT: M 525 ARG cc_start: 0.7577 (ttp-170) cc_final: 0.7259 (ttp80) REVERT: M 579 PHE cc_start: 0.7247 (p90) cc_final: 0.6712 (p90) REVERT: N 40 TYR cc_start: 0.7695 (t80) cc_final: 0.7451 (t80) REVERT: N 61 MET cc_start: 0.7174 (mtp) cc_final: 0.6798 (mtp) REVERT: N 70 GLU cc_start: 0.7496 (tt0) cc_final: 0.7230 (tt0) REVERT: N 276 SER cc_start: 0.8681 (p) cc_final: 0.8356 (m) REVERT: N 278 GLN cc_start: 0.8091 (tp40) cc_final: 0.7828 (tp40) REVERT: N 301 ARG cc_start: 0.8008 (ptm-80) cc_final: 0.7577 (tpt170) REVERT: N 302 LYS cc_start: 0.7944 (tttm) cc_final: 0.7721 (mmmt) outliers start: 218 outliers final: 141 residues processed: 626 average time/residue: 0.1941 time to fit residues: 197.8034 Evaluate side-chains 584 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 431 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 15 GLN Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 236 MET Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 319 ILE Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 424 SER Chi-restraints excluded: chain J residue 466 ILE Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 157 LYS Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 319 ILE Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 398 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 281 optimal weight: 5.9990 chunk 138 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 122 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 chunk 287 optimal weight: 0.6980 chunk 327 optimal weight: 6.9990 chunk 367 optimal weight: 7.9990 chunk 88 optimal weight: 0.9980 chunk 242 optimal weight: 0.9980 overall best weight: 1.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN ** I 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 52 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 139 GLN ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4022 r_free = 0.4022 target = 0.151922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.118410 restraints weight = 57484.652| |-----------------------------------------------------------------------------| r_work (start): 0.3577 rms_B_bonded: 2.67 r_work: 0.3443 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 35670 Z= 0.174 Angle : 0.613 8.756 49080 Z= 0.311 Chirality : 0.041 0.216 5486 Planarity : 0.004 0.045 5684 Dihedral : 17.688 171.513 6501 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 6.41 % Allowed : 28.16 % Favored : 65.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.14), residues: 3842 helix: 1.01 (0.14), residues: 1472 sheet: -0.53 (0.19), residues: 800 loop : -0.78 (0.16), residues: 1570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 529 TYR 0.019 0.002 TYR N 291 PHE 0.023 0.002 PHE E 287 TRP 0.018 0.001 TRP M 510 HIS 0.019 0.001 HIS M 52 Details of bonding type rmsd covalent geometry : bond 0.00399 (35668) covalent geometry : angle 0.61341 (49080) hydrogen bonds : bond 0.04594 ( 1469) hydrogen bonds : angle 4.69183 ( 4142) Misc. bond : bond 0.00017 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 687 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 214 poor density : 473 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8969 (OUTLIER) cc_final: 0.8378 (p90) REVERT: A 136 LYS cc_start: 0.8195 (OUTLIER) cc_final: 0.7861 (mptp) REVERT: A 213 LEU cc_start: 0.8277 (OUTLIER) cc_final: 0.7946 (mm) REVERT: A 289 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8391 (tm-30) REVERT: A 318 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8522 (m) REVERT: B 34 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8196 (mp) REVERT: B 100 MET cc_start: 0.6841 (mmm) cc_final: 0.6479 (mmm) REVERT: E 16 ASN cc_start: 0.8390 (OUTLIER) cc_final: 0.7913 (p0) REVERT: E 93 PHE cc_start: 0.9085 (OUTLIER) cc_final: 0.8343 (m-80) REVERT: E 234 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7932 (mpp) REVERT: E 492 ILE cc_start: 0.8988 (mt) cc_final: 0.8721 (mt) REVERT: E 572 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7324 (pt0) REVERT: F 249 ASP cc_start: 0.7697 (t0) cc_final: 0.7449 (t0) REVERT: F 256 GLU cc_start: 0.7905 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: I 206 ARG cc_start: 0.5934 (tpt90) cc_final: 0.5620 (ptt-90) REVERT: I 289 GLU cc_start: 0.8132 (tm-30) cc_final: 0.7804 (tm-30) REVERT: I 310 ARG cc_start: 0.6912 (ptt-90) cc_final: 0.6502 (tpt-90) REVERT: I 397 ASN cc_start: 0.6017 (m-40) cc_final: 0.5714 (t0) REVERT: I 437 HIS cc_start: 0.7332 (p-80) cc_final: 0.6999 (p-80) REVERT: I 463 LYS cc_start: 0.8227 (tppt) cc_final: 0.7868 (tppt) REVERT: I 522 ASP cc_start: 0.8524 (m-30) cc_final: 0.8109 (t0) REVERT: I 547 LEU cc_start: 0.8334 (mm) cc_final: 0.8107 (mm) REVERT: I 556 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8158 (m) REVERT: J 49 GLN cc_start: 0.8300 (pm20) cc_final: 0.7926 (pt0) REVERT: J 72 GLN cc_start: 0.7289 (mt0) cc_final: 0.6804 (tm-30) REVERT: J 100 MET cc_start: 0.6214 (ppp) cc_final: 0.6003 (ppp) REVERT: J 192 CYS cc_start: 0.6967 (t) cc_final: 0.6633 (t) REVERT: J 215 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8217 (mm) REVERT: M 332 ARG cc_start: 0.7866 (ttp-170) cc_final: 0.7623 (ptm-80) REVERT: M 381 LEU cc_start: 0.6839 (tp) cc_final: 0.6467 (tt) REVERT: M 403 TYR cc_start: 0.7066 (m-80) cc_final: 0.6622 (m-10) REVERT: M 462 ARG cc_start: 0.5055 (mtp85) cc_final: 0.4540 (mpt-90) REVERT: M 497 ARG cc_start: 0.6741 (tpp-160) cc_final: 0.5084 (tpp-160) REVERT: M 508 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.6727 (pm20) REVERT: M 525 ARG cc_start: 0.7553 (ttp-170) cc_final: 0.7319 (ttp80) REVERT: N 61 MET cc_start: 0.7268 (mtp) cc_final: 0.6973 (mtp) REVERT: N 197 MET cc_start: 0.7442 (mmp) cc_final: 0.7180 (mmp) REVERT: N 255 PHE cc_start: 0.6674 (OUTLIER) cc_final: 0.5580 (t80) REVERT: N 276 SER cc_start: 0.8702 (p) cc_final: 0.8349 (m) REVERT: N 278 GLN cc_start: 0.8128 (tp40) cc_final: 0.7852 (tp40) REVERT: N 301 ARG cc_start: 0.8125 (ptm-80) cc_final: 0.7669 (tpt170) REVERT: N 302 LYS cc_start: 0.8043 (tttm) cc_final: 0.7794 (mmmt) outliers start: 214 outliers final: 158 residues processed: 639 average time/residue: 0.2034 time to fit residues: 213.7323 Evaluate side-chains 615 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 173 poor density : 442 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 219 PHE Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 231 ILE Chi-restraints excluded: chain B residue 242 THR Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 362 ASP Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 408 MET Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 556 THR Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 125 LEU Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 244 CYS Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 407 ILE Chi-restraints excluded: chain J residue 424 SER Chi-restraints excluded: chain J residue 462 ILE Chi-restraints excluded: chain J residue 466 ILE Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 62 ILE Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 157 LYS Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain M residue 237 LEU Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 286 THR Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 398 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 221 ASP Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 372 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 86 optimal weight: 3.9990 chunk 92 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 258 optimal weight: 2.9990 chunk 362 optimal weight: 7.9990 chunk 392 optimal weight: 0.0970 chunk 94 optimal weight: 3.9990 chunk 399 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 7 ASN I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 HIS ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.150708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.119768 restraints weight = 57550.241| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.48 r_work: 0.3459 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 35670 Z= 0.166 Angle : 0.614 8.829 49080 Z= 0.312 Chirality : 0.041 0.234 5486 Planarity : 0.004 0.080 5684 Dihedral : 17.632 171.048 6501 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 6.14 % Allowed : 28.46 % Favored : 65.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.13 (0.14), residues: 3842 helix: 1.00 (0.14), residues: 1474 sheet: -0.54 (0.19), residues: 800 loop : -0.78 (0.16), residues: 1568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 47 TYR 0.021 0.002 TYR N 229 PHE 0.021 0.001 PHE E 287 TRP 0.021 0.001 TRP M 510 HIS 0.015 0.001 HIS M 52 Details of bonding type rmsd covalent geometry : bond 0.00380 (35668) covalent geometry : angle 0.61350 (49080) hydrogen bonds : bond 0.04570 ( 1469) hydrogen bonds : angle 4.68102 ( 4142) Misc. bond : bond 0.00015 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 675 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 205 poor density : 470 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8970 (OUTLIER) cc_final: 0.8358 (p90) REVERT: A 22 TRP cc_start: 0.8411 (m100) cc_final: 0.7994 (m100) REVERT: A 136 LYS cc_start: 0.8197 (OUTLIER) cc_final: 0.7869 (mptp) REVERT: A 213 LEU cc_start: 0.8292 (OUTLIER) cc_final: 0.7944 (mm) REVERT: A 289 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8391 (tm-30) REVERT: A 318 SER cc_start: 0.8787 (OUTLIER) cc_final: 0.8548 (m) REVERT: A 567 PHE cc_start: 0.6478 (m-80) cc_final: 0.6236 (m-80) REVERT: B 34 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8261 (mp) REVERT: B 100 MET cc_start: 0.6752 (mmm) cc_final: 0.6438 (mmm) REVERT: E 16 ASN cc_start: 0.8259 (OUTLIER) cc_final: 0.7802 (p0) REVERT: E 93 PHE cc_start: 0.9067 (OUTLIER) cc_final: 0.8352 (m-80) REVERT: E 244 ASN cc_start: 0.8626 (p0) cc_final: 0.8164 (t0) REVERT: E 492 ILE cc_start: 0.8972 (mt) cc_final: 0.8690 (mt) REVERT: E 572 GLU cc_start: 0.7715 (OUTLIER) cc_final: 0.7294 (pt0) REVERT: F 249 ASP cc_start: 0.7738 (t0) cc_final: 0.7506 (t0) REVERT: F 256 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7591 (tt0) REVERT: I 206 ARG cc_start: 0.5918 (tpt90) cc_final: 0.5614 (ptt-90) REVERT: I 310 ARG cc_start: 0.6961 (ptt-90) cc_final: 0.6509 (tpt-90) REVERT: I 397 ASN cc_start: 0.6251 (m-40) cc_final: 0.5885 (t0) REVERT: I 437 HIS cc_start: 0.7323 (p-80) cc_final: 0.7024 (p-80) REVERT: I 463 LYS cc_start: 0.8254 (tppt) cc_final: 0.7907 (tppt) REVERT: I 547 LEU cc_start: 0.8443 (mm) cc_final: 0.8162 (mm) REVERT: J 49 GLN cc_start: 0.8303 (pm20) cc_final: 0.7944 (pt0) REVERT: J 72 GLN cc_start: 0.7258 (mt0) cc_final: 0.6816 (tm-30) REVERT: J 195 ASN cc_start: 0.8741 (OUTLIER) cc_final: 0.8383 (t0) REVERT: J 215 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8185 (mm) REVERT: M 381 LEU cc_start: 0.6843 (tp) cc_final: 0.6509 (tt) REVERT: M 462 ARG cc_start: 0.5053 (mtp85) cc_final: 0.4584 (mpt-90) REVERT: M 497 ARG cc_start: 0.6740 (tpp-160) cc_final: 0.4926 (tpp-160) REVERT: M 508 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6743 (pm20) REVERT: M 525 ARG cc_start: 0.7552 (ttp-170) cc_final: 0.7318 (ttp80) REVERT: M 579 PHE cc_start: 0.7292 (p90) cc_final: 0.6772 (p90) REVERT: N 61 MET cc_start: 0.7275 (mtp) cc_final: 0.7036 (mtp) REVERT: N 239 GLU cc_start: 0.7692 (mp0) cc_final: 0.7441 (mp0) REVERT: N 255 PHE cc_start: 0.6852 (OUTLIER) cc_final: 0.5625 (t80) REVERT: N 276 SER cc_start: 0.8704 (p) cc_final: 0.8344 (m) REVERT: N 278 GLN cc_start: 0.8090 (tp40) cc_final: 0.7821 (tp40) REVERT: N 301 ARG cc_start: 0.8161 (ptm-80) cc_final: 0.7752 (tpt170) REVERT: N 302 LYS cc_start: 0.8029 (tttm) cc_final: 0.7827 (mmmt) outliers start: 205 outliers final: 148 residues processed: 627 average time/residue: 0.2184 time to fit residues: 224.9511 Evaluate side-chains 602 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 162 poor density : 440 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 188 ASP Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 435 ILE Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain E residue 573 ILE Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 215 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 256 GLU Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 290 LEU Chi-restraints excluded: chain F residue 293 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 299 LYS Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 405 ASP Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 474 ILE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 68 VAL Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 338 THR Chi-restraints excluded: chain J residue 362 ASP Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 424 SER Chi-restraints excluded: chain J residue 466 ILE Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 90 SER Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 319 ILE Chi-restraints excluded: chain M residue 333 THR Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 398 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 426 LEU Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 545 LYS Chi-restraints excluded: chain M residue 573 ILE Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 119 ASN Chi-restraints excluded: chain N residue 178 LEU Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 337 SER Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 276 optimal weight: 5.9990 chunk 72 optimal weight: 0.1980 chunk 207 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 197 optimal weight: 6.9990 chunk 129 optimal weight: 0.3980 chunk 73 optimal weight: 0.6980 chunk 189 optimal weight: 0.0770 chunk 370 optimal weight: 0.8980 chunk 367 optimal weight: 0.8980 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** F 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 195 ASN ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 141 HIS ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.153803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.122874 restraints weight = 57397.816| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.46 r_work: 0.3487 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 35670 Z= 0.118 Angle : 0.594 9.674 49080 Z= 0.301 Chirality : 0.040 0.236 5486 Planarity : 0.004 0.049 5684 Dihedral : 17.559 171.175 6499 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 4.55 % Allowed : 29.84 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.14), residues: 3842 helix: 1.12 (0.14), residues: 1490 sheet: -0.43 (0.19), residues: 800 loop : -0.73 (0.16), residues: 1552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 344 TYR 0.020 0.001 TYR N 229 PHE 0.020 0.001 PHE E 287 TRP 0.024 0.001 TRP M 510 HIS 0.006 0.001 HIS M 437 Details of bonding type rmsd covalent geometry : bond 0.00263 (35668) covalent geometry : angle 0.59403 (49080) hydrogen bonds : bond 0.04367 ( 1469) hydrogen bonds : angle 4.58437 ( 4142) Misc. bond : bond 0.00023 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 477 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8888 (OUTLIER) cc_final: 0.8312 (p90) REVERT: A 22 TRP cc_start: 0.8242 (m100) cc_final: 0.7883 (m100) REVERT: A 213 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7975 (mm) REVERT: A 289 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8305 (tm-30) REVERT: A 318 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8513 (m) REVERT: A 518 GLU cc_start: 0.8647 (pm20) cc_final: 0.8305 (pm20) REVERT: A 567 PHE cc_start: 0.6444 (m-80) cc_final: 0.6212 (m-80) REVERT: B 79 GLU cc_start: 0.8392 (mt-10) cc_final: 0.7761 (mm-30) REVERT: B 100 MET cc_start: 0.6709 (mmm) cc_final: 0.6408 (mmm) REVERT: B 215 LEU cc_start: 0.8603 (mt) cc_final: 0.8373 (mt) REVERT: E 93 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8297 (m-80) REVERT: E 194 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8663 (mt) REVERT: E 244 ASN cc_start: 0.8577 (p0) cc_final: 0.8124 (t0) REVERT: E 492 ILE cc_start: 0.8951 (mt) cc_final: 0.8647 (mt) REVERT: E 572 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.7235 (pt0) REVERT: F 249 ASP cc_start: 0.7718 (t0) cc_final: 0.7491 (t0) REVERT: I 206 ARG cc_start: 0.5951 (tpt90) cc_final: 0.5640 (ptt-90) REVERT: I 310 ARG cc_start: 0.6941 (ptt-90) cc_final: 0.6508 (tpt-90) REVERT: I 397 ASN cc_start: 0.6255 (m-40) cc_final: 0.5790 (t0) REVERT: I 437 HIS cc_start: 0.7292 (p-80) cc_final: 0.6666 (p-80) REVERT: I 463 LYS cc_start: 0.8286 (tppt) cc_final: 0.7907 (tppt) REVERT: I 547 LEU cc_start: 0.8397 (mm) cc_final: 0.8164 (mm) REVERT: J 49 GLN cc_start: 0.8231 (pm20) cc_final: 0.7855 (pt0) REVERT: J 72 GLN cc_start: 0.7261 (mt0) cc_final: 0.6823 (tm-30) REVERT: J 133 MET cc_start: 0.8661 (ptp) cc_final: 0.8327 (ptp) REVERT: J 195 ASN cc_start: 0.8600 (OUTLIER) cc_final: 0.8379 (t0) REVERT: J 215 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8200 (mm) REVERT: M 6 ASP cc_start: 0.7133 (OUTLIER) cc_final: 0.6828 (m-30) REVERT: M 47 ARG cc_start: 0.8127 (mtt-85) cc_final: 0.7865 (mtt-85) REVERT: M 89 TYR cc_start: 0.8134 (t80) cc_final: 0.7869 (t80) REVERT: M 343 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8475 (mm) REVERT: M 381 LEU cc_start: 0.6796 (tp) cc_final: 0.6362 (tt) REVERT: M 462 ARG cc_start: 0.5079 (mtp85) cc_final: 0.4592 (mpt-90) REVERT: M 497 ARG cc_start: 0.6606 (tpp-160) cc_final: 0.3451 (tpp-160) REVERT: M 508 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.6851 (pm20) REVERT: M 525 ARG cc_start: 0.7498 (ttp-170) cc_final: 0.7267 (ttp80) REVERT: N 61 MET cc_start: 0.7209 (mtp) cc_final: 0.6984 (mtp) REVERT: N 69 ARG cc_start: 0.7786 (ttp-110) cc_final: 0.7571 (ttp-110) REVERT: N 239 GLU cc_start: 0.7725 (mp0) cc_final: 0.7499 (mp0) REVERT: N 276 SER cc_start: 0.8686 (p) cc_final: 0.8301 (m) REVERT: N 278 GLN cc_start: 0.7983 (tp40) cc_final: 0.7707 (tp40) REVERT: N 301 ARG cc_start: 0.8175 (ptm-80) cc_final: 0.7759 (tpt170) outliers start: 152 outliers final: 109 residues processed: 596 average time/residue: 0.1859 time to fit residues: 180.7215 Evaluate side-chains 572 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 451 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 20 MET Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 467 PHE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 395 GLU Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 172 SER Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 299 LYS Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 319 ILE Chi-restraints excluded: chain M residue 343 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 545 LYS Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 309 THR Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 413 SER Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 361 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 322 optimal weight: 3.9990 chunk 152 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 372 optimal weight: 0.0670 chunk 164 optimal weight: 0.9980 chunk 183 optimal weight: 4.9990 overall best weight: 2.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 120 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN F 295 HIS ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 191 GLN J 195 ASN ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.150576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.118480 restraints weight = 57694.969| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.58 r_work: 0.3438 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 35670 Z= 0.204 Angle : 0.644 11.118 49080 Z= 0.326 Chirality : 0.042 0.278 5486 Planarity : 0.004 0.051 5684 Dihedral : 17.588 171.250 6497 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 5.30 % Allowed : 29.09 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.14), residues: 3842 helix: 0.99 (0.14), residues: 1476 sheet: -0.48 (0.19), residues: 780 loop : -0.80 (0.16), residues: 1586 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 47 TYR 0.037 0.002 TYR N 84 PHE 0.022 0.002 PHE E 287 TRP 0.026 0.001 TRP M 510 HIS 0.006 0.001 HIS E 52 Details of bonding type rmsd covalent geometry : bond 0.00466 (35668) covalent geometry : angle 0.64353 (49080) hydrogen bonds : bond 0.04611 ( 1469) hydrogen bonds : angle 4.68109 ( 4142) Misc. bond : bond 0.00042 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 630 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 177 poor density : 453 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.9003 (OUTLIER) cc_final: 0.8385 (p90) REVERT: A 22 TRP cc_start: 0.8391 (m100) cc_final: 0.7923 (m100) REVERT: A 136 LYS cc_start: 0.8164 (OUTLIER) cc_final: 0.7816 (mptp) REVERT: A 213 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8018 (mm) REVERT: A 289 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8384 (tm-30) REVERT: A 318 SER cc_start: 0.8784 (OUTLIER) cc_final: 0.8549 (m) REVERT: A 332 ARG cc_start: 0.8942 (OUTLIER) cc_final: 0.8562 (mtp180) REVERT: A 518 GLU cc_start: 0.8717 (pm20) cc_final: 0.8333 (pm20) REVERT: A 567 PHE cc_start: 0.6358 (m-80) cc_final: 0.6086 (m-10) REVERT: B 100 MET cc_start: 0.6712 (mmm) cc_final: 0.6473 (mmm) REVERT: B 280 MET cc_start: 0.8011 (tpp) cc_final: 0.7720 (tpp) REVERT: E 16 ASN cc_start: 0.8318 (OUTLIER) cc_final: 0.7802 (p0) REVERT: E 93 PHE cc_start: 0.9107 (OUTLIER) cc_final: 0.8308 (m-80) REVERT: E 234 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.7961 (mpp) REVERT: E 492 ILE cc_start: 0.9009 (mt) cc_final: 0.8756 (mt) REVERT: E 572 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7340 (pt0) REVERT: F 249 ASP cc_start: 0.7660 (t0) cc_final: 0.7411 (t0) REVERT: F 284 LEU cc_start: 0.9189 (mt) cc_final: 0.8953 (tp) REVERT: I 206 ARG cc_start: 0.5931 (tpt90) cc_final: 0.5658 (ptt-90) REVERT: I 397 ASN cc_start: 0.6286 (m-40) cc_final: 0.5879 (t0) REVERT: I 422 GLU cc_start: 0.7302 (pt0) cc_final: 0.5972 (tp30) REVERT: I 437 HIS cc_start: 0.7361 (p-80) cc_final: 0.6773 (p-80) REVERT: I 463 LYS cc_start: 0.8338 (tppt) cc_final: 0.7941 (tppt) REVERT: I 477 ASN cc_start: 0.7722 (t0) cc_final: 0.7507 (m-40) REVERT: I 547 LEU cc_start: 0.8436 (mm) cc_final: 0.8171 (mm) REVERT: J 49 GLN cc_start: 0.8330 (pm20) cc_final: 0.7897 (pt0) REVERT: J 72 GLN cc_start: 0.7259 (mt0) cc_final: 0.6808 (tm-30) REVERT: J 195 ASN cc_start: 0.8635 (OUTLIER) cc_final: 0.8374 (t0) REVERT: J 215 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8351 (mm) REVERT: M 6 ASP cc_start: 0.7338 (OUTLIER) cc_final: 0.7049 (m-30) REVERT: M 89 TYR cc_start: 0.8258 (t80) cc_final: 0.7998 (t80) REVERT: M 381 LEU cc_start: 0.6814 (tp) cc_final: 0.6348 (tt) REVERT: M 462 ARG cc_start: 0.5061 (mtp85) cc_final: 0.4644 (mpt-90) REVERT: M 508 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.6984 (pm20) REVERT: M 525 ARG cc_start: 0.7586 (ttp-170) cc_final: 0.7355 (ttp80) REVERT: N 61 MET cc_start: 0.7453 (mtp) cc_final: 0.7171 (mtp) REVERT: N 76 THR cc_start: 0.8258 (OUTLIER) cc_final: 0.8029 (p) REVERT: N 255 PHE cc_start: 0.6960 (OUTLIER) cc_final: 0.5775 (t80) REVERT: N 276 SER cc_start: 0.8699 (p) cc_final: 0.8297 (m) REVERT: N 278 GLN cc_start: 0.8195 (tp40) cc_final: 0.7848 (tp40) REVERT: N 301 ARG cc_start: 0.8248 (ptm-80) cc_final: 0.7849 (tpt170) outliers start: 177 outliers final: 130 residues processed: 584 average time/residue: 0.2253 time to fit residues: 216.5795 Evaluate side-chains 579 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 433 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 459 LEU Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 251 ASP Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 308 THR Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 465 GLU Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 224 SER Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 44 PHE Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 238 GLN Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 365 LEU Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 130 VAL Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 195 ASN Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 462 ILE Chi-restraints excluded: chain J residue 466 ILE Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 319 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 426 LEU Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 545 LYS Chi-restraints excluded: chain N residue 18 LEU Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 71 LEU Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 376 optimal weight: 0.9990 chunk 143 optimal weight: 2.9990 chunk 315 optimal weight: 0.2980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 307 optimal weight: 5.9990 chunk 119 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 overall best weight: 0.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN A 16 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 ASN F 238 GLN ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 16 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 339 ASN ** N 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.152989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.120893 restraints weight = 56994.190| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.51 r_work: 0.3481 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 35670 Z= 0.133 Angle : 0.616 10.472 49080 Z= 0.311 Chirality : 0.041 0.288 5486 Planarity : 0.004 0.053 5684 Dihedral : 17.563 171.352 6497 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.06 % Favored : 95.91 % Rotamer: Outliers : 4.46 % Allowed : 29.99 % Favored : 65.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.14 (0.14), residues: 3842 helix: 0.97 (0.14), residues: 1498 sheet: -0.43 (0.19), residues: 800 loop : -0.87 (0.16), residues: 1544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG J 301 TYR 0.025 0.001 TYR N 84 PHE 0.020 0.001 PHE M 143 TRP 0.031 0.001 TRP M 510 HIS 0.009 0.001 HIS N 289 Details of bonding type rmsd covalent geometry : bond 0.00302 (35668) covalent geometry : angle 0.61591 (49080) hydrogen bonds : bond 0.04438 ( 1469) hydrogen bonds : angle 4.61972 ( 4142) Misc. bond : bond 0.00007 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 460 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8934 (OUTLIER) cc_final: 0.8293 (p90) REVERT: A 22 TRP cc_start: 0.8303 (m100) cc_final: 0.7894 (m100) REVERT: A 213 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7975 (mm) REVERT: A 289 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8355 (tm-30) REVERT: A 319 ILE cc_start: 0.8390 (pt) cc_final: 0.8172 (pt) REVERT: A 332 ARG cc_start: 0.8842 (OUTLIER) cc_final: 0.8517 (mtp180) REVERT: A 567 PHE cc_start: 0.6357 (m-80) cc_final: 0.6099 (m-10) REVERT: B 100 MET cc_start: 0.6763 (mmm) cc_final: 0.6492 (mmm) REVERT: B 280 MET cc_start: 0.7975 (tpp) cc_final: 0.7630 (tpp) REVERT: E 16 ASN cc_start: 0.8077 (OUTLIER) cc_final: 0.7823 (p0) REVERT: E 93 PHE cc_start: 0.9053 (OUTLIER) cc_final: 0.8212 (m-80) REVERT: E 194 ILE cc_start: 0.8837 (OUTLIER) cc_final: 0.8609 (mt) REVERT: E 244 ASN cc_start: 0.8623 (p0) cc_final: 0.8171 (t0) REVERT: E 492 ILE cc_start: 0.8959 (mt) cc_final: 0.8699 (mt) REVERT: E 572 GLU cc_start: 0.7767 (OUTLIER) cc_final: 0.7297 (pt0) REVERT: F 249 ASP cc_start: 0.7625 (t0) cc_final: 0.7349 (t0) REVERT: F 396 LYS cc_start: 0.7616 (tmtt) cc_final: 0.7356 (tmtt) REVERT: I 206 ARG cc_start: 0.5858 (tpt90) cc_final: 0.5583 (ptt-90) REVERT: I 397 ASN cc_start: 0.6171 (m-40) cc_final: 0.5779 (t0) REVERT: I 422 GLU cc_start: 0.7312 (pt0) cc_final: 0.5925 (tp30) REVERT: I 437 HIS cc_start: 0.7354 (p-80) cc_final: 0.6787 (p-80) REVERT: I 463 LYS cc_start: 0.8360 (tppt) cc_final: 0.7944 (tppt) REVERT: I 477 ASN cc_start: 0.7585 (t0) cc_final: 0.7382 (m-40) REVERT: I 547 LEU cc_start: 0.8442 (mm) cc_final: 0.8190 (mm) REVERT: J 49 GLN cc_start: 0.8315 (pm20) cc_final: 0.7861 (pt0) REVERT: J 72 GLN cc_start: 0.7250 (mt0) cc_final: 0.6807 (tm-30) REVERT: J 214 LYS cc_start: 0.8544 (ttpt) cc_final: 0.7920 (mtpt) REVERT: J 215 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8197 (mm) REVERT: J 301 ARG cc_start: 0.8385 (mtt90) cc_final: 0.7777 (mtm-85) REVERT: M 6 ASP cc_start: 0.7352 (OUTLIER) cc_final: 0.7025 (m-30) REVERT: M 89 TYR cc_start: 0.8191 (t80) cc_final: 0.7967 (t80) REVERT: M 381 LEU cc_start: 0.6833 (tp) cc_final: 0.6392 (tt) REVERT: M 508 GLU cc_start: 0.7341 (OUTLIER) cc_final: 0.7024 (pm20) REVERT: M 525 ARG cc_start: 0.7524 (ttp-170) cc_final: 0.7297 (ttp80) REVERT: N 69 ARG cc_start: 0.7947 (ttp-110) cc_final: 0.7721 (ttp-110) REVERT: N 239 GLU cc_start: 0.7828 (mp0) cc_final: 0.7624 (mm-30) REVERT: N 255 PHE cc_start: 0.6786 (OUTLIER) cc_final: 0.5699 (t80) REVERT: N 276 SER cc_start: 0.8657 (p) cc_final: 0.8249 (m) REVERT: N 278 GLN cc_start: 0.8155 (tp40) cc_final: 0.7803 (tp40) REVERT: N 301 ARG cc_start: 0.8270 (ptm-80) cc_final: 0.7892 (tpt170) outliers start: 149 outliers final: 120 residues processed: 575 average time/residue: 0.2272 time to fit residues: 214.4039 Evaluate side-chains 570 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 132 poor density : 438 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 GLN Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 347 VAL Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 375 THR Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 215 LEU Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 462 ILE Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 317 VAL Chi-restraints excluded: chain M residue 319 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 545 LYS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 365 optimal weight: 7.9990 chunk 372 optimal weight: 6.9990 chunk 315 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 392 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 399 optimal weight: 10.0000 chunk 75 optimal weight: 0.6980 chunk 118 optimal weight: 1.9990 chunk 277 optimal weight: 3.9990 chunk 353 optimal weight: 8.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 15 GLN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 333 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN I 16 ASN I 133 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 72 GLN ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 238 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 289 HIS ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.156416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.124790 restraints weight = 59309.140| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.74 r_work: 0.3589 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 moved from start: 0.3586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 35670 Z= 0.211 Angle : 0.663 11.938 49080 Z= 0.335 Chirality : 0.042 0.306 5486 Planarity : 0.004 0.089 5684 Dihedral : 17.598 171.551 6497 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 13.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.10 % Favored : 94.87 % Rotamer: Outliers : 4.52 % Allowed : 30.02 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.14), residues: 3842 helix: 0.89 (0.14), residues: 1478 sheet: -0.54 (0.19), residues: 784 loop : -0.94 (0.16), residues: 1580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 462 TYR 0.029 0.002 TYR N 84 PHE 0.023 0.002 PHE M 579 TRP 0.033 0.001 TRP M 510 HIS 0.009 0.001 HIS A 12 Details of bonding type rmsd covalent geometry : bond 0.00487 (35668) covalent geometry : angle 0.66307 (49080) hydrogen bonds : bond 0.04629 ( 1469) hydrogen bonds : angle 4.75331 ( 4142) Misc. bond : bond 0.00040 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7684 Ramachandran restraints generated. 3842 Oldfield, 0 Emsley, 3842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 582 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 151 poor density : 431 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 HIS cc_start: 0.8976 (OUTLIER) cc_final: 0.8394 (p90) REVERT: A 22 TRP cc_start: 0.8331 (m100) cc_final: 0.7882 (m100) REVERT: A 136 LYS cc_start: 0.8183 (OUTLIER) cc_final: 0.7785 (mptp) REVERT: A 213 LEU cc_start: 0.8335 (OUTLIER) cc_final: 0.8010 (mm) REVERT: A 289 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8424 (tm-30) REVERT: A 318 SER cc_start: 0.8802 (OUTLIER) cc_final: 0.8576 (m) REVERT: A 332 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8490 (mtp180) REVERT: A 567 PHE cc_start: 0.6395 (m-80) cc_final: 0.6131 (m-10) REVERT: B 280 MET cc_start: 0.7965 (tpp) cc_final: 0.7624 (tpp) REVERT: E 93 PHE cc_start: 0.9088 (OUTLIER) cc_final: 0.8305 (m-80) REVERT: E 132 MET cc_start: 0.8913 (ptm) cc_final: 0.8590 (ptm) REVERT: E 244 ASN cc_start: 0.8653 (p0) cc_final: 0.8178 (t0) REVERT: E 492 ILE cc_start: 0.9007 (mt) cc_final: 0.8728 (mt) REVERT: E 572 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7365 (pt0) REVERT: F 249 ASP cc_start: 0.7630 (t0) cc_final: 0.7369 (t0) REVERT: I 206 ARG cc_start: 0.5958 (tpt90) cc_final: 0.5694 (ptt-90) REVERT: I 397 ASN cc_start: 0.6142 (m-40) cc_final: 0.5767 (t0) REVERT: I 422 GLU cc_start: 0.7356 (pt0) cc_final: 0.5973 (tp30) REVERT: I 437 HIS cc_start: 0.7344 (p-80) cc_final: 0.6796 (p-80) REVERT: I 463 LYS cc_start: 0.8300 (tppt) cc_final: 0.7848 (tppt) REVERT: I 547 LEU cc_start: 0.8433 (mm) cc_final: 0.8168 (mm) REVERT: J 49 GLN cc_start: 0.8351 (pm20) cc_final: 0.7910 (pt0) REVERT: J 72 GLN cc_start: 0.7273 (mt0) cc_final: 0.6824 (tm-30) REVERT: J 214 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8073 (mtpt) REVERT: J 301 ARG cc_start: 0.8421 (mtt90) cc_final: 0.7819 (mtm-85) REVERT: M 6 ASP cc_start: 0.7426 (OUTLIER) cc_final: 0.7095 (m-30) REVERT: M 153 ASP cc_start: 0.8117 (t70) cc_final: 0.7840 (t0) REVERT: M 260 LYS cc_start: 0.8335 (mtmt) cc_final: 0.7961 (ptpt) REVERT: M 381 LEU cc_start: 0.6863 (tp) cc_final: 0.6365 (tt) REVERT: M 508 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.6946 (pm20) REVERT: M 525 ARG cc_start: 0.7555 (ttp-170) cc_final: 0.7332 (ttp80) REVERT: N 69 ARG cc_start: 0.7938 (ttp-110) cc_final: 0.7729 (ttp-110) REVERT: N 76 THR cc_start: 0.8340 (OUTLIER) cc_final: 0.8111 (p) REVERT: N 239 GLU cc_start: 0.7820 (mp0) cc_final: 0.7601 (mm-30) REVERT: N 255 PHE cc_start: 0.7197 (OUTLIER) cc_final: 0.5954 (t80) REVERT: N 276 SER cc_start: 0.8708 (p) cc_final: 0.8258 (m) REVERT: N 278 GLN cc_start: 0.8244 (tp40) cc_final: 0.7910 (tp40) REVERT: N 301 ARG cc_start: 0.8399 (ptm-80) cc_final: 0.8019 (tpt170) outliers start: 151 outliers final: 126 residues processed: 545 average time/residue: 0.2261 time to fit residues: 202.3188 Evaluate side-chains 558 residues out of total 3342 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 420 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 ASN Chi-restraints excluded: chain A residue 19 HIS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain A residue 136 LYS Chi-restraints excluded: chain A residue 161 VAL Chi-restraints excluded: chain A residue 206 ARG Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 317 VAL Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 331 LEU Chi-restraints excluded: chain A residue 332 ARG Chi-restraints excluded: chain A residue 333 THR Chi-restraints excluded: chain A residue 359 LEU Chi-restraints excluded: chain A residue 404 ILE Chi-restraints excluded: chain A residue 478 VAL Chi-restraints excluded: chain A residue 557 VAL Chi-restraints excluded: chain A residue 583 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 18 LEU Chi-restraints excluded: chain B residue 157 CYS Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 244 CYS Chi-restraints excluded: chain B residue 281 GLN Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 312 THR Chi-restraints excluded: chain B residue 394 VAL Chi-restraints excluded: chain B residue 435 ASN Chi-restraints excluded: chain B residue 462 ILE Chi-restraints excluded: chain B residue 473 MET Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 16 ASN Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 93 PHE Chi-restraints excluded: chain E residue 94 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 PHE Chi-restraints excluded: chain E residue 194 ILE Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain E residue 211 CYS Chi-restraints excluded: chain E residue 234 MET Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 311 THR Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain E residue 331 LEU Chi-restraints excluded: chain E residue 350 LEU Chi-restraints excluded: chain E residue 407 ILE Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 572 GLU Chi-restraints excluded: chain F residue 16 GLU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 61 MET Chi-restraints excluded: chain F residue 96 VAL Chi-restraints excluded: chain F residue 110 LEU Chi-restraints excluded: chain F residue 180 ILE Chi-restraints excluded: chain F residue 182 ILE Chi-restraints excluded: chain F residue 188 LEU Chi-restraints excluded: chain F residue 242 THR Chi-restraints excluded: chain F residue 244 CYS Chi-restraints excluded: chain F residue 247 VAL Chi-restraints excluded: chain F residue 255 PHE Chi-restraints excluded: chain F residue 285 SER Chi-restraints excluded: chain F residue 337 SER Chi-restraints excluded: chain F residue 345 VAL Chi-restraints excluded: chain F residue 436 ASN Chi-restraints excluded: chain F residue 466 ILE Chi-restraints excluded: chain F residue 468 ASP Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain I residue 121 ILE Chi-restraints excluded: chain I residue 126 LEU Chi-restraints excluded: chain I residue 149 THR Chi-restraints excluded: chain I residue 219 PHE Chi-restraints excluded: chain I residue 232 ASN Chi-restraints excluded: chain I residue 244 ASN Chi-restraints excluded: chain I residue 286 THR Chi-restraints excluded: chain I residue 331 LEU Chi-restraints excluded: chain I residue 349 THR Chi-restraints excluded: chain I residue 467 PHE Chi-restraints excluded: chain I residue 561 CYS Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 28 THR Chi-restraints excluded: chain J residue 166 HIS Chi-restraints excluded: chain J residue 276 SER Chi-restraints excluded: chain J residue 345 VAL Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain J residue 388 GLN Chi-restraints excluded: chain J residue 394 VAL Chi-restraints excluded: chain J residue 424 SER Chi-restraints excluded: chain J residue 462 ILE Chi-restraints excluded: chain J residue 473 MET Chi-restraints excluded: chain M residue 6 ASP Chi-restraints excluded: chain M residue 19 HIS Chi-restraints excluded: chain M residue 77 SER Chi-restraints excluded: chain M residue 82 LEU Chi-restraints excluded: chain M residue 93 PHE Chi-restraints excluded: chain M residue 108 LEU Chi-restraints excluded: chain M residue 117 VAL Chi-restraints excluded: chain M residue 164 LEU Chi-restraints excluded: chain M residue 189 PHE Chi-restraints excluded: chain M residue 254 THR Chi-restraints excluded: chain M residue 267 ASP Chi-restraints excluded: chain M residue 314 VAL Chi-restraints excluded: chain M residue 317 VAL Chi-restraints excluded: chain M residue 319 ILE Chi-restraints excluded: chain M residue 348 VAL Chi-restraints excluded: chain M residue 349 THR Chi-restraints excluded: chain M residue 352 SER Chi-restraints excluded: chain M residue 425 ILE Chi-restraints excluded: chain M residue 426 LEU Chi-restraints excluded: chain M residue 508 GLU Chi-restraints excluded: chain M residue 544 ILE Chi-restraints excluded: chain M residue 545 LYS Chi-restraints excluded: chain N residue 28 THR Chi-restraints excluded: chain N residue 76 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 180 ILE Chi-restraints excluded: chain N residue 185 ASP Chi-restraints excluded: chain N residue 188 LEU Chi-restraints excluded: chain N residue 190 ARG Chi-restraints excluded: chain N residue 241 THR Chi-restraints excluded: chain N residue 242 THR Chi-restraints excluded: chain N residue 244 CYS Chi-restraints excluded: chain N residue 255 PHE Chi-restraints excluded: chain N residue 258 VAL Chi-restraints excluded: chain N residue 289 HIS Chi-restraints excluded: chain N residue 345 VAL Chi-restraints excluded: chain N residue 394 VAL Chi-restraints excluded: chain N residue 397 GLU Chi-restraints excluded: chain N residue 429 THR Chi-restraints excluded: chain N residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 402 random chunks: chunk 296 optimal weight: 0.8980 chunk 169 optimal weight: 0.9980 chunk 339 optimal weight: 4.9990 chunk 219 optimal weight: 2.9990 chunk 387 optimal weight: 2.9990 chunk 153 optimal weight: 0.8980 chunk 313 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 342 optimal weight: 0.0040 chunk 188 optimal weight: 2.9990 chunk 98 optimal weight: 0.8980 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 16 ASN ** A 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 297 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 238 GLN ** F 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 436 ASN I 16 ASN I 120 ASN ** I 441 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 238 GLN N 289 HIS ** N 295 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 415 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.159468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.128593 restraints weight = 58671.103| |-----------------------------------------------------------------------------| r_work (start): 0.3786 rms_B_bonded: 2.57 r_work: 0.3648 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.3630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 35670 Z= 0.128 Angle : 0.629 12.025 49080 Z= 0.316 Chirality : 0.041 0.293 5486 Planarity : 0.004 0.053 5684 Dihedral : 17.564 172.168 6497 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.93 % Favored : 96.04 % Rotamer: Outliers : 4.31 % Allowed : 30.56 % Favored : 65.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.17 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.15 (0.14), residues: 3842 helix: 0.96 (0.14), residues: 1502 sheet: -0.41 (0.19), residues: 800 loop : -0.90 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG I 462 TYR 0.024 0.001 TYR N 229 PHE 0.028 0.001 PHE F 21 TRP 0.035 0.001 TRP M 510 HIS 0.009 0.001 HIS N 289 Details of bonding type rmsd covalent geometry : bond 0.00290 (35668) covalent geometry : angle 0.62887 (49080) hydrogen bonds : bond 0.04418 ( 1469) hydrogen bonds : angle 4.67147 ( 4142) Misc. bond : bond 0.00014 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8686.89 seconds wall clock time: 150 minutes 7.60 seconds (9007.60 seconds total)