Starting phenix.real_space_refine on Sun Oct 12 10:11:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7jz2_22528/10_2025/7jz2_22528_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7jz2_22528/10_2025/7jz2_22528.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7jz2_22528/10_2025/7jz2_22528.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7jz2_22528/10_2025/7jz2_22528.map" model { file = "/net/cci-nas-00/data/ceres_data/7jz2_22528/10_2025/7jz2_22528_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7jz2_22528/10_2025/7jz2_22528_neut.cif" } resolution = 2.5 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.172 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Fe 30 7.16 5 P 9 5.49 5 S 186 5.16 5 Na 3 4.78 5 C 14520 2.51 5 N 3921 2.21 5 O 4197 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 54 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 22866 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3707 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 463} Chain breaks: 1 Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 220} Chain: "C" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 972 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "D" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 898 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 111} Chain: "A" Number of atoms: 54 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 54 Unusual residues: {' NA': 1, 'FAD': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 19 Unusual residues: {'F3S': 1, 'FES': 1, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 37 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 66 Unusual residues: {'HEM': 1, 'UQ2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'3PE': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'UQ2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 80 Unusual residues: {'3PE': 1, 'HEM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 14 Chain: "L" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'UQ2': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4298 SG CYS B 75 79.724 104.845 57.102 1.00 25.54 S ATOM 4931 SG CYS B 155 76.201 91.973 66.627 1.00 22.51 S ATOM 5407 SG CYS B 216 71.860 97.703 66.077 1.00 23.12 S ATOM 4892 SG CYS B 149 73.317 91.509 61.104 1.00 26.11 S ATOM 4914 SG CYS B 152 78.004 96.628 62.112 1.00 22.99 S ATOM 4956 SG CYS B 159 78.230 89.297 74.675 1.00 23.87 S Restraints were copied for chains: E, I, F, J, G, K, H, L Time building chain proxies: 5.89, per 1000 atoms: 0.26 Number of scatterers: 22866 At special positions: 0 Unit cell: (131.76, 135, 133.92, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 30 26.01 S 186 16.00 P 9 15.00 Na 3 11.00 O 4197 8.00 N 3921 7.00 C 14520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" F3S B 303 " pdb="FE1 F3S B 303 " - pdb=" SG CYS B 159 " pdb="FE3 F3S B 303 " - pdb=" SG CYS B 206 " pdb="FE4 F3S B 303 " - pdb=" SG CYS B 212 " pdb=" F3S F 303 " pdb="FE1 F3S F 303 " - pdb=" SG CYS F 159 " pdb="FE3 F3S F 303 " - pdb=" SG CYS F 206 " pdb="FE4 F3S F 303 " - pdb=" SG CYS F 212 " pdb=" F3S J 303 " pdb="FE1 F3S J 303 " - pdb=" SG CYS J 159 " pdb="FE3 F3S J 303 " - pdb=" SG CYS J 206 " pdb="FE4 F3S J 303 " - pdb=" SG CYS J 212 " pdb=" FES B 301 " pdb="FE1 FES B 301 " - pdb=" SG CYS B 75 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 55 " pdb="FE2 FES B 301 " - pdb=" SG CYS B 60 " pdb=" FES F 301 " pdb="FE1 FES F 301 " - pdb=" SG CYS F 75 " pdb="FE2 FES F 301 " - pdb=" SG CYS F 55 " pdb="FE2 FES F 301 " - pdb=" SG CYS F 60 " pdb=" FES J 301 " pdb="FE1 FES J 301 " - pdb=" SG CYS J 75 " pdb="FE2 FES J 301 " - pdb=" SG CYS J 55 " pdb="FE2 FES J 301 " - pdb=" SG CYS J 60 " pdb=" SF4 B 302 " pdb="FE4 SF4 B 302 " - pdb=" SG CYS B 152 " pdb="FE1 SF4 B 302 " - pdb=" SG CYS B 155 " pdb="FE3 SF4 B 302 " - pdb=" SG CYS B 149 " pdb="FE2 SF4 B 302 " - pdb=" SG CYS B 216 " pdb=" SF4 F 302 " pdb="FE4 SF4 F 302 " - pdb=" SG CYS F 152 " pdb="FE1 SF4 F 302 " - pdb=" SG CYS F 155 " pdb="FE3 SF4 F 302 " - pdb=" SG CYS F 149 " pdb="FE2 SF4 F 302 " - pdb=" SG CYS F 216 " pdb=" SF4 J 302 " pdb="FE4 SF4 J 302 " - pdb=" SG CYS J 152 " pdb="FE1 SF4 J 302 " - pdb=" SG CYS J 155 " pdb="FE3 SF4 J 302 " - pdb=" SG CYS J 149 " pdb="FE2 SF4 J 302 " - pdb=" SG CYS J 216 " Number of angles added : 75 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5274 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 52.1% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 16 through 29 Processing helix chain 'A' and resid 44 through 49 Processing helix chain 'A' and resid 64 through 76 removed outlier: 4.275A pdb=" N HIS A 68 " --> pdb=" O ASN A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 103 Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 140 through 157 Processing helix chain 'A' and resid 205 through 209 Processing helix chain 'A' and resid 220 through 230 Processing helix chain 'A' and resid 402 through 418 removed outlier: 3.859A pdb=" N LEU A 406 " --> pdb=" O GLY A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 427 Processing helix chain 'A' and resid 433 through 450 removed outlier: 3.969A pdb=" N VAL A 437 " --> pdb=" O SER A 433 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU A 438 " --> pdb=" O GLU A 434 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG A 443 " --> pdb=" O ALA A 439 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU A 444 " --> pdb=" O SER A 440 " (cutoff:3.500A) Processing helix chain 'A' and resid 455 through 471 Processing helix chain 'A' and resid 476 through 495 Processing helix chain 'A' and resid 507 through 533 removed outlier: 3.680A pdb=" N VAL A 511 " --> pdb=" O ASN A 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 44 Processing helix chain 'B' and resid 75 through 77 No H-bonds generated for 'chain 'B' and resid 75 through 77' Processing helix chain 'B' and resid 78 through 83 removed outlier: 3.892A pdb=" N LEU B 82 " --> pdb=" O PRO B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 117 removed outlier: 3.787A pdb=" N ILE B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 142 Processing helix chain 'B' and resid 155 through 158 Processing helix chain 'B' and resid 159 through 165 Processing helix chain 'B' and resid 171 through 184 Processing helix chain 'B' and resid 189 through 197 removed outlier: 3.685A pdb=" N ARG B 193 " --> pdb=" O GLU B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 216 Processing helix chain 'B' and resid 221 through 238 removed outlier: 3.522A pdb=" N ALA B 225 " --> pdb=" O ASN B 221 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 54 removed outlier: 3.954A pdb=" N GLY C 42 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 66 Processing helix chain 'C' and resid 67 through 97 Processing helix chain 'C' and resid 102 through 129 removed outlier: 3.503A pdb=" N LEU C 127 " --> pdb=" O LEU C 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 40 Processing helix chain 'D' and resid 44 through 52 Processing helix chain 'D' and resid 54 through 84 Processing helix chain 'D' and resid 86 through 113 Processing helix chain 'E' and resid 16 through 29 Processing helix chain 'E' and resid 44 through 49 Processing helix chain 'E' and resid 64 through 76 removed outlier: 4.275A pdb=" N HIS E 68 " --> pdb=" O ASN E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 81 through 103 Proline residue: E 93 - end of helix Processing helix chain 'E' and resid 140 through 157 Processing helix chain 'E' and resid 205 through 209 Processing helix chain 'E' and resid 220 through 230 Processing helix chain 'E' and resid 402 through 418 removed outlier: 3.858A pdb=" N LEU E 406 " --> pdb=" O GLY E 402 " (cutoff:3.500A) Processing helix chain 'E' and resid 418 through 427 Processing helix chain 'E' and resid 433 through 450 removed outlier: 3.969A pdb=" N VAL E 437 " --> pdb=" O SER E 433 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU E 438 " --> pdb=" O GLU E 434 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG E 443 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU E 444 " --> pdb=" O SER E 440 " (cutoff:3.500A) Processing helix chain 'E' and resid 455 through 471 Processing helix chain 'E' and resid 476 through 495 Processing helix chain 'E' and resid 507 through 533 removed outlier: 3.680A pdb=" N VAL E 511 " --> pdb=" O ASN E 507 " (cutoff:3.500A) Processing helix chain 'F' and resid 34 through 44 Processing helix chain 'F' and resid 75 through 77 No H-bonds generated for 'chain 'F' and resid 75 through 77' Processing helix chain 'F' and resid 78 through 83 removed outlier: 3.891A pdb=" N LEU F 82 " --> pdb=" O PRO F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 117 removed outlier: 3.786A pdb=" N ILE F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 136 through 142 Processing helix chain 'F' and resid 155 through 158 Processing helix chain 'F' and resid 159 through 165 Processing helix chain 'F' and resid 171 through 184 Processing helix chain 'F' and resid 189 through 197 removed outlier: 3.684A pdb=" N ARG F 193 " --> pdb=" O GLU F 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 216 Processing helix chain 'F' and resid 221 through 238 removed outlier: 3.521A pdb=" N ALA F 225 " --> pdb=" O ASN F 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 54 removed outlier: 3.954A pdb=" N GLY G 42 " --> pdb=" O PHE G 38 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N SER G 54 " --> pdb=" O THR G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 54 through 66 Processing helix chain 'G' and resid 67 through 97 Processing helix chain 'G' and resid 102 through 129 removed outlier: 3.503A pdb=" N LEU G 127 " --> pdb=" O LEU G 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 40 Processing helix chain 'H' and resid 44 through 52 Processing helix chain 'H' and resid 54 through 84 Processing helix chain 'H' and resid 86 through 113 Processing helix chain 'I' and resid 16 through 29 Processing helix chain 'I' and resid 44 through 49 Processing helix chain 'I' and resid 64 through 76 removed outlier: 4.276A pdb=" N HIS I 68 " --> pdb=" O ASN I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 103 Proline residue: I 93 - end of helix Processing helix chain 'I' and resid 140 through 157 Processing helix chain 'I' and resid 205 through 209 Processing helix chain 'I' and resid 220 through 230 Processing helix chain 'I' and resid 402 through 418 removed outlier: 3.859A pdb=" N LEU I 406 " --> pdb=" O GLY I 402 " (cutoff:3.500A) Processing helix chain 'I' and resid 418 through 427 Processing helix chain 'I' and resid 433 through 450 removed outlier: 3.970A pdb=" N VAL I 437 " --> pdb=" O SER I 433 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU I 438 " --> pdb=" O GLU I 434 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N ARG I 443 " --> pdb=" O ALA I 439 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LEU I 444 " --> pdb=" O SER I 440 " (cutoff:3.500A) Processing helix chain 'I' and resid 455 through 471 Processing helix chain 'I' and resid 476 through 495 Processing helix chain 'I' and resid 507 through 533 removed outlier: 3.679A pdb=" N VAL I 511 " --> pdb=" O ASN I 507 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 44 Processing helix chain 'J' and resid 75 through 77 No H-bonds generated for 'chain 'J' and resid 75 through 77' Processing helix chain 'J' and resid 78 through 83 removed outlier: 3.892A pdb=" N LEU J 82 " --> pdb=" O PRO J 78 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 117 removed outlier: 3.787A pdb=" N ILE J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 142 Processing helix chain 'J' and resid 155 through 158 Processing helix chain 'J' and resid 159 through 165 Processing helix chain 'J' and resid 171 through 184 Processing helix chain 'J' and resid 189 through 197 removed outlier: 3.685A pdb=" N ARG J 193 " --> pdb=" O GLU J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 211 through 216 Processing helix chain 'J' and resid 221 through 238 removed outlier: 3.521A pdb=" N ALA J 225 " --> pdb=" O ASN J 221 " (cutoff:3.500A) Processing helix chain 'K' and resid 21 through 54 removed outlier: 3.955A pdb=" N GLY K 42 " --> pdb=" O PHE K 38 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N SER K 54 " --> pdb=" O THR K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 54 through 66 Processing helix chain 'K' and resid 67 through 97 Processing helix chain 'K' and resid 102 through 129 removed outlier: 3.504A pdb=" N LEU K 127 " --> pdb=" O LEU K 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 40 Processing helix chain 'L' and resid 44 through 52 Processing helix chain 'L' and resid 54 through 84 Processing helix chain 'L' and resid 86 through 113 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 7 removed outlier: 6.299A pdb=" N ARG A 6 " --> pdb=" O LYS A 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL A 177 " --> pdb=" O LYS A 171 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS A 171 " --> pdb=" O VAL A 177 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY A 179 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU A 169 " --> pdb=" O GLY A 179 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 181 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.910A pdb=" N THR A 159 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA A 10 " --> pdb=" O ALA A 34 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU A 36 " --> pdb=" O ALA A 10 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL A 12 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA A 368 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'A' and resid 233 through 234 removed outlier: 3.606A pdb=" N VAL A 233 " --> pdb=" O TYR A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 239 through 242 removed outlier: 6.623A pdb=" N GLN A 240 " --> pdb=" O HIS A 354 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 361 removed outlier: 5.520A pdb=" N ILE A 360 " --> pdb=" O CYS A 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 536 through 537 Processing sheet with id=AA8, first strand: chain 'B' and resid 19 through 25 Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 7 removed outlier: 6.299A pdb=" N ARG E 6 " --> pdb=" O LYS E 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL E 177 " --> pdb=" O LYS E 171 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS E 171 " --> pdb=" O VAL E 177 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLY E 179 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU E 169 " --> pdb=" O GLY E 179 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR E 181 " --> pdb=" O LEU E 167 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 159 through 161 removed outlier: 3.911A pdb=" N THR E 159 " --> pdb=" O CYS E 33 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA E 10 " --> pdb=" O ALA E 34 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU E 36 " --> pdb=" O ALA E 10 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL E 12 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA E 368 " --> pdb=" O VAL E 380 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'E' and resid 233 through 234 removed outlier: 3.606A pdb=" N VAL E 233 " --> pdb=" O TYR E 559 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 239 through 242 removed outlier: 6.622A pdb=" N GLN E 240 " --> pdb=" O HIS E 354 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 360 through 361 removed outlier: 5.521A pdb=" N ILE E 360 " --> pdb=" O CYS E 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 536 through 537 Processing sheet with id=AB7, first strand: chain 'F' and resid 19 through 25 Processing sheet with id=AB8, first strand: chain 'I' and resid 5 through 7 removed outlier: 6.298A pdb=" N ARG I 6 " --> pdb=" O LYS I 194 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL I 177 " --> pdb=" O LYS I 171 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS I 171 " --> pdb=" O VAL I 177 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N GLY I 179 " --> pdb=" O LEU I 169 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LEU I 169 " --> pdb=" O GLY I 179 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR I 181 " --> pdb=" O LEU I 167 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 159 through 161 removed outlier: 3.911A pdb=" N THR I 159 " --> pdb=" O CYS I 33 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA I 10 " --> pdb=" O ALA I 34 " (cutoff:3.500A) removed outlier: 7.527A pdb=" N LEU I 36 " --> pdb=" O ALA I 10 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N VAL I 12 " --> pdb=" O LEU I 36 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N ALA I 368 " --> pdb=" O VAL I 380 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 53 through 54 Processing sheet with id=AC2, first strand: chain 'I' and resid 233 through 234 removed outlier: 3.606A pdb=" N VAL I 233 " --> pdb=" O TYR I 559 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'I' and resid 239 through 242 removed outlier: 6.622A pdb=" N GLN I 240 " --> pdb=" O HIS I 354 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'I' and resid 360 through 361 removed outlier: 5.520A pdb=" N ILE I 360 " --> pdb=" O CYS I 391 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 536 through 537 Processing sheet with id=AC6, first strand: chain 'J' and resid 19 through 25 1221 hydrogen bonds defined for protein. 3519 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.41 Time building geometry restraints manager: 2.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.74: 23046 1.74 - 2.29: 321 2.29 - 2.84: 9 2.84 - 3.40: 0 3.40 - 3.95: 9 Bond restraints: 23385 Sorted by residual: bond pdb=" S4 F3S J 303 " pdb="FE1 F3S J 303 " ideal model delta sigma weight residual 2.233 3.935 -1.702 2.00e-02 2.50e+03 7.24e+03 bond pdb=" S4 F3S B 303 " pdb="FE1 F3S B 303 " ideal model delta sigma weight residual 2.233 3.935 -1.702 2.00e-02 2.50e+03 7.24e+03 bond pdb=" S4 F3S F 303 " pdb="FE1 F3S F 303 " ideal model delta sigma weight residual 2.233 3.934 -1.701 2.00e-02 2.50e+03 7.23e+03 bond pdb=" S2 F3S B 303 " pdb="FE3 F3S B 303 " ideal model delta sigma weight residual 2.300 3.951 -1.651 2.00e-02 2.50e+03 6.81e+03 bond pdb=" S2 F3S F 303 " pdb="FE3 F3S F 303 " ideal model delta sigma weight residual 2.300 3.950 -1.650 2.00e-02 2.50e+03 6.81e+03 ... (remaining 23380 not shown) Histogram of bond angle deviations from ideal: 0.00 - 9.99: 31725 9.99 - 19.97: 15 19.97 - 29.96: 3 29.96 - 39.95: 21 39.95 - 49.93: 6 Bond angle restraints: 31770 Sorted by residual: angle pdb=" S1 F3S J 303 " pdb="FE4 F3S J 303 " pdb=" S3 F3S J 303 " ideal model delta sigma weight residual 114.75 64.82 49.93 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S1 F3S F 303 " pdb="FE4 F3S F 303 " pdb=" S3 F3S F 303 " ideal model delta sigma weight residual 114.75 64.82 49.93 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S1 F3S B 303 " pdb="FE4 F3S B 303 " pdb=" S3 F3S B 303 " ideal model delta sigma weight residual 114.75 64.83 49.92 3.00e+00 1.11e-01 2.77e+02 angle pdb=" S3 F3S J 303 " pdb="FE1 F3S J 303 " pdb=" S4 F3S J 303 " ideal model delta sigma weight residual 112.59 64.30 48.29 3.00e+00 1.11e-01 2.59e+02 angle pdb=" S3 F3S F 303 " pdb="FE1 F3S F 303 " pdb=" S4 F3S F 303 " ideal model delta sigma weight residual 112.59 64.31 48.28 3.00e+00 1.11e-01 2.59e+02 ... (remaining 31765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 12488 16.63 - 33.25: 972 33.25 - 49.88: 292 49.88 - 66.50: 90 66.50 - 83.13: 36 Dihedral angle restraints: 13878 sinusoidal: 5664 harmonic: 8214 Sorted by residual: dihedral pdb=" C2D HEM K 201 " pdb=" C3D HEM K 201 " pdb=" CAD HEM K 201 " pdb=" CBD HEM K 201 " ideal model delta sinusoidal sigma weight residual 0.00 67.81 -67.81 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" C2D HEM D 201 " pdb=" C3D HEM D 201 " pdb=" CAD HEM D 201 " pdb=" CBD HEM D 201 " ideal model delta sinusoidal sigma weight residual 0.00 67.71 -67.71 2 2.00e+01 2.50e-03 1.03e+01 dihedral pdb=" C2D HEM G 201 " pdb=" C3D HEM G 201 " pdb=" CAD HEM G 201 " pdb=" CBD HEM G 201 " ideal model delta sinusoidal sigma weight residual 0.00 67.70 -67.70 2 2.00e+01 2.50e-03 1.03e+01 ... (remaining 13875 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 3.605: 3504 3.605 - 7.210: 0 7.210 - 10.816: 0 10.816 - 14.421: 0 14.421 - 18.026: 3 Chirality restraints: 3507 Sorted by residual: chirality pdb=" S2 F3S B 303 " pdb="FE1 F3S B 303 " pdb="FE3 F3S B 303 " pdb="FE4 F3S B 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.26 18.03 2.00e-01 2.50e+01 8.12e+03 chirality pdb=" S2 F3S F 303 " pdb="FE1 F3S F 303 " pdb="FE3 F3S F 303 " pdb="FE4 F3S F 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.25 18.02 2.00e-01 2.50e+01 8.12e+03 chirality pdb=" S2 F3S J 303 " pdb="FE1 F3S J 303 " pdb="FE3 F3S J 303 " pdb="FE4 F3S J 303 " both_signs ideal model delta sigma weight residual False 10.77 -7.25 18.02 2.00e-01 2.50e+01 8.12e+03 ... (remaining 3504 not shown) Planarity restraints: 4029 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 113 " 0.007 2.00e-02 2.50e+03 5.32e-03 7.07e-01 pdb=" CG TRP L 113 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TRP L 113 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP L 113 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 113 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP L 113 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP L 113 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 113 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 113 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 113 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 109 " 0.004 2.00e-02 2.50e+03 8.38e-03 7.02e-01 pdb=" C PHE D 109 " -0.014 2.00e-02 2.50e+03 pdb=" O PHE D 109 " 0.005 2.00e-02 2.50e+03 pdb=" N VAL D 110 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE L 109 " -0.004 2.00e-02 2.50e+03 8.36e-03 6.98e-01 pdb=" C PHE L 109 " 0.014 2.00e-02 2.50e+03 pdb=" O PHE L 109 " -0.005 2.00e-02 2.50e+03 pdb=" N VAL L 110 " -0.005 2.00e-02 2.50e+03 ... (remaining 4026 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 395 2.64 - 3.20: 22686 3.20 - 3.77: 36860 3.77 - 4.33: 52080 4.33 - 4.90: 85072 Nonbonded interactions: 197093 Sorted by model distance: nonbonded pdb=" OD1 ASP J 46 " pdb=" OG SER J 48 " model vdw 2.070 3.040 nonbonded pdb=" OD1 ASP F 46 " pdb=" OG SER F 48 " model vdw 2.070 3.040 nonbonded pdb=" OD1 ASP B 46 " pdb=" OG SER B 48 " model vdw 2.070 3.040 nonbonded pdb=" NH1 ARG J 205 " pdb=" OD1 ASP L 82 " model vdw 2.114 3.120 nonbonded pdb=" OE1 GLU E 94 " pdb=" NH1 ARG E 413 " model vdw 2.115 3.120 ... (remaining 197088 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' } ncs_group { reference = (chain 'C' and resid 5 through 129) selection = (chain 'G' and resid 5 through 129) selection = (chain 'K' and resid 5 through 129) } ncs_group { reference = (chain 'D' and resid 3 through 115) selection = (chain 'H' and resid 3 through 115) selection = (chain 'L' and resid 3 through 115) } 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: 0.010 Normalize map: mean=0, sd=1: 0.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.500 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 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 : 0.042 1.702 23420 Z= 1.972 Angle : 1.922 70.119 31845 Z= 0.548 Chirality : 0.528 18.026 3507 Planarity : 0.002 0.019 4029 Dihedral : 14.261 83.128 8604 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 35.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.38 % Allowed : 2.39 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.16 (0.14), residues: 2841 helix: 0.25 (0.13), residues: 1404 sheet: -3.15 (0.28), residues: 165 loop : -3.27 (0.15), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 413 TYR 0.011 0.001 TYR B 8 PHE 0.010 0.001 PHE E 411 TRP 0.015 0.001 TRP L 113 HIS 0.003 0.000 HIS E 147 Details of bonding type rmsd covalent geometry : bond 0.03272 (23385) covalent geometry : angle 1.28065 (31770) hydrogen bonds : bond 0.12098 ( 1221) hydrogen bonds : angle 5.65316 ( 3519) metal coordination : bond 0.71833 ( 30) metal coordination : angle 29.55529 ( 75) Misc. bond : bond 0.38835 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 631 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 598 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 225 MET cc_start: 0.6830 (mtp) cc_final: 0.6593 (mtp) REVERT: A 227 ILE cc_start: 0.7298 (mt) cc_final: 0.6841 (mt) REVERT: A 236 MET cc_start: 0.7449 (mmp) cc_final: 0.6907 (mmp) REVERT: A 443 ARG cc_start: 0.7869 (ttp80) cc_final: 0.7646 (ttp80) REVERT: B 1 MET cc_start: 0.5214 (ptt) cc_final: 0.4115 (mpp) REVERT: B 41 GLN cc_start: 0.6981 (tt0) cc_final: 0.6644 (mt0) REVERT: D 77 TRP cc_start: 0.7643 (t60) cc_final: 0.7348 (t-100) REVERT: E 209 TYR cc_start: 0.7159 (m-80) cc_final: 0.6879 (m-80) REVERT: E 227 ILE cc_start: 0.7479 (mt) cc_final: 0.7077 (mt) REVERT: E 568 ARG cc_start: 0.7382 (mtt180) cc_final: 0.7083 (mtt180) REVERT: F 9 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7309 (mmm160) REVERT: F 232 MET cc_start: 0.7783 (mtp) cc_final: 0.7388 (mtp) REVERT: G 93 MET cc_start: 0.6906 (mtp) cc_final: 0.6495 (mtp) REVERT: H 56 PHE cc_start: 0.7072 (t80) cc_final: 0.5613 (m-80) REVERT: I 227 ILE cc_start: 0.7064 (mt) cc_final: 0.6598 (mt) REVERT: I 420 GLN cc_start: 0.6644 (tp40) cc_final: 0.6319 (tp40) REVERT: I 446 ARG cc_start: 0.7473 (tmm160) cc_final: 0.7234 (tmm160) REVERT: I 471 PHE cc_start: 0.6564 (m-80) cc_final: 0.6330 (m-80) REVERT: I 568 ARG cc_start: 0.7437 (mtt180) cc_final: 0.7118 (mtt-85) REVERT: J 67 MET cc_start: 0.6782 (mtm) cc_final: 0.6422 (mtm) REVERT: J 235 GLN cc_start: 0.7010 (mm-40) cc_final: 0.6774 (mm110) REVERT: L 45 TYR cc_start: 0.7261 (t80) cc_final: 0.7059 (t80) REVERT: L 56 PHE cc_start: 0.7054 (t80) cc_final: 0.5779 (m-80) outliers start: 33 outliers final: 7 residues processed: 626 average time/residue: 0.6734 time to fit residues: 481.7660 Evaluate side-chains 492 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 485 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 352 THR Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 10.0000 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 5.9990 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 6.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS A 173 GLN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 450 ASN A 452 ASN A 531 ASN B 71 ASN B 123 ASN B 133 HIS B 207 HIS B 211 ASN B 237 ASN C 91 HIS D 14 HIS ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 50 GLN ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS E 173 GLN ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN E 452 ASN E 496 ASN E 518 ASN E 531 ASN F 71 ASN F 207 HIS F 211 ASN F 228 HIS F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 91 HIS H 14 HIS ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 143 HIS ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN I 450 ASN I 452 ASN I 518 ASN I 531 ASN J 71 ASN J 123 ASN J 133 HIS J 207 HIS J 228 HIS J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 91 HIS L 14 HIS L 94 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.160804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.143903 restraints weight = 30053.575| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.06 r_work: 0.3668 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7025 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.297 23420 Z= 0.266 Angle : 1.578 65.593 31845 Z= 0.492 Chirality : 0.063 1.586 3507 Planarity : 0.005 0.044 4029 Dihedral : 9.197 76.836 3437 Min Nonbonded Distance : 1.508 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.27 % Allowed : 12.56 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.15), residues: 2841 helix: 1.21 (0.13), residues: 1437 sheet: -2.76 (0.28), residues: 189 loop : -2.51 (0.16), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 578 TYR 0.022 0.002 TYR B 8 PHE 0.023 0.002 PHE D 60 TRP 0.018 0.002 TRP H 113 HIS 0.006 0.002 HIS A 556 Details of bonding type rmsd covalent geometry : bond 0.00580 (23385) covalent geometry : angle 1.25272 (31770) hydrogen bonds : bond 0.05287 ( 1221) hydrogen bonds : angle 4.75948 ( 3519) metal coordination : bond 0.02658 ( 30) metal coordination : angle 19.81618 ( 75) Misc. bond : bond 0.18319 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 538 time to evaluate : 0.837 Fit side-chains revert: symmetry clash REVERT: A 9 ASP cc_start: 0.7325 (m-30) cc_final: 0.6800 (m-30) REVERT: A 31 GLN cc_start: 0.7400 (mm-40) cc_final: 0.6864 (mp10) REVERT: A 46 THR cc_start: 0.8650 (OUTLIER) cc_final: 0.8408 (m) REVERT: A 236 MET cc_start: 0.7707 (mmp) cc_final: 0.7504 (mmp) REVERT: A 438 GLU cc_start: 0.7110 (OUTLIER) cc_final: 0.6862 (tt0) REVERT: A 471 PHE cc_start: 0.7054 (m-80) cc_final: 0.6518 (m-80) REVERT: A 476 GLU cc_start: 0.7146 (tm-30) cc_final: 0.6593 (mt-10) REVERT: A 488 LYS cc_start: 0.5735 (OUTLIER) cc_final: 0.5505 (mmmm) REVERT: A 490 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.6854 (mp) REVERT: A 568 ARG cc_start: 0.7715 (mtt180) cc_final: 0.7111 (mtt180) REVERT: B 1 MET cc_start: 0.5876 (ptt) cc_final: 0.4545 (mpp) REVERT: B 2 ARG cc_start: 0.6892 (ptm160) cc_final: 0.6196 (ptm160) REVERT: B 9 ARG cc_start: 0.7782 (mmm-85) cc_final: 0.7413 (mmm-85) REVERT: B 33 MET cc_start: 0.7193 (OUTLIER) cc_final: 0.6769 (ptt) REVERT: B 144 ASP cc_start: 0.7999 (m-30) cc_final: 0.7570 (m-30) REVERT: C 101 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7150 (mt-10) REVERT: D 27 THR cc_start: 0.6853 (p) cc_final: 0.6300 (m) REVERT: D 77 TRP cc_start: 0.7926 (t60) cc_final: 0.7222 (t-100) REVERT: E 31 GLN cc_start: 0.7440 (mm-40) cc_final: 0.6064 (mp10) REVERT: E 46 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8189 (m) REVERT: E 196 ARG cc_start: 0.7238 (mtp180) cc_final: 0.7016 (mtp180) REVERT: E 227 ILE cc_start: 0.7532 (mt) cc_final: 0.7247 (mt) REVERT: E 352 THR cc_start: 0.7992 (t) cc_final: 0.7547 (m) REVERT: E 438 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7102 (tp30) REVERT: E 449 ASN cc_start: 0.6472 (m-40) cc_final: 0.6084 (m-40) REVERT: E 455 ASP cc_start: 0.7496 (t0) cc_final: 0.7271 (t0) REVERT: E 568 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7450 (mtt180) REVERT: E 578 ARG cc_start: 0.6835 (ttt90) cc_final: 0.6582 (tpt-90) REVERT: E 581 PHE cc_start: 0.8343 (m-80) cc_final: 0.7903 (m-80) REVERT: F 2 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.6565 (ttt90) REVERT: F 33 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6639 (ptt) REVERT: F 102 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7701 (t70) REVERT: F 235 GLN cc_start: 0.7328 (OUTLIER) cc_final: 0.7058 (mm110) REVERT: G 81 LEU cc_start: 0.7352 (tp) cc_final: 0.7124 (tt) REVERT: G 93 MET cc_start: 0.7384 (mtp) cc_final: 0.6977 (mtp) REVERT: G 123 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7333 (mp) REVERT: H 56 PHE cc_start: 0.7464 (t80) cc_final: 0.5078 (m-80) REVERT: I 31 GLN cc_start: 0.7482 (mm-40) cc_final: 0.6917 (mm110) REVERT: I 46 THR cc_start: 0.8729 (OUTLIER) cc_final: 0.8427 (m) REVERT: I 187 THR cc_start: 0.7501 (OUTLIER) cc_final: 0.7300 (p) REVERT: I 227 ILE cc_start: 0.7408 (mt) cc_final: 0.7144 (mt) REVERT: I 420 GLN cc_start: 0.7026 (tp40) cc_final: 0.6636 (tp40) REVERT: I 450 ASN cc_start: 0.6681 (OUTLIER) cc_final: 0.6475 (t0) REVERT: I 455 ASP cc_start: 0.7734 (t0) cc_final: 0.7450 (t0) REVERT: I 520 MET cc_start: 0.8459 (tpt) cc_final: 0.8027 (tpt) REVERT: I 572 ASN cc_start: 0.7129 (t0) cc_final: 0.6733 (t0) REVERT: J 2 ARG cc_start: 0.6758 (OUTLIER) cc_final: 0.6359 (ptm-80) REVERT: J 67 MET cc_start: 0.7071 (mtm) cc_final: 0.6749 (mtm) REVERT: J 102 ASP cc_start: 0.7823 (OUTLIER) cc_final: 0.7346 (t70) REVERT: J 109 GLN cc_start: 0.8138 (mt0) cc_final: 0.7921 (mt0) REVERT: J 235 GLN cc_start: 0.7054 (mm-40) cc_final: 0.6712 (mm110) REVERT: K 101 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7148 (mt-10) REVERT: L 56 PHE cc_start: 0.7512 (t80) cc_final: 0.5381 (m-80) REVERT: L 77 TRP cc_start: 0.7911 (t60) cc_final: 0.7142 (t-100) outliers start: 102 outliers final: 34 residues processed: 583 average time/residue: 0.6253 time to fit residues: 418.9430 Evaluate side-chains 553 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 500 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain F residue 2 ARG Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 211 ASN Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 177 VAL Chi-restraints excluded: chain I residue 187 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 437 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 242 optimal weight: 10.0000 chunk 175 optimal weight: 9.9990 chunk 253 optimal weight: 4.9990 chunk 164 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 241 optimal weight: 0.9980 chunk 220 optimal weight: 20.0000 chunk 7 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 281 optimal weight: 2.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 153 ASN ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN A 518 ASN B 71 ASN B 237 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN E 367 GLN E 452 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 122 GLN I 173 GLN ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 ASN I 452 ASN J 71 ASN J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.161206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.144343 restraints weight = 30500.213| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.09 r_work: 0.3674 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.235 23420 Z= 0.174 Angle : 1.463 85.618 31845 Z= 0.441 Chirality : 0.059 1.468 3507 Planarity : 0.005 0.049 4029 Dihedral : 8.262 77.353 3433 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.89 % Allowed : 15.91 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.16), residues: 2841 helix: 1.61 (0.14), residues: 1434 sheet: -2.28 (0.31), residues: 189 loop : -2.15 (0.17), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 56 TYR 0.028 0.002 TYR H 45 PHE 0.018 0.002 PHE D 60 TRP 0.022 0.002 TRP H 113 HIS 0.005 0.001 HIS E 143 Details of bonding type rmsd covalent geometry : bond 0.00383 (23385) covalent geometry : angle 1.11187 (31770) hydrogen bonds : bond 0.04880 ( 1221) hydrogen bonds : angle 4.58166 ( 3519) metal coordination : bond 0.00970 ( 30) metal coordination : angle 19.63786 ( 75) Misc. bond : bond 0.14536 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 611 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 518 time to evaluate : 0.876 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7513 (mm-40) cc_final: 0.6909 (mp10) REVERT: A 46 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8400 (m) REVERT: A 168 ASP cc_start: 0.7755 (m-30) cc_final: 0.7484 (t0) REVERT: A 374 LYS cc_start: 0.8628 (ttmt) cc_final: 0.8298 (ttmp) REVERT: A 438 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6871 (tp30) REVERT: A 471 PHE cc_start: 0.7092 (m-80) cc_final: 0.6489 (m-80) REVERT: A 476 GLU cc_start: 0.7068 (tm-30) cc_final: 0.6625 (mt-10) REVERT: A 490 ILE cc_start: 0.7218 (OUTLIER) cc_final: 0.6741 (mp) REVERT: B 1 MET cc_start: 0.5818 (ptt) cc_final: 0.5590 (ptt) REVERT: B 2 ARG cc_start: 0.6884 (ptm160) cc_final: 0.6349 (ttt90) REVERT: B 33 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6721 (ptt) REVERT: B 56 ARG cc_start: 0.8079 (ttp-110) cc_final: 0.7876 (ttp-170) REVERT: C 71 LYS cc_start: 0.6461 (mmtm) cc_final: 0.6256 (mmtm) REVERT: C 123 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7193 (mp) REVERT: D 6 SER cc_start: 0.8002 (OUTLIER) cc_final: 0.7761 (t) REVERT: D 27 THR cc_start: 0.6784 (p) cc_final: 0.6305 (m) REVERT: E 46 THR cc_start: 0.8602 (OUTLIER) cc_final: 0.8195 (m) REVERT: E 196 ARG cc_start: 0.7292 (mtp180) cc_final: 0.7077 (mtp180) REVERT: E 210 GLN cc_start: 0.6853 (tt0) cc_final: 0.6340 (mt0) REVERT: E 227 ILE cc_start: 0.7524 (mt) cc_final: 0.7266 (mt) REVERT: E 352 THR cc_start: 0.7961 (t) cc_final: 0.7497 (m) REVERT: E 357 MET cc_start: 0.6410 (mmm) cc_final: 0.6206 (mmm) REVERT: E 367 GLN cc_start: 0.7151 (OUTLIER) cc_final: 0.6884 (mt0) REVERT: E 438 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7074 (tp30) REVERT: E 455 ASP cc_start: 0.7502 (t0) cc_final: 0.7238 (t0) REVERT: E 545 PHE cc_start: 0.6044 (m-80) cc_final: 0.5786 (m-10) REVERT: E 568 ARG cc_start: 0.7693 (mtt180) cc_final: 0.7382 (mtt180) REVERT: F 33 MET cc_start: 0.7156 (OUTLIER) cc_final: 0.6672 (ptt) REVERT: F 168 LYS cc_start: 0.7860 (OUTLIER) cc_final: 0.7616 (mttt) REVERT: F 235 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.7106 (mp10) REVERT: G 81 LEU cc_start: 0.7329 (tp) cc_final: 0.7107 (tt) REVERT: G 123 LEU cc_start: 0.7761 (OUTLIER) cc_final: 0.7342 (mp) REVERT: H 27 THR cc_start: 0.7061 (p) cc_final: 0.6850 (m) REVERT: I 31 GLN cc_start: 0.7493 (mm-40) cc_final: 0.6920 (mm110) REVERT: I 46 THR cc_start: 0.8705 (OUTLIER) cc_final: 0.8386 (m) REVERT: I 66 GLU cc_start: 0.6098 (mt-10) cc_final: 0.5650 (mp0) REVERT: I 130 GLN cc_start: 0.6721 (mm-40) cc_final: 0.6496 (mm-40) REVERT: I 227 ILE cc_start: 0.7429 (mt) cc_final: 0.7184 (mt) REVERT: I 420 GLN cc_start: 0.7085 (tp40) cc_final: 0.6690 (tp40) REVERT: I 450 ASN cc_start: 0.6756 (OUTLIER) cc_final: 0.6546 (OUTLIER) REVERT: I 455 ASP cc_start: 0.7692 (t0) cc_final: 0.7452 (t0) REVERT: I 471 PHE cc_start: 0.6934 (m-80) cc_final: 0.6690 (m-80) REVERT: I 476 GLU cc_start: 0.6337 (OUTLIER) cc_final: 0.6061 (mp0) REVERT: I 520 MET cc_start: 0.8418 (tpt) cc_final: 0.7953 (tpt) REVERT: I 568 ARG cc_start: 0.7785 (mtt-85) cc_final: 0.7250 (mtt-85) REVERT: I 572 ASN cc_start: 0.7082 (t0) cc_final: 0.6748 (t0) REVERT: J 2 ARG cc_start: 0.6798 (OUTLIER) cc_final: 0.6360 (ptm-80) REVERT: J 67 MET cc_start: 0.7023 (mtm) cc_final: 0.6705 (mtm) REVERT: J 102 ASP cc_start: 0.7733 (OUTLIER) cc_final: 0.7227 (t70) REVERT: J 235 GLN cc_start: 0.7098 (mm-40) cc_final: 0.6756 (mm110) REVERT: K 101 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.7085 (mt-10) REVERT: L 6 SER cc_start: 0.7915 (OUTLIER) cc_final: 0.7600 (p) REVERT: L 56 PHE cc_start: 0.7584 (t80) cc_final: 0.5410 (m-80) outliers start: 93 outliers final: 29 residues processed: 563 average time/residue: 0.6148 time to fit residues: 397.9059 Evaluate side-chains 536 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 488 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 367 GLN Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 124 optimal weight: 0.9990 chunk 204 optimal weight: 10.0000 chunk 105 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 4.9990 chunk 113 optimal weight: 9.9990 chunk 213 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 159 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 100 optimal weight: 9.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN B 71 ASN B 237 ASN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 240 GLN I 367 GLN I 448 ASN I 450 ASN I 531 ASN J 71 ASN J 109 GLN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.159108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.142231 restraints weight = 30784.122| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 2.08 r_work: 0.3651 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.262 23420 Z= 0.215 Angle : 1.400 84.387 31845 Z= 0.454 Chirality : 0.059 1.404 3507 Planarity : 0.005 0.049 4029 Dihedral : 8.083 77.935 3433 Min Nonbonded Distance : 1.784 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 4.27 % Allowed : 18.51 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.16), residues: 2841 helix: 1.57 (0.13), residues: 1437 sheet: -2.12 (0.31), residues: 189 loop : -2.11 (0.17), residues: 1215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 21 TYR 0.032 0.002 TYR L 45 PHE 0.021 0.002 PHE L 60 TRP 0.024 0.002 TRP D 113 HIS 0.007 0.001 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00489 (23385) covalent geometry : angle 1.13530 (31770) hydrogen bonds : bond 0.05344 ( 1221) hydrogen bonds : angle 4.61353 ( 3519) metal coordination : bond 0.01210 ( 30) metal coordination : angle 16.90580 ( 75) Misc. bond : bond 0.15779 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 503 time to evaluate : 0.804 Fit side-chains REVERT: A 31 GLN cc_start: 0.7362 (mm-40) cc_final: 0.6700 (mp10) REVERT: A 374 LYS cc_start: 0.8645 (ttmt) cc_final: 0.8285 (ttmp) REVERT: A 438 GLU cc_start: 0.7223 (OUTLIER) cc_final: 0.6893 (tp30) REVERT: A 476 GLU cc_start: 0.7175 (tm-30) cc_final: 0.6684 (mt-10) REVERT: A 490 ILE cc_start: 0.7279 (OUTLIER) cc_final: 0.6792 (mp) REVERT: A 517 ASP cc_start: 0.7144 (m-30) cc_final: 0.6881 (m-30) REVERT: A 568 ARG cc_start: 0.7629 (mtt180) cc_final: 0.7196 (mtt180) REVERT: B 1 MET cc_start: 0.5492 (ptt) cc_final: 0.5268 (ptt) REVERT: B 2 ARG cc_start: 0.6694 (ptm160) cc_final: 0.5990 (ptm160) REVERT: B 9 ARG cc_start: 0.7722 (mmm-85) cc_final: 0.7493 (mmm-85) REVERT: B 33 MET cc_start: 0.7181 (OUTLIER) cc_final: 0.6770 (ptt) REVERT: B 56 ARG cc_start: 0.8123 (ttp-110) cc_final: 0.7915 (ttp-170) REVERT: B 144 ASP cc_start: 0.7943 (m-30) cc_final: 0.7512 (m-30) REVERT: C 71 LYS cc_start: 0.6519 (mmtm) cc_final: 0.6295 (mmtm) REVERT: C 101 GLU cc_start: 0.7534 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: C 123 LEU cc_start: 0.7691 (OUTLIER) cc_final: 0.7242 (mp) REVERT: D 6 SER cc_start: 0.7987 (OUTLIER) cc_final: 0.7682 (t) REVERT: D 27 THR cc_start: 0.6868 (p) cc_final: 0.6436 (m) REVERT: E 46 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8241 (m) REVERT: E 50 GLN cc_start: 0.8288 (OUTLIER) cc_final: 0.7915 (mt0) REVERT: E 62 GLU cc_start: 0.7085 (tt0) cc_final: 0.6589 (pt0) REVERT: E 196 ARG cc_start: 0.7293 (mtp180) cc_final: 0.7069 (mtp180) REVERT: E 210 GLN cc_start: 0.6815 (tt0) cc_final: 0.6337 (mt0) REVERT: E 227 ILE cc_start: 0.7528 (mt) cc_final: 0.7304 (mt) REVERT: E 438 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7235 (tp30) REVERT: E 455 ASP cc_start: 0.7589 (t0) cc_final: 0.7302 (t0) REVERT: E 568 ARG cc_start: 0.7660 (mtt180) cc_final: 0.7358 (mtt180) REVERT: F 33 MET cc_start: 0.7254 (OUTLIER) cc_final: 0.6714 (ptt) REVERT: F 142 LYS cc_start: 0.7154 (mmtp) cc_final: 0.6791 (mppt) REVERT: F 168 LYS cc_start: 0.7938 (OUTLIER) cc_final: 0.7661 (mttt) REVERT: F 235 GLN cc_start: 0.7290 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: G 53 SER cc_start: 0.7800 (t) cc_final: 0.7055 (p) REVERT: G 81 LEU cc_start: 0.7347 (tp) cc_final: 0.7125 (tt) REVERT: G 119 VAL cc_start: 0.8264 (t) cc_final: 0.8054 (t) REVERT: G 123 LEU cc_start: 0.7777 (OUTLIER) cc_final: 0.7374 (mp) REVERT: H 56 PHE cc_start: 0.7434 (t80) cc_final: 0.5137 (m-80) REVERT: I 31 GLN cc_start: 0.7475 (mm-40) cc_final: 0.6903 (mm110) REVERT: I 66 GLU cc_start: 0.6163 (mt-10) cc_final: 0.5700 (mp0) REVERT: I 227 ILE cc_start: 0.7465 (mt) cc_final: 0.7255 (mt) REVERT: I 367 GLN cc_start: 0.6695 (OUTLIER) cc_final: 0.6272 (mt0) REVERT: I 420 GLN cc_start: 0.7031 (tp40) cc_final: 0.6647 (tp40) REVERT: I 450 ASN cc_start: 0.6813 (OUTLIER) cc_final: 0.6587 (OUTLIER) REVERT: I 455 ASP cc_start: 0.7711 (t0) cc_final: 0.7460 (t0) REVERT: I 471 PHE cc_start: 0.7098 (m-80) cc_final: 0.6871 (m-80) REVERT: I 476 GLU cc_start: 0.6408 (OUTLIER) cc_final: 0.6092 (mp0) REVERT: I 480 MET cc_start: 0.7614 (mtm) cc_final: 0.7334 (mtt) REVERT: I 490 ILE cc_start: 0.6710 (OUTLIER) cc_final: 0.6336 (mp) REVERT: I 520 MET cc_start: 0.8411 (tpt) cc_final: 0.7978 (tpt) REVERT: I 572 ASN cc_start: 0.7137 (t0) cc_final: 0.6719 (t0) REVERT: J 2 ARG cc_start: 0.6764 (OUTLIER) cc_final: 0.6288 (ptm-80) REVERT: J 67 MET cc_start: 0.6907 (mtm) cc_final: 0.6662 (mtm) REVERT: J 102 ASP cc_start: 0.7845 (OUTLIER) cc_final: 0.7290 (t70) REVERT: K 92 MET cc_start: 0.7744 (mtm) cc_final: 0.7430 (mmm) REVERT: K 101 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7080 (mt-10) REVERT: L 6 SER cc_start: 0.7925 (OUTLIER) cc_final: 0.7576 (t) REVERT: L 56 PHE cc_start: 0.7582 (t80) cc_final: 0.5468 (m-80) REVERT: L 90 ARG cc_start: 0.6860 (ttp-110) cc_final: 0.6634 (ttp-110) outliers start: 102 outliers final: 45 residues processed: 553 average time/residue: 0.6249 time to fit residues: 398.7220 Evaluate side-chains 553 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 488 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 40 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 379 VAL Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 144 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 367 GLN Chi-restraints excluded: chain I residue 407 ASP Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 262 optimal weight: 2.9990 chunk 174 optimal weight: 3.9990 chunk 151 optimal weight: 0.1980 chunk 32 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 158 optimal weight: 0.9980 chunk 252 optimal weight: 1.9990 chunk 196 optimal weight: 9.9990 chunk 260 optimal weight: 0.4980 chunk 12 optimal weight: 5.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 218 ASN A 452 ASN B 71 ASN B 237 ASN ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN E 496 ASN F 71 ASN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 64 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 450 ASN I 452 ASN I 531 ASN J 71 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.163533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.146318 restraints weight = 29984.402| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 2.13 r_work: 0.3739 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3648 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7061 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.176 23420 Z= 0.150 Angle : 1.320 84.306 31845 Z= 0.428 Chirality : 0.058 1.435 3507 Planarity : 0.004 0.050 4029 Dihedral : 7.598 78.479 3431 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.52 % Allowed : 20.81 % Favored : 75.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.16), residues: 2841 helix: 1.90 (0.14), residues: 1437 sheet: -2.02 (0.31), residues: 225 loop : -1.93 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 451 TYR 0.030 0.001 TYR L 45 PHE 0.017 0.001 PHE L 52 TRP 0.025 0.001 TRP H 113 HIS 0.005 0.001 HIS A 68 Details of bonding type rmsd covalent geometry : bond 0.00317 (23385) covalent geometry : angle 1.09859 (31770) hydrogen bonds : bond 0.04619 ( 1221) hydrogen bonds : angle 4.45941 ( 3519) metal coordination : bond 0.00767 ( 30) metal coordination : angle 15.10321 ( 75) Misc. bond : bond 0.10654 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 510 time to evaluate : 0.867 Fit side-chains REVERT: A 31 GLN cc_start: 0.7369 (mm-40) cc_final: 0.6691 (mp10) REVERT: A 438 GLU cc_start: 0.7237 (mm-30) cc_final: 0.6868 (tp30) REVERT: A 476 GLU cc_start: 0.6963 (tm-30) cc_final: 0.6689 (mt-10) REVERT: A 568 ARG cc_start: 0.7676 (mtt180) cc_final: 0.7267 (mtt180) REVERT: B 1 MET cc_start: 0.5572 (ptt) cc_final: 0.5332 (ptt) REVERT: B 2 ARG cc_start: 0.6711 (ptm160) cc_final: 0.6094 (ptm160) REVERT: B 9 ARG cc_start: 0.7728 (mmm-85) cc_final: 0.7431 (mmm-85) REVERT: B 33 MET cc_start: 0.7152 (OUTLIER) cc_final: 0.6749 (ptt) REVERT: B 144 ASP cc_start: 0.7937 (m-30) cc_final: 0.7540 (m-30) REVERT: C 71 LYS cc_start: 0.6632 (mmtm) cc_final: 0.6344 (mmtm) REVERT: C 123 LEU cc_start: 0.7654 (OUTLIER) cc_final: 0.7395 (mm) REVERT: D 6 SER cc_start: 0.7923 (OUTLIER) cc_final: 0.7653 (t) REVERT: D 27 THR cc_start: 0.6994 (p) cc_final: 0.6543 (m) REVERT: E 46 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8205 (m) REVERT: E 50 GLN cc_start: 0.8329 (OUTLIER) cc_final: 0.7931 (mt0) REVERT: E 62 GLU cc_start: 0.7092 (tt0) cc_final: 0.6606 (pt0) REVERT: E 210 GLN cc_start: 0.6803 (tt0) cc_final: 0.6385 (mt0) REVERT: E 227 ILE cc_start: 0.7561 (mt) cc_final: 0.7349 (mt) REVERT: E 243 PRO cc_start: 0.6273 (Cg_endo) cc_final: 0.6049 (Cg_exo) REVERT: E 355 TYR cc_start: 0.8105 (t80) cc_final: 0.7884 (t80) REVERT: E 405 LEU cc_start: 0.6891 (mm) cc_final: 0.6430 (mt) REVERT: E 438 GLU cc_start: 0.7384 (OUTLIER) cc_final: 0.7136 (tp30) REVERT: E 455 ASP cc_start: 0.7546 (t0) cc_final: 0.7239 (t0) REVERT: E 568 ARG cc_start: 0.7653 (mtt180) cc_final: 0.7373 (mtt180) REVERT: E 574 GLU cc_start: 0.7587 (OUTLIER) cc_final: 0.6723 (pp20) REVERT: F 2 ARG cc_start: 0.7093 (ttt90) cc_final: 0.6892 (ttt90) REVERT: F 33 MET cc_start: 0.7133 (OUTLIER) cc_final: 0.6637 (ptt) REVERT: F 142 LYS cc_start: 0.7149 (mmtp) cc_final: 0.6813 (mppt) REVERT: F 168 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7626 (mttt) REVERT: G 53 SER cc_start: 0.7815 (t) cc_final: 0.7113 (p) REVERT: G 81 LEU cc_start: 0.7304 (tp) cc_final: 0.7085 (tt) REVERT: G 93 MET cc_start: 0.7211 (mtp) cc_final: 0.6948 (mtm) REVERT: G 123 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7228 (mp) REVERT: H 27 THR cc_start: 0.7100 (p) cc_final: 0.6896 (m) REVERT: I 31 GLN cc_start: 0.7448 (mm-40) cc_final: 0.7001 (mm110) REVERT: I 66 GLU cc_start: 0.6083 (mt-10) cc_final: 0.5717 (mp0) REVERT: I 227 ILE cc_start: 0.7582 (mt) cc_final: 0.7363 (mt) REVERT: I 420 GLN cc_start: 0.7086 (tp40) cc_final: 0.6715 (tp40) REVERT: I 438 GLU cc_start: 0.6887 (tp30) cc_final: 0.6566 (tp30) REVERT: I 455 ASP cc_start: 0.7699 (t0) cc_final: 0.7453 (t0) REVERT: I 471 PHE cc_start: 0.6828 (m-80) cc_final: 0.6609 (m-80) REVERT: I 476 GLU cc_start: 0.6436 (OUTLIER) cc_final: 0.6113 (mp0) REVERT: I 480 MET cc_start: 0.7484 (mtm) cc_final: 0.7259 (mtp) REVERT: I 490 ILE cc_start: 0.6972 (OUTLIER) cc_final: 0.6518 (mp) REVERT: I 520 MET cc_start: 0.8473 (tpt) cc_final: 0.8088 (tpt) REVERT: I 572 ASN cc_start: 0.7144 (t0) cc_final: 0.6687 (t0) REVERT: I 574 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.6661 (pp20) REVERT: J 2 ARG cc_start: 0.6825 (OUTLIER) cc_final: 0.6193 (ttt90) REVERT: J 9 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.7288 (mmm-85) REVERT: J 67 MET cc_start: 0.6884 (mtm) cc_final: 0.6668 (mtm) REVERT: J 235 GLN cc_start: 0.6686 (OUTLIER) cc_final: 0.6291 (mm-40) REVERT: K 92 MET cc_start: 0.7784 (mtm) cc_final: 0.7520 (mmm) REVERT: L 6 SER cc_start: 0.7637 (OUTLIER) cc_final: 0.7321 (t) REVERT: L 26 LEU cc_start: 0.8441 (OUTLIER) cc_final: 0.8198 (mm) REVERT: L 56 PHE cc_start: 0.7486 (t80) cc_final: 0.5339 (m-80) outliers start: 84 outliers final: 33 residues processed: 550 average time/residue: 0.6217 time to fit residues: 393.3266 Evaluate side-chains 539 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 488 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 438 GLU Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 116 LYS Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 27 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 234 optimal weight: 9.9990 chunk 258 optimal weight: 2.9990 chunk 128 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 34 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 226 optimal weight: 8.9990 chunk 247 optimal weight: 6.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 237 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN E 452 ASN F 71 ASN F 235 GLN F 237 ASN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 448 ASN I 531 ASN J 71 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.162045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144834 restraints weight = 30256.050| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.15 r_work: 0.3721 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.236 23420 Z= 0.181 Angle : 1.341 84.554 31845 Z= 0.442 Chirality : 0.059 1.410 3507 Planarity : 0.005 0.051 4029 Dihedral : 7.637 79.280 3430 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.36 % Allowed : 21.11 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.16), residues: 2841 helix: 1.85 (0.14), residues: 1437 sheet: -1.86 (0.31), residues: 225 loop : -1.94 (0.17), residues: 1179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 578 TYR 0.035 0.002 TYR L 45 PHE 0.022 0.002 PHE L 52 TRP 0.025 0.002 TRP D 113 HIS 0.005 0.001 HIS I 143 Details of bonding type rmsd covalent geometry : bond 0.00404 (23385) covalent geometry : angle 1.12058 (31770) hydrogen bonds : bond 0.04958 ( 1221) hydrogen bonds : angle 4.50921 ( 3519) metal coordination : bond 0.00960 ( 30) metal coordination : angle 15.22242 ( 75) Misc. bond : bond 0.13668 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 504 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7376 (mm-40) cc_final: 0.6722 (mp10) REVERT: A 196 ARG cc_start: 0.7273 (mtp180) cc_final: 0.7019 (mtp180) REVERT: A 438 GLU cc_start: 0.7318 (OUTLIER) cc_final: 0.6988 (tp30) REVERT: A 476 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6748 (mt-10) REVERT: A 490 ILE cc_start: 0.7295 (OUTLIER) cc_final: 0.6863 (mp) REVERT: A 568 ARG cc_start: 0.7671 (mtt180) cc_final: 0.7278 (mtt180) REVERT: B 2 ARG cc_start: 0.6669 (ptm160) cc_final: 0.6016 (ptm160) REVERT: B 9 ARG cc_start: 0.7749 (mmm-85) cc_final: 0.7401 (mmm-85) REVERT: B 33 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6903 (ptt) REVERT: B 41 GLN cc_start: 0.7187 (tt0) cc_final: 0.6351 (mt0) REVERT: B 136 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7818 (mmm) REVERT: C 46 TRP cc_start: 0.7142 (t60) cc_final: 0.6704 (t60) REVERT: C 53 SER cc_start: 0.7802 (t) cc_final: 0.7178 (p) REVERT: C 71 LYS cc_start: 0.6641 (mmtm) cc_final: 0.6353 (mmtm) REVERT: C 123 LEU cc_start: 0.7669 (OUTLIER) cc_final: 0.7449 (mm) REVERT: D 6 SER cc_start: 0.7966 (OUTLIER) cc_final: 0.7694 (t) REVERT: D 27 THR cc_start: 0.6928 (p) cc_final: 0.6515 (m) REVERT: E 46 THR cc_start: 0.8645 (OUTLIER) cc_final: 0.8339 (m) REVERT: E 50 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.7954 (mt0) REVERT: E 62 GLU cc_start: 0.7086 (tt0) cc_final: 0.6650 (pt0) REVERT: E 210 GLN cc_start: 0.6875 (tt0) cc_final: 0.6450 (mt0) REVERT: E 227 ILE cc_start: 0.7605 (mt) cc_final: 0.7392 (mt) REVERT: E 243 PRO cc_start: 0.6137 (Cg_endo) cc_final: 0.5932 (Cg_exo) REVERT: E 355 TYR cc_start: 0.8165 (t80) cc_final: 0.7889 (t80) REVERT: E 438 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7174 (tp30) REVERT: E 449 ASN cc_start: 0.6373 (m-40) cc_final: 0.5951 (m-40) REVERT: E 568 ARG cc_start: 0.7675 (mtt180) cc_final: 0.7408 (mtt180) REVERT: E 574 GLU cc_start: 0.7636 (OUTLIER) cc_final: 0.6759 (pp20) REVERT: F 33 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6702 (ptt) REVERT: F 142 LYS cc_start: 0.7157 (mmtp) cc_final: 0.6834 (mppt) REVERT: F 168 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7654 (mttt) REVERT: F 235 GLN cc_start: 0.7256 (OUTLIER) cc_final: 0.6899 (mp10) REVERT: G 53 SER cc_start: 0.7813 (t) cc_final: 0.7214 (p) REVERT: G 81 LEU cc_start: 0.7319 (tp) cc_final: 0.7093 (tt) REVERT: G 93 MET cc_start: 0.7283 (mtp) cc_final: 0.6966 (mtm) REVERT: G 123 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7275 (mp) REVERT: I 31 GLN cc_start: 0.7443 (mm-40) cc_final: 0.6716 (mm110) REVERT: I 66 GLU cc_start: 0.6103 (mt-10) cc_final: 0.5730 (mp0) REVERT: I 130 GLN cc_start: 0.6663 (mm-40) cc_final: 0.5904 (tp-100) REVERT: I 210 GLN cc_start: 0.6698 (tt0) cc_final: 0.6214 (mt0) REVERT: I 438 GLU cc_start: 0.6935 (tp30) cc_final: 0.6574 (mm-30) REVERT: I 455 ASP cc_start: 0.7729 (t0) cc_final: 0.7482 (t0) REVERT: I 471 PHE cc_start: 0.6997 (m-80) cc_final: 0.6783 (m-80) REVERT: I 476 GLU cc_start: 0.6567 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: I 490 ILE cc_start: 0.6868 (OUTLIER) cc_final: 0.6463 (mp) REVERT: I 520 MET cc_start: 0.8423 (tpt) cc_final: 0.8012 (tpt) REVERT: I 568 ARG cc_start: 0.7941 (mtt180) cc_final: 0.7428 (mtt-85) REVERT: I 572 ASN cc_start: 0.7184 (t0) cc_final: 0.6753 (t0) REVERT: I 574 GLU cc_start: 0.7722 (OUTLIER) cc_final: 0.6698 (pp20) REVERT: J 2 ARG cc_start: 0.6784 (OUTLIER) cc_final: 0.6138 (ttt90) REVERT: J 9 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7132 (mmm-85) REVERT: J 67 MET cc_start: 0.6855 (mtm) cc_final: 0.6650 (mtm) REVERT: J 102 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7149 (t70) REVERT: J 235 GLN cc_start: 0.6729 (OUTLIER) cc_final: 0.6350 (mm-40) REVERT: K 92 MET cc_start: 0.7795 (mtm) cc_final: 0.7549 (mmm) REVERT: K 93 MET cc_start: 0.7498 (mtp) cc_final: 0.7099 (ptp) REVERT: K 101 GLU cc_start: 0.7543 (OUTLIER) cc_final: 0.7017 (mt-10) REVERT: L 6 SER cc_start: 0.7730 (OUTLIER) cc_final: 0.7416 (t) REVERT: L 26 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8202 (mm) REVERT: L 56 PHE cc_start: 0.7554 (t80) cc_final: 0.5458 (m-80) outliers start: 104 outliers final: 48 residues processed: 549 average time/residue: 0.5927 time to fit residues: 376.0182 Evaluate side-chains 562 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 491 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 393 SER Chi-restraints excluded: chain E residue 450 ASN Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 20 MET Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 476 GLU Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 31 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 54 optimal weight: 10.0000 chunk 204 optimal weight: 9.9990 chunk 5 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 127 optimal weight: 10.0000 chunk 279 optimal weight: 4.9990 chunk 81 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN A 496 ASN B 71 ASN B 228 HIS B 237 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 367 GLN E 452 ASN F 71 ASN F 237 ASN G 12 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN I 448 ASN I 452 ASN I 531 ASN J 71 ASN J 123 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.157757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.140674 restraints weight = 30425.151| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.13 r_work: 0.3681 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.335 23420 Z= 0.337 Angle : 1.505 85.081 31845 Z= 0.515 Chirality : 0.064 1.393 3507 Planarity : 0.006 0.057 4029 Dihedral : 8.463 78.457 3430 Min Nonbonded Distance : 1.783 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.94 % Allowed : 20.98 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.15), residues: 2841 helix: 1.11 (0.13), residues: 1455 sheet: -1.76 (0.31), residues: 219 loop : -2.22 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 578 TYR 0.035 0.003 TYR L 45 PHE 0.036 0.003 PHE L 60 TRP 0.026 0.003 TRP D 113 HIS 0.008 0.002 HIS A 143 Details of bonding type rmsd covalent geometry : bond 0.00789 (23385) covalent geometry : angle 1.23436 (31770) hydrogen bonds : bond 0.06417 ( 1221) hydrogen bonds : angle 4.91227 ( 3519) metal coordination : bond 0.01849 ( 30) metal coordination : angle 17.77452 ( 75) Misc. bond : bond 0.19712 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 490 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7418 (mm-40) cc_final: 0.6585 (mp10) REVERT: A 228 ARG cc_start: 0.7832 (mtm-85) cc_final: 0.7524 (mtt-85) REVERT: A 476 GLU cc_start: 0.7372 (tm-30) cc_final: 0.7013 (mt-10) REVERT: A 490 ILE cc_start: 0.7517 (OUTLIER) cc_final: 0.7097 (mp) REVERT: A 568 ARG cc_start: 0.7720 (mtt180) cc_final: 0.7343 (mtt-85) REVERT: B 2 ARG cc_start: 0.6794 (ptm160) cc_final: 0.6091 (ptm160) REVERT: B 33 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6796 (ptt) REVERT: B 136 MET cc_start: 0.8129 (OUTLIER) cc_final: 0.7895 (mmm) REVERT: C 53 SER cc_start: 0.7970 (t) cc_final: 0.7354 (p) REVERT: C 71 LYS cc_start: 0.6710 (mmtm) cc_final: 0.6463 (mmtm) REVERT: C 123 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7273 (mp) REVERT: D 6 SER cc_start: 0.8097 (OUTLIER) cc_final: 0.7739 (t) REVERT: D 27 THR cc_start: 0.6950 (p) cc_final: 0.6589 (m) REVERT: E 50 GLN cc_start: 0.8313 (OUTLIER) cc_final: 0.7947 (mt0) REVERT: E 62 GLU cc_start: 0.7089 (tt0) cc_final: 0.6312 (pm20) REVERT: E 65 TRP cc_start: 0.6357 (p-90) cc_final: 0.6065 (p-90) REVERT: E 210 GLN cc_start: 0.7067 (tt0) cc_final: 0.6646 (mt0) REVERT: E 449 ASN cc_start: 0.6441 (m-40) cc_final: 0.6104 (m-40) REVERT: E 568 ARG cc_start: 0.7757 (mtt180) cc_final: 0.7487 (mtt180) REVERT: E 572 ASN cc_start: 0.7331 (t0) cc_final: 0.7076 (t0) REVERT: E 574 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6864 (pp20) REVERT: F 33 MET cc_start: 0.7329 (OUTLIER) cc_final: 0.6740 (ptt) REVERT: F 142 LYS cc_start: 0.7113 (mmtp) cc_final: 0.6431 (mppt) REVERT: F 168 LYS cc_start: 0.8141 (OUTLIER) cc_final: 0.7819 (mtmt) REVERT: G 46 TRP cc_start: 0.7391 (t60) cc_final: 0.7080 (t60) REVERT: G 93 MET cc_start: 0.7405 (mtp) cc_final: 0.7083 (mtm) REVERT: G 119 VAL cc_start: 0.8221 (t) cc_final: 0.8010 (t) REVERT: G 123 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7476 (mp) REVERT: H 56 PHE cc_start: 0.7482 (t80) cc_final: 0.5205 (m-80) REVERT: I 31 GLN cc_start: 0.7548 (mm-40) cc_final: 0.6735 (mm110) REVERT: I 66 GLU cc_start: 0.6212 (mt-10) cc_final: 0.5884 (mp0) REVERT: I 196 ARG cc_start: 0.7363 (mtp85) cc_final: 0.6976 (mtp85) REVERT: I 210 GLN cc_start: 0.6900 (tt0) cc_final: 0.6656 (tt0) REVERT: I 367 GLN cc_start: 0.7170 (OUTLIER) cc_final: 0.6737 (mt0) REVERT: I 373 GLU cc_start: 0.8189 (pt0) cc_final: 0.7945 (pm20) REVERT: I 438 GLU cc_start: 0.7077 (tp30) cc_final: 0.6749 (tp30) REVERT: I 455 ASP cc_start: 0.7746 (t0) cc_final: 0.7481 (t0) REVERT: I 476 GLU cc_start: 0.6761 (mt-10) cc_final: 0.6387 (mp0) REVERT: I 490 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6607 (mp) REVERT: I 531 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7589 (m-40) REVERT: I 568 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7601 (mtt-85) REVERT: I 584 LYS cc_start: 0.6365 (mtpp) cc_final: 0.5906 (mmmm) REVERT: J 2 ARG cc_start: 0.6821 (OUTLIER) cc_final: 0.6127 (ttt90) REVERT: J 9 ARG cc_start: 0.7793 (OUTLIER) cc_final: 0.7184 (mmm-85) REVERT: J 33 MET cc_start: 0.7193 (ptp) cc_final: 0.6907 (ptt) REVERT: J 102 ASP cc_start: 0.8030 (OUTLIER) cc_final: 0.7067 (t70) REVERT: J 235 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.6376 (mm-40) REVERT: K 53 SER cc_start: 0.8072 (t) cc_final: 0.7527 (p) REVERT: K 92 MET cc_start: 0.7823 (mtm) cc_final: 0.7556 (mmm) REVERT: K 93 MET cc_start: 0.7544 (mtp) cc_final: 0.7128 (OUTLIER) REVERT: K 101 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7274 (mt-10) REVERT: L 56 PHE cc_start: 0.7554 (t80) cc_final: 0.5510 (m-80) outliers start: 118 outliers final: 64 residues processed: 547 average time/residue: 0.6243 time to fit residues: 392.7931 Evaluate side-chains 555 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 474 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 531 ASN Chi-restraints excluded: chain A residue 584 LYS Chi-restraints excluded: chain B residue 20 MET Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain D residue 6 SER Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain I residue 42 THR Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 367 GLN Chi-restraints excluded: chain I residue 407 ASP Chi-restraints excluded: chain I residue 450 ASN Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 31 ILE Chi-restraints excluded: chain L residue 47 VAL Chi-restraints excluded: chain L residue 96 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 6 optimal weight: 10.0000 chunk 130 optimal weight: 2.9990 chunk 267 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 189 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 chunk 175 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 71 ASN B 237 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 235 GLN F 237 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 531 ASN J 71 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.161081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.143856 restraints weight = 29927.466| |-----------------------------------------------------------------------------| r_work (start): 0.3775 rms_B_bonded: 2.13 r_work: 0.3716 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.243 23420 Z= 0.187 Angle : 1.370 84.589 31845 Z= 0.458 Chirality : 0.060 1.417 3507 Planarity : 0.005 0.051 4029 Dihedral : 8.022 78.729 3430 Min Nonbonded Distance : 1.786 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 3.89 % Allowed : 22.78 % Favored : 73.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.16), residues: 2841 helix: 1.58 (0.13), residues: 1437 sheet: -1.66 (0.32), residues: 219 loop : -2.03 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 2 TYR 0.034 0.002 TYR H 45 PHE 0.023 0.002 PHE L 60 TRP 0.029 0.002 TRP D 113 HIS 0.004 0.001 HIS E 395 Details of bonding type rmsd covalent geometry : bond 0.00415 (23385) covalent geometry : angle 1.14660 (31770) hydrogen bonds : bond 0.05292 ( 1221) hydrogen bonds : angle 4.69205 ( 3519) metal coordination : bond 0.01084 ( 30) metal coordination : angle 15.48769 ( 75) Misc. bond : bond 0.14507 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 498 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 31 GLN cc_start: 0.7412 (mm-40) cc_final: 0.6634 (mp10) REVERT: A 196 ARG cc_start: 0.7251 (mtp85) cc_final: 0.6995 (mtp180) REVERT: A 210 GLN cc_start: 0.6624 (OUTLIER) cc_final: 0.6387 (mt0) REVERT: A 228 ARG cc_start: 0.7772 (mtm-85) cc_final: 0.7511 (mtt-85) REVERT: A 430 ARG cc_start: 0.7593 (mtm-85) cc_final: 0.7347 (mtm110) REVERT: A 476 GLU cc_start: 0.7128 (tm-30) cc_final: 0.6790 (mt-10) REVERT: A 490 ILE cc_start: 0.7220 (OUTLIER) cc_final: 0.6777 (mp) REVERT: A 568 ARG cc_start: 0.7614 (mtt180) cc_final: 0.7388 (mtt-85) REVERT: B 2 ARG cc_start: 0.6674 (ptm160) cc_final: 0.5993 (ptm160) REVERT: B 33 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.6933 (ptt) REVERT: C 53 SER cc_start: 0.7918 (OUTLIER) cc_final: 0.7308 (p) REVERT: C 71 LYS cc_start: 0.6615 (mmtm) cc_final: 0.6359 (mmtm) REVERT: C 123 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7477 (mm) REVERT: D 27 THR cc_start: 0.6920 (p) cc_final: 0.6535 (m) REVERT: D 77 TRP cc_start: 0.7986 (t60) cc_final: 0.7208 (t-100) REVERT: E 46 THR cc_start: 0.8612 (OUTLIER) cc_final: 0.8334 (m) REVERT: E 50 GLN cc_start: 0.8357 (OUTLIER) cc_final: 0.7993 (mt0) REVERT: E 62 GLU cc_start: 0.7025 (tt0) cc_final: 0.6298 (pm20) REVERT: E 210 GLN cc_start: 0.6933 (tt0) cc_final: 0.6494 (mt0) REVERT: E 405 LEU cc_start: 0.6816 (mm) cc_final: 0.6413 (mt) REVERT: E 430 ARG cc_start: 0.7321 (mtm-85) cc_final: 0.7116 (ttp80) REVERT: E 449 ASN cc_start: 0.6309 (m-40) cc_final: 0.5911 (m-40) REVERT: E 545 PHE cc_start: 0.5974 (m-80) cc_final: 0.5610 (m-10) REVERT: E 568 ARG cc_start: 0.7678 (mtt180) cc_final: 0.7413 (mtt180) REVERT: E 572 ASN cc_start: 0.7343 (t0) cc_final: 0.7057 (t0) REVERT: E 574 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.6788 (pp20) REVERT: F 2 ARG cc_start: 0.6898 (ttt90) cc_final: 0.6679 (ttt90) REVERT: F 33 MET cc_start: 0.7219 (OUTLIER) cc_final: 0.6685 (ptt) REVERT: F 142 LYS cc_start: 0.7127 (mmtp) cc_final: 0.6825 (mppt) REVERT: F 168 LYS cc_start: 0.8051 (OUTLIER) cc_final: 0.7739 (mtmt) REVERT: F 235 GLN cc_start: 0.7269 (OUTLIER) cc_final: 0.7026 (mp10) REVERT: G 46 TRP cc_start: 0.7350 (t60) cc_final: 0.7036 (t60) REVERT: G 53 SER cc_start: 0.7858 (t) cc_final: 0.7236 (p) REVERT: G 93 MET cc_start: 0.7353 (mtp) cc_final: 0.7027 (mtm) REVERT: G 123 LEU cc_start: 0.7810 (OUTLIER) cc_final: 0.7352 (mp) REVERT: H 56 PHE cc_start: 0.7428 (t80) cc_final: 0.5151 (m-80) REVERT: I 31 GLN cc_start: 0.7477 (mm-40) cc_final: 0.7091 (mm110) REVERT: I 66 GLU cc_start: 0.6101 (mt-10) cc_final: 0.5794 (mp0) REVERT: I 210 GLN cc_start: 0.6744 (tt0) cc_final: 0.6513 (tt0) REVERT: I 228 ARG cc_start: 0.7562 (mtt90) cc_final: 0.7260 (mtt-85) REVERT: I 420 GLN cc_start: 0.7071 (tp40) cc_final: 0.6700 (tp40) REVERT: I 438 GLU cc_start: 0.6982 (tp30) cc_final: 0.6644 (tp30) REVERT: I 455 ASP cc_start: 0.7762 (t0) cc_final: 0.7381 (t0) REVERT: I 480 MET cc_start: 0.8133 (mtp) cc_final: 0.7775 (mtm) REVERT: I 490 ILE cc_start: 0.6823 (OUTLIER) cc_final: 0.6457 (mp) REVERT: I 520 MET cc_start: 0.8454 (tpt) cc_final: 0.7992 (tpt) REVERT: I 531 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7512 (m-40) REVERT: I 568 ARG cc_start: 0.8050 (mtt180) cc_final: 0.7577 (mtt180) REVERT: I 574 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.6764 (pp20) REVERT: I 584 LYS cc_start: 0.6372 (mtpp) cc_final: 0.5890 (mmmm) REVERT: J 2 ARG cc_start: 0.6800 (OUTLIER) cc_final: 0.6187 (ttt90) REVERT: J 9 ARG cc_start: 0.7701 (OUTLIER) cc_final: 0.7333 (mmm-85) REVERT: J 33 MET cc_start: 0.7080 (OUTLIER) cc_final: 0.6811 (ptt) REVERT: J 235 GLN cc_start: 0.6773 (OUTLIER) cc_final: 0.6395 (mm-40) REVERT: K 93 MET cc_start: 0.7458 (mtp) cc_final: 0.7107 (ptp) REVERT: K 101 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: L 6 SER cc_start: 0.7811 (OUTLIER) cc_final: 0.7497 (t) REVERT: L 26 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8317 (mm) REVERT: L 56 PHE cc_start: 0.7535 (t80) cc_final: 0.5445 (m-80) outliers start: 93 outliers final: 49 residues processed: 540 average time/residue: 0.6270 time to fit residues: 389.6679 Evaluate side-chains 556 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 485 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 116 LYS Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain C residue 123 LEU Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 195 optimal weight: 5.9990 chunk 174 optimal weight: 10.0000 chunk 39 optimal weight: 0.0030 chunk 260 optimal weight: 9.9990 chunk 271 optimal weight: 9.9990 chunk 21 optimal weight: 8.9990 chunk 99 optimal weight: 9.9990 chunk 204 optimal weight: 8.9990 chunk 263 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 232 optimal weight: 9.9990 overall best weight: 6.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 367 GLN B 71 ASN B 237 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 143 HIS ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 235 GLN F 237 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN I 448 ASN I 452 ASN I 531 ASN J 71 ASN J 123 ASN J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.157612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.140768 restraints weight = 30617.940| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.08 r_work: 0.3640 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3548 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3548 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.2866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.290 23420 Z= 0.272 Angle : 1.450 85.006 31845 Z= 0.496 Chirality : 0.062 1.388 3507 Planarity : 0.006 0.054 4029 Dihedral : 8.342 79.261 3430 Min Nonbonded Distance : 1.788 Molprobity Statistics. All-atom Clashscore : 12.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.23 % Allowed : 22.74 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.49 (0.15), residues: 2841 helix: 1.24 (0.13), residues: 1455 sheet: -1.66 (0.32), residues: 219 loop : -2.16 (0.17), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 578 TYR 0.040 0.003 TYR H 45 PHE 0.028 0.002 PHE D 60 TRP 0.028 0.003 TRP D 113 HIS 0.006 0.002 HIS E 45 Details of bonding type rmsd covalent geometry : bond 0.00631 (23385) covalent geometry : angle 1.20723 (31770) hydrogen bonds : bond 0.05997 ( 1221) hydrogen bonds : angle 4.85685 ( 3519) metal coordination : bond 0.01488 ( 30) metal coordination : angle 16.60622 ( 75) Misc. bond : bond 0.17623 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 579 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 478 time to evaluate : 0.910 Fit side-chains REVERT: A 196 ARG cc_start: 0.7213 (mtp85) cc_final: 0.6992 (mtp180) REVERT: A 210 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.6412 (mt0) REVERT: A 476 GLU cc_start: 0.7246 (tm-30) cc_final: 0.6845 (mt-10) REVERT: A 490 ILE cc_start: 0.7243 (OUTLIER) cc_final: 0.6878 (mp) REVERT: A 568 ARG cc_start: 0.7592 (OUTLIER) cc_final: 0.7191 (mtt-85) REVERT: B 2 ARG cc_start: 0.6640 (ptm160) cc_final: 0.6131 (ptm160) REVERT: B 33 MET cc_start: 0.7453 (OUTLIER) cc_final: 0.7024 (ptt) REVERT: B 136 MET cc_start: 0.8088 (OUTLIER) cc_final: 0.7841 (mmm) REVERT: C 53 SER cc_start: 0.7872 (OUTLIER) cc_final: 0.7223 (p) REVERT: C 71 LYS cc_start: 0.6637 (mmtm) cc_final: 0.6394 (mmtm) REVERT: C 101 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7149 (mt-10) REVERT: D 27 THR cc_start: 0.6968 (p) cc_final: 0.6610 (m) REVERT: D 77 TRP cc_start: 0.7840 (t60) cc_final: 0.7170 (t-100) REVERT: E 46 THR cc_start: 0.8584 (OUTLIER) cc_final: 0.8261 (m) REVERT: E 50 GLN cc_start: 0.8263 (OUTLIER) cc_final: 0.7837 (mt0) REVERT: E 62 GLU cc_start: 0.7094 (tt0) cc_final: 0.6282 (pm20) REVERT: E 163 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6694 (mt-10) REVERT: E 196 ARG cc_start: 0.7333 (mtp85) cc_final: 0.6975 (mtm180) REVERT: E 210 GLN cc_start: 0.7009 (tt0) cc_final: 0.6560 (mt0) REVERT: E 430 ARG cc_start: 0.7373 (mtm-85) cc_final: 0.7164 (ttp80) REVERT: E 449 ASN cc_start: 0.6377 (m-40) cc_final: 0.6062 (m-40) REVERT: E 568 ARG cc_start: 0.7688 (mtt180) cc_final: 0.7409 (mtt180) REVERT: E 572 ASN cc_start: 0.7281 (t0) cc_final: 0.6972 (t0) REVERT: E 574 GLU cc_start: 0.7773 (OUTLIER) cc_final: 0.6837 (pp20) REVERT: F 2 ARG cc_start: 0.6780 (ttt90) cc_final: 0.6521 (ttt90) REVERT: F 33 MET cc_start: 0.7282 (OUTLIER) cc_final: 0.6713 (ptt) REVERT: F 142 LYS cc_start: 0.7149 (mmtp) cc_final: 0.6398 (mppt) REVERT: F 168 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7738 (mtmt) REVERT: F 235 GLN cc_start: 0.7404 (OUTLIER) cc_final: 0.7054 (mp10) REVERT: G 46 TRP cc_start: 0.7317 (t60) cc_final: 0.7025 (t60) REVERT: G 93 MET cc_start: 0.7244 (mtp) cc_final: 0.6937 (mtm) REVERT: G 123 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7397 (mp) REVERT: H 56 PHE cc_start: 0.7312 (t80) cc_final: 0.5042 (m-80) REVERT: I 31 GLN cc_start: 0.7473 (mm-40) cc_final: 0.6609 (mm110) REVERT: I 66 GLU cc_start: 0.6114 (mt-10) cc_final: 0.5674 (mp0) REVERT: I 196 ARG cc_start: 0.7336 (mtp85) cc_final: 0.6978 (mtp85) REVERT: I 210 GLN cc_start: 0.6734 (tt0) cc_final: 0.6478 (tt0) REVERT: I 367 GLN cc_start: 0.6910 (OUTLIER) cc_final: 0.6472 (mt0) REVERT: I 455 ASP cc_start: 0.7739 (t0) cc_final: 0.7390 (t0) REVERT: I 476 GLU cc_start: 0.6128 (mt-10) cc_final: 0.5791 (mp0) REVERT: I 490 ILE cc_start: 0.6756 (OUTLIER) cc_final: 0.6469 (mp) REVERT: I 492 GLU cc_start: 0.7184 (mm-30) cc_final: 0.6800 (mp0) REVERT: I 531 ASN cc_start: 0.8027 (OUTLIER) cc_final: 0.7515 (m-40) REVERT: I 568 ARG cc_start: 0.8015 (mtt180) cc_final: 0.7525 (mtt180) REVERT: I 574 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.6778 (pp20) REVERT: I 584 LYS cc_start: 0.6230 (mtpp) cc_final: 0.5647 (mmmt) REVERT: J 2 ARG cc_start: 0.6694 (OUTLIER) cc_final: 0.6007 (ttt90) REVERT: J 9 ARG cc_start: 0.7698 (OUTLIER) cc_final: 0.7125 (mmm-85) REVERT: J 33 MET cc_start: 0.7226 (ptp) cc_final: 0.6936 (ptt) REVERT: J 102 ASP cc_start: 0.8018 (OUTLIER) cc_final: 0.6960 (t70) REVERT: J 235 GLN cc_start: 0.6653 (OUTLIER) cc_final: 0.6265 (mm-40) REVERT: K 53 SER cc_start: 0.8057 (t) cc_final: 0.7456 (p) REVERT: K 93 MET cc_start: 0.7460 (mtp) cc_final: 0.7060 (ptp) REVERT: K 101 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7204 (mt-10) REVERT: L 6 SER cc_start: 0.7867 (OUTLIER) cc_final: 0.7473 (t) REVERT: L 56 PHE cc_start: 0.7614 (t80) cc_final: 0.5498 (m-80) outliers start: 101 outliers final: 56 residues processed: 529 average time/residue: 0.6300 time to fit residues: 383.7185 Evaluate side-chains 543 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 462 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain A residue 568 ARG Chi-restraints excluded: chain B residue 24 THR Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain E residue 42 THR Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 170 VAL Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain H residue 47 VAL Chi-restraints excluded: chain H residue 96 VAL Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 367 GLN Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 514 LEU Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 102 ASP Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 0 optimal weight: 10.0000 chunk 154 optimal weight: 0.5980 chunk 7 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 203 optimal weight: 4.9990 chunk 237 optimal weight: 0.9980 chunk 263 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 224 optimal weight: 5.9990 chunk 207 optimal weight: 9.9990 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 ASN B 71 ASN B 237 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 235 GLN F 237 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 GLN I 531 ASN J 71 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.161065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.144012 restraints weight = 30189.517| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 2.13 r_work: 0.3717 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3625 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.233 23420 Z= 0.192 Angle : 1.389 84.662 31845 Z= 0.469 Chirality : 0.060 1.410 3507 Planarity : 0.005 0.050 4029 Dihedral : 8.007 79.234 3428 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.48 % Allowed : 23.58 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.16), residues: 2841 helix: 1.59 (0.14), residues: 1437 sheet: -1.58 (0.32), residues: 219 loop : -2.04 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 578 TYR 0.041 0.002 TYR H 45 PHE 0.024 0.002 PHE E 471 TRP 0.029 0.002 TRP D 113 HIS 0.004 0.001 HIS I 143 Details of bonding type rmsd covalent geometry : bond 0.00430 (23385) covalent geometry : angle 1.16898 (31770) hydrogen bonds : bond 0.05362 ( 1221) hydrogen bonds : angle 4.76231 ( 3519) metal coordination : bond 0.01120 ( 30) metal coordination : angle 15.49321 ( 75) Misc. bond : bond 0.14177 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5682 Ramachandran restraints generated. 2841 Oldfield, 0 Emsley, 2841 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 483 time to evaluate : 0.920 Fit side-chains REVERT: A 196 ARG cc_start: 0.7241 (mtp85) cc_final: 0.6984 (mtp180) REVERT: A 210 GLN cc_start: 0.6557 (OUTLIER) cc_final: 0.6329 (mt0) REVERT: A 430 ARG cc_start: 0.7650 (mmm-85) cc_final: 0.7443 (mtm110) REVERT: A 476 GLU cc_start: 0.7144 (tm-30) cc_final: 0.6817 (mt-10) REVERT: A 490 ILE cc_start: 0.7211 (OUTLIER) cc_final: 0.6799 (mp) REVERT: A 568 ARG cc_start: 0.7697 (mtt180) cc_final: 0.7255 (mtt-85) REVERT: B 2 ARG cc_start: 0.6653 (ptm160) cc_final: 0.5966 (ptm160) REVERT: B 33 MET cc_start: 0.7327 (OUTLIER) cc_final: 0.6943 (ptt) REVERT: C 53 SER cc_start: 0.7898 (OUTLIER) cc_final: 0.7280 (p) REVERT: C 71 LYS cc_start: 0.6659 (mmtm) cc_final: 0.6414 (mmtm) REVERT: C 93 MET cc_start: 0.7213 (mtp) cc_final: 0.6805 (mtt) REVERT: D 27 THR cc_start: 0.6918 (p) cc_final: 0.6526 (m) REVERT: D 77 TRP cc_start: 0.7980 (t60) cc_final: 0.7193 (t-100) REVERT: E 46 THR cc_start: 0.8590 (OUTLIER) cc_final: 0.8330 (m) REVERT: E 62 GLU cc_start: 0.7058 (tt0) cc_final: 0.6314 (pm20) REVERT: E 163 GLU cc_start: 0.6810 (OUTLIER) cc_final: 0.6550 (mt-10) REVERT: E 210 GLN cc_start: 0.6932 (tt0) cc_final: 0.6491 (mt0) REVERT: E 405 LEU cc_start: 0.6769 (mm) cc_final: 0.6402 (mt) REVERT: E 430 ARG cc_start: 0.7340 (mtm-85) cc_final: 0.7134 (ttp80) REVERT: E 449 ASN cc_start: 0.6335 (m-40) cc_final: 0.5936 (m-40) REVERT: E 545 PHE cc_start: 0.5916 (m-80) cc_final: 0.5559 (m-10) REVERT: E 568 ARG cc_start: 0.7707 (mtt180) cc_final: 0.7442 (mtt180) REVERT: E 572 ASN cc_start: 0.7284 (t0) cc_final: 0.6991 (t0) REVERT: E 574 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.6823 (pp20) REVERT: F 33 MET cc_start: 0.7290 (OUTLIER) cc_final: 0.6751 (ptt) REVERT: F 142 LYS cc_start: 0.7133 (mmtp) cc_final: 0.6805 (mppt) REVERT: F 168 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7751 (mtmt) REVERT: F 235 GLN cc_start: 0.7281 (OUTLIER) cc_final: 0.6965 (mp10) REVERT: G 46 TRP cc_start: 0.7363 (t60) cc_final: 0.7056 (t60) REVERT: G 53 SER cc_start: 0.7877 (t) cc_final: 0.7249 (p) REVERT: G 123 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7315 (mp) REVERT: H 33 MET cc_start: 0.7741 (mmt) cc_final: 0.7447 (mmt) REVERT: H 56 PHE cc_start: 0.7342 (t80) cc_final: 0.5092 (m-80) REVERT: I 66 GLU cc_start: 0.6241 (mt-10) cc_final: 0.5821 (mp0) REVERT: I 130 GLN cc_start: 0.6949 (mm-40) cc_final: 0.6252 (tp-100) REVERT: I 196 ARG cc_start: 0.7328 (mtp85) cc_final: 0.6980 (mtp85) REVERT: I 210 GLN cc_start: 0.6747 (tt0) cc_final: 0.6527 (tt0) REVERT: I 367 GLN cc_start: 0.6408 (OUTLIER) cc_final: 0.5884 (mt0) REVERT: I 455 ASP cc_start: 0.7713 (t0) cc_final: 0.7392 (t0) REVERT: I 480 MET cc_start: 0.8064 (mtp) cc_final: 0.7683 (mtm) REVERT: I 490 ILE cc_start: 0.6814 (OUTLIER) cc_final: 0.6462 (mp) REVERT: I 520 MET cc_start: 0.8549 (tpt) cc_final: 0.7897 (tpt) REVERT: I 531 ASN cc_start: 0.8092 (OUTLIER) cc_final: 0.7542 (m-40) REVERT: I 568 ARG cc_start: 0.7990 (mtt180) cc_final: 0.7533 (mtt180) REVERT: I 574 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6764 (pp20) REVERT: I 584 LYS cc_start: 0.6396 (mtpp) cc_final: 0.5919 (mmmm) REVERT: J 2 ARG cc_start: 0.6747 (OUTLIER) cc_final: 0.6254 (ttt90) REVERT: J 9 ARG cc_start: 0.7719 (OUTLIER) cc_final: 0.7362 (mmm-85) REVERT: J 33 MET cc_start: 0.7078 (OUTLIER) cc_final: 0.6739 (ptt) REVERT: J 235 GLN cc_start: 0.6707 (OUTLIER) cc_final: 0.6334 (mm-40) REVERT: K 93 MET cc_start: 0.7525 (mtp) cc_final: 0.7144 (ptp) REVERT: K 101 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7143 (mt-10) REVERT: L 6 SER cc_start: 0.7790 (OUTLIER) cc_final: 0.7478 (t) REVERT: L 26 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8321 (mm) REVERT: L 56 PHE cc_start: 0.7536 (t80) cc_final: 0.5463 (m-80) outliers start: 83 outliers final: 52 residues processed: 523 average time/residue: 0.6361 time to fit residues: 382.5242 Evaluate side-chains 549 residues out of total 2388 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 475 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 THR Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 210 GLN Chi-restraints excluded: chain A residue 213 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 506 PHE Chi-restraints excluded: chain A residue 514 LEU Chi-restraints excluded: chain B residue 33 MET Chi-restraints excluded: chain B residue 127 ASN Chi-restraints excluded: chain B residue 136 MET Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain B residue 188 THR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 17 THR Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 102 THR Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain E residue 46 THR Chi-restraints excluded: chain E residue 163 GLU Chi-restraints excluded: chain E residue 177 VAL Chi-restraints excluded: chain E residue 178 VAL Chi-restraints excluded: chain E residue 223 VAL Chi-restraints excluded: chain E residue 364 VAL Chi-restraints excluded: chain E residue 455 ASP Chi-restraints excluded: chain E residue 490 ILE Chi-restraints excluded: chain E residue 574 GLU Chi-restraints excluded: chain F residue 20 MET Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain F residue 102 ASP Chi-restraints excluded: chain F residue 127 ASN Chi-restraints excluded: chain F residue 136 MET Chi-restraints excluded: chain F residue 158 SER Chi-restraints excluded: chain F residue 168 LYS Chi-restraints excluded: chain F residue 188 THR Chi-restraints excluded: chain F residue 190 THR Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 235 GLN Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 19 ARG Chi-restraints excluded: chain G residue 102 THR Chi-restraints excluded: chain G residue 123 LEU Chi-restraints excluded: chain H residue 26 LEU Chi-restraints excluded: chain H residue 31 ILE Chi-restraints excluded: chain H residue 40 SER Chi-restraints excluded: chain I residue 198 THR Chi-restraints excluded: chain I residue 223 VAL Chi-restraints excluded: chain I residue 364 VAL Chi-restraints excluded: chain I residue 367 GLN Chi-restraints excluded: chain I residue 487 LEU Chi-restraints excluded: chain I residue 490 ILE Chi-restraints excluded: chain I residue 531 ASN Chi-restraints excluded: chain I residue 574 GLU Chi-restraints excluded: chain J residue 1 MET Chi-restraints excluded: chain J residue 2 ARG Chi-restraints excluded: chain J residue 9 ARG Chi-restraints excluded: chain J residue 20 MET Chi-restraints excluded: chain J residue 24 THR Chi-restraints excluded: chain J residue 33 MET Chi-restraints excluded: chain J residue 116 LYS Chi-restraints excluded: chain J residue 158 SER Chi-restraints excluded: chain J residue 188 THR Chi-restraints excluded: chain J residue 190 THR Chi-restraints excluded: chain J residue 235 GLN Chi-restraints excluded: chain K residue 17 THR Chi-restraints excluded: chain K residue 19 ARG Chi-restraints excluded: chain K residue 101 GLU Chi-restraints excluded: chain K residue 102 THR Chi-restraints excluded: chain K residue 123 LEU Chi-restraints excluded: chain L residue 6 SER Chi-restraints excluded: chain L residue 26 LEU Chi-restraints excluded: chain L residue 47 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 113 optimal weight: 4.9990 chunk 174 optimal weight: 9.9990 chunk 18 optimal weight: 8.9990 chunk 84 optimal weight: 2.9990 chunk 235 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 64 optimal weight: 5.9990 chunk 243 optimal weight: 1.9990 chunk 197 optimal weight: 8.9990 chunk 204 optimal weight: 0.7980 chunk 268 optimal weight: 4.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 143 HIS ** A 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN ** D 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 452 ASN F 71 ASN F 237 ASN ** I 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 452 ASN I 470 ASN I 531 ASN J 71 ASN J 237 ASN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.161604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.144594 restraints weight = 29960.507| |-----------------------------------------------------------------------------| r_work (start): 0.3782 rms_B_bonded: 2.12 r_work: 0.3723 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3632 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.224 23420 Z= 0.187 Angle : 1.376 84.690 31845 Z= 0.466 Chirality : 0.060 1.408 3507 Planarity : 0.005 0.080 4029 Dihedral : 7.878 79.794 3428 Min Nonbonded Distance : 1.792 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.56 % Allowed : 23.70 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.16), residues: 2841 helix: 1.65 (0.14), residues: 1437 sheet: -1.50 (0.33), residues: 219 loop : -2.00 (0.17), residues: 1185 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG F 2 TYR 0.040 0.002 TYR H 45 PHE 0.023 0.002 PHE E 471 TRP 0.029 0.002 TRP D 113 HIS 0.004 0.001 HIS I 143 Details of bonding type rmsd covalent geometry : bond 0.00420 (23385) covalent geometry : angle 1.16525 (31770) hydrogen bonds : bond 0.05240 ( 1221) hydrogen bonds : angle 4.72672 ( 3519) metal coordination : bond 0.01061 ( 30) metal coordination : angle 15.12534 ( 75) Misc. bond : bond 0.13923 ( 5) =============================================================================== Job complete usr+sys time: 10266.07 seconds wall clock time: 175 minutes 11.61 seconds (10511.61 seconds total)