Starting phenix.real_space_refine on Sat Sep 12 16:19:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6muu_9256/09_2026/6muu_9256_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6muu_9256/09_2026/6muu_9256.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6muu_9256/09_2026/6muu_9256_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6muu_9256/09_2026/6muu_9256_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6muu_9256/09_2026/6muu_9256.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6muu_9256/09_2026/6muu_9256.map" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 P 24 5.49 5 S 49 5.16 5 C 10573 2.51 5 N 2925 2.21 5 O 3142 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 51 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16716 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 6211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 780, 6211 Classifications: {'peptide': 780} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 36, 'TRANS': 743} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 25 Chain: "B" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 941 Classifications: {'peptide': 136} Incomplete info: {'truncation_to_alanine': 45} Link IDs: {'PTRANS': 4, 'TRANS': 131} Chain breaks: 3 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 183 Unresolved non-hydrogen angles: 235 Unresolved non-hydrogen dihedrals: 160 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 2, 'TRP:plan': 2, 'TYR:plan': 3, 'PHE:plan': 2, 'ASP:plan': 3, 'ASN:plan1': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 100 Chain: "C" Number of atoms: 2202 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2202 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 12, 'TRANS': 263} Chain breaks: 1 Chain: "D" Number of atoms: 2254 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2254 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 12, 'TRANS': 270} Chain breaks: 1 Chain: "E" Number of atoms: 2257 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2257 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 20, 'TRANS': 264} Chain: "F" Number of atoms: 2302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 2302 Classifications: {'peptide': 323} Incomplete info: {'truncation_to_alanine': 87} Link IDs: {'PTRANS': 16, 'TRANS': 306} Chain breaks: 13 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 338 Unresolved non-hydrogen angles: 432 Unresolved non-hydrogen dihedrals: 290 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'ASN:plan1': 6, 'ASP:plan': 6, 'GLU:plan': 7, 'TYR:plan': 6, 'TRP:plan': 2, 'PHE:plan': 4, 'HIS:plan': 1, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 183 Chain: "G" Number of atoms: 546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 546 Classifications: {'RNA': 25} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 8, 'rna3p_pyr': 4} Link IDs: {'rna2p': 13, 'rna3p': 11} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3135 SG CYS A 389 46.938 73.949 98.475 1.00 37.02 S ATOM 3155 SG CYS A 392 44.894 70.349 97.471 1.00 35.05 S ATOM 3310 SG CYS A 413 45.189 71.721 101.524 1.00 38.54 S ATOM 7967 SG CYS C 113 54.582 99.125 83.196 1.00 38.63 S ATOM 8034 SG CYS C 122 55.964 100.205 79.685 1.00 28.96 S ATOM 8054 SG CYS C 125 54.673 96.603 80.577 1.00 28.10 S ATOM 10221 SG CYS D 113 85.911 85.116 80.930 1.00 41.91 S ATOM 10288 SG CYS D 122 88.208 87.178 78.386 1.00 45.54 S ATOM 10308 SG CYS D 125 84.793 84.588 77.509 1.00 38.51 S Time building chain proxies: 3.71, per 1000 atoms: 0.22 Number of scatterers: 16716 At special positions: 0 Unit cell: (137.214, 124.146, 145.926, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 49 16.00 P 24 15.00 O 3142 8.00 N 2925 7.00 C 10573 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.35 Conformation dependent library (CDL) restraints added in 649.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" NE2 HIS C 111 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 122 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 125 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " Number of angles added : 6 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3810 Finding SS restraints... Secondary structure from input PDB file: 82 helices and 28 sheets defined 43.2% alpha, 14.5% beta 0 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.579A pdb=" N LEU A 6 " --> pdb=" O GLU A 2 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU A 12 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing helix chain 'A' and resid 16 through 23 removed outlier: 3.651A pdb=" N VAL A 20 " --> pdb=" O ILE A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 44 Processing helix chain 'A' and resid 49 through 59 removed outlier: 4.555A pdb=" N LEU A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N PHE A 56 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 69 through 78 Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 104 removed outlier: 3.594A pdb=" N ALA A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU A 94 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 removed outlier: 3.728A pdb=" N GLU A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU A 164 " --> pdb=" O ARG A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 183 Proline residue: A 177 - end of helix removed outlier: 3.631A pdb=" N TYR A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 216 Processing helix chain 'A' and resid 219 through 224 Processing helix chain 'A' and resid 243 through 248 removed outlier: 3.606A pdb=" N TYR A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 281 removed outlier: 3.607A pdb=" N ALA A 261 " --> pdb=" O LYS A 257 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER A 263 " --> pdb=" O LEU A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 303 through 325 removed outlier: 3.541A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ARG A 323 " --> pdb=" O GLU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 368 removed outlier: 3.557A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 426 removed outlier: 3.566A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 420 " --> pdb=" O CYS A 416 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 421 " --> pdb=" O ASN A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 507 Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 530 through 532 No H-bonds generated for 'chain 'A' and resid 530 through 532' Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.576A pdb=" N ARG A 543 " --> pdb=" O ALA A 539 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ASP A 546 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE A 548 " --> pdb=" O PHE A 544 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.793A pdb=" N ILE A 556 " --> pdb=" O TYR A 552 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.635A pdb=" N GLU A 601 " --> pdb=" O ASP A 597 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG A 607 " --> pdb=" O ALA A 603 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 645 removed outlier: 3.532A pdb=" N ASP A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 645 through 650 removed outlier: 4.163A pdb=" N GLU A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 688 removed outlier: 3.537A pdb=" N ALA A 685 " --> pdb=" O TRP A 681 " (cutoff:3.500A) Proline residue: A 686 - end of helix Processing helix chain 'A' and resid 702 through 719 removed outlier: 3.575A pdb=" N LEU A 706 " --> pdb=" O LYS A 702 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N TRP A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) Processing helix chain 'A' and resid 724 through 736 removed outlier: 3.807A pdb=" N LEU A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 729 " --> pdb=" O TRP A 725 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 746 removed outlier: 3.741A pdb=" N VAL A 746 " --> pdb=" O PRO A 743 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 755 removed outlier: 3.855A pdb=" N ARG A 755 " --> pdb=" O LYS A 751 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 775 removed outlier: 4.246A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 44 removed outlier: 3.865A pdb=" N MET B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU B 42 " --> pdb=" O ILE B 38 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY B 44 " --> pdb=" O LYS B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 53 removed outlier: 3.961A pdb=" N GLN B 53 " --> pdb=" O TRP B 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 49 through 53' Processing helix chain 'B' and resid 53 through 63 removed outlier: 3.552A pdb=" N ALA B 63 " --> pdb=" O VAL B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 88 removed outlier: 3.692A pdb=" N LEU B 75 " --> pdb=" O PRO B 71 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N SER B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLN B 88 " --> pdb=" O TYR B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 110 removed outlier: 4.071A pdb=" N LYS B 97 " --> pdb=" O ASN B 93 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ILE B 98 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR B 105 " --> pdb=" O MET B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 141 through 158 removed outlier: 3.566A pdb=" N PHE B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 3.516A pdb=" N VAL B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY B 158 " --> pdb=" O GLU B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 183 removed outlier: 3.696A pdb=" N ASN B 164 " --> pdb=" O PRO B 160 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N PHE B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N GLU B 166 " --> pdb=" O LYS B 162 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ASP B 170 " --> pdb=" O GLU B 166 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALA B 174 " --> pdb=" O ASP B 170 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 181 " --> pdb=" O ALA B 177 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE B 182 " --> pdb=" O TYR B 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 69 Processing helix chain 'C' and resid 78 through 84 removed outlier: 3.675A pdb=" N ALA C 82 " --> pdb=" O PRO C 79 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN C 83 " --> pdb=" O SER C 80 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N TYR C 84 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 153 through 159 Processing helix chain 'C' and resid 205 through 220 Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.810A pdb=" N TYR C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ARG C 252 " --> pdb=" O LEU C 248 " (cutoff:3.500A) Processing helix chain 'C' and resid 274 through 280 removed outlier: 3.702A pdb=" N SER C 278 " --> pdb=" O SER C 274 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N PHE C 280 " --> pdb=" O PHE C 276 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 287 Processing helix chain 'D' and resid 51 through 69 removed outlier: 3.523A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 122 through 129 removed outlier: 3.902A pdb=" N LEU D 127 " --> pdb=" O PRO D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 149 through 159 removed outlier: 3.710A pdb=" N GLU D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N TRP D 156 " --> pdb=" O TRP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 221 removed outlier: 4.032A pdb=" N ASP D 209 " --> pdb=" O HIS D 205 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA D 218 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 254 removed outlier: 3.563A pdb=" N ARG D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 273 removed outlier: 3.902A pdb=" N ILE D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'D' and resid 282 through 287 removed outlier: 3.833A pdb=" N LYS D 286 " --> pdb=" O GLU D 282 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.625A pdb=" N ALA E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER E 33 " --> pdb=" O GLY E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 50 removed outlier: 3.581A pdb=" N VAL E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 43 " --> pdb=" O SER E 39 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.847A pdb=" N VAL E 73 " --> pdb=" O PRO E 70 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLU E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 74' Processing helix chain 'E' and resid 76 through 81 Processing helix chain 'E' and resid 88 through 98 Processing helix chain 'E' and resid 104 through 112 removed outlier: 3.657A pdb=" N LEU E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG E 112 " --> pdb=" O GLU E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 171 removed outlier: 3.557A pdb=" N GLY E 170 " --> pdb=" O GLU E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 182 removed outlier: 3.872A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP E 181 " --> pdb=" O ARG E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 187 through 191 Processing helix chain 'F' and resid 36 through 46 removed outlier: 3.521A pdb=" N LEU F 40 " --> pdb=" O ASP F 36 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ASP F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ASN F 46 " --> pdb=" O ASN F 42 " (cutoff:3.500A) Processing helix chain 'F' and resid 51 through 60 removed outlier: 3.674A pdb=" N ASN F 60 " --> pdb=" O ALA F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 74 Processing helix chain 'F' and resid 113 through 133 removed outlier: 3.585A pdb=" N GLY F 119 " --> pdb=" O SER F 115 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE F 121 " --> pdb=" O LEU F 117 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N CYS F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 138 through 142 Processing helix chain 'F' and resid 160 through 169 removed outlier: 3.570A pdb=" N MET F 165 " --> pdb=" O LEU F 161 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N SER F 166 " --> pdb=" O ASP F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 178 through 183 removed outlier: 4.126A pdb=" N LEU F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 204 removed outlier: 3.629A pdb=" N ARG F 203 " --> pdb=" O GLU F 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 257 through 263 removed outlier: 3.577A pdb=" N ARG F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU F 262 " --> pdb=" O GLU F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 277 Processing helix chain 'F' and resid 280 through 305 removed outlier: 4.927A pdb=" N GLU F 286 " --> pdb=" O GLY F 282 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP F 287 " --> pdb=" O GLU F 283 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N TYR F 297 " --> pdb=" O VAL F 293 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA F 299 " --> pdb=" O GLU F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 324 removed outlier: 3.679A pdb=" N PHE F 321 " --> pdb=" O GLN F 317 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA F 323 " --> pdb=" O ARG F 319 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 345 Processing helix chain 'F' and resid 346 through 349 Processing helix chain 'F' and resid 357 through 364 removed outlier: 3.946A pdb=" N LYS F 363 " --> pdb=" O ASN F 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 119 through 120 removed outlier: 4.345A pdb=" N LEU A 119 " --> pdb=" O TYR A 129 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.614A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 345 through 346 Processing sheet with id=AA4, first strand: chain 'A' and resid 386 through 388 Processing sheet with id=AA5, first strand: chain 'A' and resid 402 through 403 Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.619A pdb=" N GLY A 431 " --> pdb=" O TYR A 454 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ILE A 465 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N TYR A 485 " --> pdb=" O ILE A 465 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N VAL A 467 " --> pdb=" O TYR A 485 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 580 through 584 removed outlier: 6.678A pdb=" N PHE A 591 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU A 620 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N PHE A 656 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N VAL A 622 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 689 through 691 removed outlier: 6.399A pdb=" N ARG A 694 " --> pdb=" O ALA A 690 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 141 through 143 removed outlier: 4.064A pdb=" N PHE C 147 " --> pdb=" O GLU C 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 141 through 143 removed outlier: 3.532A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLY C 7 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N LYS C 14 " --> pdb=" O PHE C 240 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N PHE C 240 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LYS C 16 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N PHE C 238 " --> pdb=" O LYS C 16 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 88 removed outlier: 5.080A pdb=" N SER C 85 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE C 101 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLY C 87 " --> pdb=" O PHE C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB4, first strand: chain 'C' and resid 163 through 168 Processing sheet with id=AB5, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.674A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.635A pdb=" N GLY D 13 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N LYS D 8 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N PHE D 245 " --> pdb=" O LYS D 8 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL D 10 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N PHE D 243 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS D 12 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE D 243 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 85 through 88 removed outlier: 5.327A pdb=" N SER D 85 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N PHE D 101 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N GLY D 87 " --> pdb=" O PHE D 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB9, first strand: chain 'D' and resid 163 through 171 Processing sheet with id=AC1, first strand: chain 'E' and resid 53 through 61 removed outlier: 5.657A pdb=" N ILE E 54 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER E 162 " --> pdb=" O ILE E 54 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N SER E 56 " --> pdb=" O LEU E 160 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU E 160 " --> pdb=" O SER E 56 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 66 through 68 Processing sheet with id=AC3, first strand: chain 'E' and resid 124 through 131 Processing sheet with id=AC4, first strand: chain 'E' and resid 252 through 254 Processing sheet with id=AC5, first strand: chain 'E' and resid 229 through 236 removed outlier: 6.625A pdb=" N LEU E 230 " --> pdb=" O THR E 245 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N THR E 245 " --> pdb=" O LEU E 230 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS E 232 " --> pdb=" O ARG E 243 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N ARG E 243 " --> pdb=" O LYS E 232 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N GLY E 234 " --> pdb=" O LYS E 241 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 261 through 263 Processing sheet with id=AC7, first strand: chain 'F' and resid 248 through 251 removed outlier: 3.762A pdb=" N VAL F 251 " --> pdb=" O ARG F 4 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.729A pdb=" N ILE F 100 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'F' and resid 209 through 210 Processing sheet with id=AD1, first strand: chain 'F' and resid 223 through 226 613 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 3.19 Time building geometry restraints manager: 1.79 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4048 1.33 - 1.45: 3797 1.45 - 1.58: 9149 1.58 - 1.70: 49 1.70 - 1.82: 80 Bond restraints: 17123 Sorted by residual: bond pdb=" C GLU E 74 " pdb=" N PRO E 75 " ideal model delta sigma weight residual 1.335 1.388 -0.052 1.36e-02 5.41e+03 1.47e+01 bond pdb=" N GLU F 280 " pdb=" CA GLU F 280 " ideal model delta sigma weight residual 1.457 1.488 -0.032 9.10e-03 1.21e+04 1.21e+01 bond pdb=" N THR F 16 " pdb=" CA THR F 16 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.15e+01 bond pdb=" N GLY F 279 " pdb=" CA GLY F 279 " ideal model delta sigma weight residual 1.446 1.476 -0.030 9.70e-03 1.06e+04 9.65e+00 bond pdb=" N ILE F 197 " pdb=" CA ILE F 197 " ideal model delta sigma weight residual 1.458 1.495 -0.037 1.19e-02 7.06e+03 9.58e+00 ... (remaining 17118 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.61: 22472 2.61 - 5.23: 700 5.23 - 7.84: 70 7.84 - 10.45: 18 10.45 - 13.06: 2 Bond angle restraints: 23262 Sorted by residual: angle pdb=" N PRO F 61 " pdb=" CA PRO F 61 " pdb=" CB PRO F 61 " ideal model delta sigma weight residual 103.08 110.83 -7.75 9.70e-01 1.06e+00 6.39e+01 angle pdb=" CA GLY F 279 " pdb=" C GLY F 279 " pdb=" O GLY F 279 " ideal model delta sigma weight residual 122.22 117.31 4.91 6.50e-01 2.37e+00 5.70e+01 angle pdb=" N PRO F 62 " pdb=" CA PRO F 62 " pdb=" CB PRO F 62 " ideal model delta sigma weight residual 103.00 110.59 -7.59 1.10e+00 8.26e-01 4.76e+01 angle pdb=" N PRO F 191 " pdb=" CA PRO F 191 " pdb=" CB PRO F 191 " ideal model delta sigma weight residual 103.00 110.41 -7.41 1.10e+00 8.26e-01 4.54e+01 angle pdb=" N PRO B 54 " pdb=" CA PRO B 54 " pdb=" CB PRO B 54 " ideal model delta sigma weight residual 103.52 110.18 -6.66 1.06e+00 8.90e-01 3.95e+01 ... (remaining 23257 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.12: 10093 35.12 - 70.24: 152 70.24 - 105.37: 8 105.37 - 140.49: 0 140.49 - 175.61: 2 Dihedral angle restraints: 10255 sinusoidal: 4309 harmonic: 5946 Sorted by residual: dihedral pdb=" O4' U G 2 " pdb=" C1' U G 2 " pdb=" N1 U G 2 " pdb=" C2 U G 2 " ideal model delta sinusoidal sigma weight residual -128.00 47.61 -175.61 1 1.70e+01 3.46e-03 6.63e+01 dihedral pdb=" O4' C G 14 " pdb=" C1' C G 14 " pdb=" N1 C G 14 " pdb=" C2 C G 14 " ideal model delta sinusoidal sigma weight residual -128.00 39.93 -167.93 1 1.70e+01 3.46e-03 6.57e+01 dihedral pdb=" C THR F 16 " pdb=" N THR F 16 " pdb=" CA THR F 16 " pdb=" CB THR F 16 " ideal model delta harmonic sigma weight residual -122.00 -139.81 17.81 0 2.50e+00 1.60e-01 5.08e+01 ... (remaining 10252 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 2326 0.112 - 0.224: 195 0.224 - 0.335: 26 0.335 - 0.447: 0 0.447 - 0.559: 1 Chirality restraints: 2548 Sorted by residual: chirality pdb=" CA THR F 16 " pdb=" N THR F 16 " pdb=" C THR F 16 " pdb=" CB THR F 16 " both_signs ideal model delta sigma weight residual False 2.53 1.97 0.56 2.00e-01 2.50e+01 7.81e+00 chirality pdb=" CA LYS A 257 " pdb=" N LYS A 257 " pdb=" C LYS A 257 " pdb=" CB LYS A 257 " both_signs ideal model delta sigma weight residual False 2.51 2.81 -0.30 2.00e-01 2.50e+01 2.25e+00 chirality pdb=" CA ILE C 239 " pdb=" N ILE C 239 " pdb=" C ILE C 239 " pdb=" CB ILE C 239 " both_signs ideal model delta sigma weight residual False 2.43 2.73 -0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 2545 not shown) Planarity restraints: 2909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 264 " 0.014 2.00e-02 2.50e+03 2.94e-02 8.62e+00 pdb=" C GLU E 264 " -0.051 2.00e-02 2.50e+03 pdb=" O GLU E 264 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU E 265 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 22 " 0.245 9.50e-02 1.11e+02 1.10e-01 7.40e+00 pdb=" NE ARG A 22 " -0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 22 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 22 " -0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 22 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 389 " 0.041 5.00e-02 4.00e+02 6.20e-02 6.15e+00 pdb=" N PRO A 390 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " 0.034 5.00e-02 4.00e+02 ... (remaining 2906 not shown) Histogram of nonbonded interaction distances: 1.87 - 2.47: 82 2.47 - 3.08: 9957 3.08 - 3.69: 25251 3.69 - 4.29: 37616 4.29 - 4.90: 62035 Nonbonded interactions: 134941 Sorted by model distance: nonbonded pdb=" O2' G G 22 " pdb=" O5' U G 23 " model vdw 1.866 3.040 nonbonded pdb=" O VAL F 34 " pdb=" CB ASP F 81 " model vdw 1.883 3.440 nonbonded pdb=" O2' U G 24 " pdb=" O4' U G 25 " model vdw 1.948 3.040 nonbonded pdb=" CB GLN A 114 " pdb=" NE ARG A 117 " model vdw 1.985 3.520 nonbonded pdb=" O2' U G 24 " pdb=" C6 U G 25 " model vdw 2.042 3.340 ... (remaining 134936 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 'C' selection = (chain 'D' and (resid 4 through 26 or resid 35 through 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.460 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: 0.020 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 19.600 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 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 : 0.011 0.506 17134 Z= 0.483 Angle : 1.106 38.217 23268 Z= 0.652 Chirality : 0.066 0.559 2548 Planarity : 0.008 0.110 2909 Dihedral : 12.492 175.609 6445 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.34 % Favored : 93.51 % Rotamer: Outliers : 0.67 % Allowed : 4.59 % Favored : 94.73 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.66 (0.14), residues: 2035 helix: -4.18 (0.09), residues: 807 sheet: -1.11 (0.29), residues: 273 loop : -2.60 (0.16), residues: 955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 177 TYR 0.037 0.003 TYR A 265 PHE 0.029 0.003 PHE E 15 TRP 0.030 0.003 TRP A 131 HIS 0.008 0.002 HIS D 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00738 / 0.40 (17123) covalent geometry : angle 1.04784 / 0.65 (23262) hydrogen bonds : bond 0.28902 / 19.54 ( 609) hydrogen bonds : angle 10.00895 / 6.95 ( 1752) metal coordination : bond 0.31788 / 17.92 ( 11) metal coordination : angle 22.09373 / 12.23 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 470 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.7747 (mmp) cc_final: 0.7317 (mtt) REVERT: A 308 LYS cc_start: 0.8308 (tttt) cc_final: 0.7925 (mtpp) REVERT: A 411 LYS cc_start: 0.8487 (mptt) cc_final: 0.8226 (mmmm) REVERT: A 584 TYR cc_start: 0.7405 (t80) cc_final: 0.7081 (t80) REVERT: A 684 TYR cc_start: 0.7966 (m-80) cc_final: 0.7651 (m-80) REVERT: D 2 ASP cc_start: 0.6946 (t0) cc_final: 0.6673 (t70) REVERT: D 244 GLU cc_start: 0.7302 (tt0) cc_final: 0.7079 (tt0) REVERT: E 255 ASN cc_start: 0.7891 (t0) cc_final: 0.7606 (p0) REVERT: F 6 LEU cc_start: 0.6575 (pp) cc_final: 0.6310 (pp) REVERT: F 116 SER cc_start: 0.7960 (t) cc_final: 0.7406 (p) REVERT: F 287 ASP cc_start: 0.6360 (t70) cc_final: 0.5932 (m-30) REVERT: F 384 ARG cc_start: 0.6416 (mpp80) cc_final: 0.5907 (mtp180) outliers start: 11 outliers final: 2 residues processed: 476 average time/residue: 0.6623 time to fit residues: 347.6187 Evaluate side-chains 286 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 284 time to evaluate : 0.614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain B residue 178 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 98 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 200 optimal weight: 9.9990 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 61 HIS A 64 HIS A 67 ASN A 102 ASN A 481 GLN B 72 ASN C 179 ASN C 183 ASN C 205 HIS D 37 ASN D 94 GLN D 136 ASN D 183 ASN D 202 ASN D 205 HIS F 18 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.165743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127765 restraints weight = 22110.125| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.82 r_work: 0.3177 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17134 Z= 0.162 Angle : 0.720 14.989 23268 Z= 0.369 Chirality : 0.046 0.207 2548 Planarity : 0.006 0.064 2909 Dihedral : 12.143 174.511 2683 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.04 % Allowed : 15.00 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.16 (0.15), residues: 2035 helix: -2.30 (0.14), residues: 821 sheet: -0.87 (0.30), residues: 271 loop : -2.20 (0.17), residues: 943 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 150 TYR 0.019 0.002 TYR A 265 PHE 0.033 0.002 PHE C 280 TRP 0.018 0.001 TRP A 131 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.16 (17123) covalent geometry : angle 0.71854 / 0.37 (23262) hydrogen bonds : bond 0.06240 / 4.25 ( 609) hydrogen bonds : angle 5.92073 / 4.10 ( 1752) metal coordination : bond 0.01147 / 0.65 ( 11) metal coordination : angle 3.23021 / 1.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 300 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 167 LYS cc_start: 0.8465 (mtpm) cc_final: 0.7864 (mmmt) REVERT: A 257 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8744 (ttmm) REVERT: A 308 LYS cc_start: 0.8535 (tttt) cc_final: 0.8223 (mttt) REVERT: A 411 LYS cc_start: 0.8716 (mptt) cc_final: 0.8378 (mmmm) REVERT: A 513 ARG cc_start: 0.8034 (ptm-80) cc_final: 0.7491 (ptm-80) REVERT: A 584 TYR cc_start: 0.7998 (t80) cc_final: 0.7636 (t80) REVERT: A 644 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8439 (tp) REVERT: B 103 ARG cc_start: 0.7300 (ttm110) cc_final: 0.7075 (mtm-85) REVERT: D 2 ASP cc_start: 0.7579 (t0) cc_final: 0.7061 (t70) REVERT: D 244 GLU cc_start: 0.7705 (tt0) cc_final: 0.7402 (tp30) REVERT: E 140 ASP cc_start: 0.8631 (m-30) cc_final: 0.8312 (m-30) REVERT: E 148 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7770 (tp30) REVERT: E 223 THR cc_start: 0.9089 (t) cc_final: 0.8853 (m) REVERT: E 255 ASN cc_start: 0.8686 (t0) cc_final: 0.8010 (p0) REVERT: F 116 SER cc_start: 0.7279 (t) cc_final: 0.7008 (p) REVERT: F 287 ASP cc_start: 0.6515 (t70) cc_final: 0.5912 (m-30) REVERT: F 345 THR cc_start: 0.5472 (m) cc_final: 0.5065 (p) outliers start: 66 outliers final: 31 residues processed: 337 average time/residue: 0.6096 time to fit residues: 229.0469 Evaluate side-chains 278 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 245 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain B residue 176 VAL Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 182 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 78 GLU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 268 SER Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 302 LYS Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 333 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 5.9990 chunk 163 optimal weight: 0.9990 chunk 149 optimal weight: 1.9990 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 198 optimal weight: 0.8980 chunk 74 optimal weight: 0.0000 chunk 171 optimal weight: 0.9980 chunk 127 optimal weight: 4.9990 chunk 105 optimal weight: 2.9990 overall best weight: 0.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN D 202 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.165728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.128034 restraints weight = 22381.721| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 2.87 r_work: 0.3193 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.3033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17134 Z= 0.139 Angle : 0.636 13.101 23268 Z= 0.322 Chirality : 0.044 0.185 2548 Planarity : 0.005 0.049 2909 Dihedral : 11.861 174.935 2681 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 4.04 % Allowed : 15.80 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.21 (0.17), residues: 2035 helix: -1.14 (0.16), residues: 827 sheet: -0.77 (0.29), residues: 281 loop : -1.93 (0.18), residues: 927 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 513 TYR 0.018 0.002 TYR F 297 PHE 0.017 0.001 PHE C 243 TRP 0.011 0.001 TRP A 131 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (17123) covalent geometry : angle 0.63473 / 0.32 (23262) hydrogen bonds : bond 0.04837 / 3.31 ( 609) hydrogen bonds : angle 5.25073 / 3.63 ( 1752) metal coordination : bond 0.00936 / 0.48 ( 11) metal coordination : angle 2.65863 / 1.37 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 256 time to evaluate : 0.654 Fit side-chains revert: symmetry clash REVERT: A 4 ASP cc_start: 0.8491 (p0) cc_final: 0.8264 (p0) REVERT: A 21 GLN cc_start: 0.7706 (tp40) cc_final: 0.7482 (tp40) REVERT: A 71 MET cc_start: 0.8044 (mmp) cc_final: 0.7555 (mtt) REVERT: A 167 LYS cc_start: 0.8513 (mtpm) cc_final: 0.7897 (mmmt) REVERT: A 257 LYS cc_start: 0.9193 (OUTLIER) cc_final: 0.8913 (mtmm) REVERT: A 308 LYS cc_start: 0.8783 (tttt) cc_final: 0.8552 (mtpp) REVERT: A 411 LYS cc_start: 0.8786 (mptt) cc_final: 0.8396 (mmmm) REVERT: A 584 TYR cc_start: 0.8354 (t80) cc_final: 0.7942 (t80) REVERT: A 644 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8430 (tp) REVERT: B 103 ARG cc_start: 0.7246 (ttm110) cc_final: 0.7044 (mtm-85) REVERT: D 2 ASP cc_start: 0.7878 (t0) cc_final: 0.7201 (t70) REVERT: D 160 GLU cc_start: 0.7372 (mt-10) cc_final: 0.6543 (mp0) REVERT: D 244 GLU cc_start: 0.8072 (tt0) cc_final: 0.7578 (tp30) REVERT: E 46 ASP cc_start: 0.8234 (m-30) cc_final: 0.8012 (m-30) REVERT: E 98 LYS cc_start: 0.8684 (OUTLIER) cc_final: 0.8390 (pttm) REVERT: E 140 ASP cc_start: 0.8801 (m-30) cc_final: 0.8499 (m-30) REVERT: E 223 THR cc_start: 0.9232 (t) cc_final: 0.9007 (m) REVERT: E 255 ASN cc_start: 0.8863 (t0) cc_final: 0.8254 (p0) REVERT: F 287 ASP cc_start: 0.6640 (t70) cc_final: 0.6046 (m-30) REVERT: F 319 ARG cc_start: 0.4603 (mmt180) cc_final: 0.4268 (mmm160) REVERT: F 346 ILE cc_start: 0.6596 (OUTLIER) cc_final: 0.6224 (pp) outliers start: 66 outliers final: 35 residues processed: 295 average time/residue: 0.6091 time to fit residues: 200.6439 Evaluate side-chains 281 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 242 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 197 ILE Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 120 optimal weight: 0.0030 chunk 73 optimal weight: 6.9990 chunk 188 optimal weight: 40.0000 chunk 66 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 185 optimal weight: 2.9990 overall best weight: 1.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS B 72 ASN D 94 GLN D 202 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.163764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.126005 restraints weight = 22048.787| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 2.81 r_work: 0.3159 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17134 Z= 0.175 Angle : 0.643 11.790 23268 Z= 0.324 Chirality : 0.045 0.200 2548 Planarity : 0.005 0.059 2909 Dihedral : 11.767 174.453 2681 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 4.59 % Allowed : 16.23 % Favored : 79.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2035 helix: -0.63 (0.17), residues: 834 sheet: -0.62 (0.29), residues: 281 loop : -1.83 (0.19), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 654 TYR 0.021 0.002 TYR F 297 PHE 0.017 0.002 PHE E 15 TRP 0.014 0.001 TRP A 131 HIS 0.006 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00408 / 0.17 (17123) covalent geometry : angle 0.64126 / 0.32 (23262) hydrogen bonds : bond 0.04517 / 3.08 ( 609) hydrogen bonds : angle 5.06807 / 3.50 ( 1752) metal coordination : bond 0.01357 / 0.68 ( 11) metal coordination : angle 2.78654 / 1.47 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 257 time to evaluate : 0.654 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ASP cc_start: 0.8518 (p0) cc_final: 0.8248 (p0) REVERT: A 21 GLN cc_start: 0.7848 (tp40) cc_final: 0.7316 (tm-30) REVERT: A 59 PHE cc_start: 0.7481 (m-10) cc_final: 0.7221 (m-80) REVERT: A 71 MET cc_start: 0.8086 (mmp) cc_final: 0.7634 (mtt) REVERT: A 257 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8989 (mtmm) REVERT: A 308 LYS cc_start: 0.8790 (tttt) cc_final: 0.8552 (mtpp) REVERT: A 411 LYS cc_start: 0.8822 (mptt) cc_final: 0.8427 (mmmm) REVERT: A 577 GLU cc_start: 0.7737 (pp20) cc_final: 0.7516 (pp20) REVERT: A 584 TYR cc_start: 0.8363 (t80) cc_final: 0.7995 (t80) REVERT: A 644 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8443 (tp) REVERT: B 103 ARG cc_start: 0.7501 (ttm110) cc_final: 0.7160 (mtm-85) REVERT: C 257 GLU cc_start: 0.7299 (tm-30) cc_final: 0.6962 (tm-30) REVERT: C 282 GLU cc_start: 0.6939 (tp30) cc_final: 0.6575 (tp30) REVERT: D 2 ASP cc_start: 0.7979 (t0) cc_final: 0.7306 (t70) REVERT: D 92 ASP cc_start: 0.7055 (OUTLIER) cc_final: 0.6125 (p0) REVERT: D 243 PHE cc_start: 0.8407 (OUTLIER) cc_final: 0.7927 (t80) REVERT: D 244 GLU cc_start: 0.8089 (tt0) cc_final: 0.7621 (tp30) REVERT: D 267 LYS cc_start: 0.7817 (pmtt) cc_final: 0.7473 (pptt) REVERT: E 53 ARG cc_start: 0.8683 (mtt-85) cc_final: 0.8082 (ttm170) REVERT: E 89 ARG cc_start: 0.7366 (OUTLIER) cc_final: 0.7076 (mtt-85) REVERT: E 140 ASP cc_start: 0.8829 (m-30) cc_final: 0.8493 (m-30) REVERT: E 255 ASN cc_start: 0.8844 (t0) cc_final: 0.8225 (p0) REVERT: F 287 ASP cc_start: 0.6617 (t70) cc_final: 0.6015 (m-30) REVERT: F 346 ILE cc_start: 0.6563 (OUTLIER) cc_final: 0.6177 (pp) REVERT: F 395 VAL cc_start: 0.6522 (t) cc_final: 0.6287 (p) outliers start: 75 outliers final: 44 residues processed: 301 average time/residue: 0.5893 time to fit residues: 198.6853 Evaluate side-chains 292 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 242 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 257 LYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 243 PHE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 262 ILE Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 42 optimal weight: 3.9990 chunk 200 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 139 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 153 optimal weight: 0.5980 chunk 195 optimal weight: 0.9990 chunk 120 optimal weight: 0.0980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN D 94 GLN ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.165022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.127129 restraints weight = 22106.891| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.84 r_work: 0.3179 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17134 Z= 0.136 Angle : 0.614 11.529 23268 Z= 0.307 Chirality : 0.044 0.191 2548 Planarity : 0.004 0.059 2909 Dihedral : 11.733 174.731 2681 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 4.04 % Allowed : 16.96 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.18), residues: 2035 helix: -0.24 (0.18), residues: 840 sheet: -0.54 (0.29), residues: 295 loop : -1.76 (0.19), residues: 900 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 513 TYR 0.018 0.001 TYR E 124 PHE 0.014 0.001 PHE F 288 TRP 0.012 0.001 TRP A 131 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.14 (17123) covalent geometry : angle 0.61268 / 0.31 (23262) hydrogen bonds : bond 0.04100 / 2.80 ( 609) hydrogen bonds : angle 4.88830 / 3.37 ( 1752) metal coordination : bond 0.00946 / 0.49 ( 11) metal coordination : angle 2.49579 / 1.28 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 254 time to evaluate : 0.738 Fit side-chains revert: symmetry clash REVERT: A 4 ASP cc_start: 0.8592 (p0) cc_final: 0.8327 (p0) REVERT: A 21 GLN cc_start: 0.7849 (tp40) cc_final: 0.7284 (tm-30) REVERT: A 33 GLN cc_start: 0.8386 (mt0) cc_final: 0.8185 (mt0) REVERT: A 71 MET cc_start: 0.8085 (mmp) cc_final: 0.7652 (mtt) REVERT: A 308 LYS cc_start: 0.8767 (tttt) cc_final: 0.8486 (mtpp) REVERT: A 411 LYS cc_start: 0.8822 (mptt) cc_final: 0.8426 (mmmm) REVERT: A 577 GLU cc_start: 0.7619 (pp20) cc_final: 0.7384 (pp20) REVERT: A 584 TYR cc_start: 0.8442 (t80) cc_final: 0.8075 (t80) REVERT: A 644 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8480 (tp) REVERT: B 180 LYS cc_start: 0.6010 (ttpt) cc_final: 0.5777 (ttpp) REVERT: C 90 ARG cc_start: 0.8008 (ttp80) cc_final: 0.7658 (ttp-110) REVERT: C 257 GLU cc_start: 0.7334 (tm-30) cc_final: 0.6953 (tm-30) REVERT: C 282 GLU cc_start: 0.7020 (tp30) cc_final: 0.6548 (tp30) REVERT: D 2 ASP cc_start: 0.7859 (t0) cc_final: 0.7114 (t70) REVERT: D 92 ASP cc_start: 0.7114 (OUTLIER) cc_final: 0.6160 (p0) REVERT: D 243 PHE cc_start: 0.8408 (OUTLIER) cc_final: 0.7921 (t80) REVERT: D 244 GLU cc_start: 0.8049 (tt0) cc_final: 0.7589 (tp30) REVERT: E 89 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6887 (mtt-85) REVERT: E 140 ASP cc_start: 0.8777 (m-30) cc_final: 0.8467 (m-30) REVERT: E 255 ASN cc_start: 0.8824 (t0) cc_final: 0.8272 (p0) REVERT: F 215 LYS cc_start: 0.6928 (pttt) cc_final: 0.6621 (pttp) REVERT: F 287 ASP cc_start: 0.6639 (t70) cc_final: 0.6066 (m-30) REVERT: F 319 ARG cc_start: 0.4382 (mmt180) cc_final: 0.4141 (mmm160) REVERT: F 346 ILE cc_start: 0.6608 (OUTLIER) cc_final: 0.6317 (pp) outliers start: 66 outliers final: 37 residues processed: 302 average time/residue: 0.6073 time to fit residues: 205.2640 Evaluate side-chains 284 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 242 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 255 THR Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 688 ILE Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 77 LYS Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 243 PHE Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 136 optimal weight: 6.9990 chunk 189 optimal weight: 20.0000 chunk 172 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 ASN D 94 GLN D 202 ASN E 139 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.164841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126843 restraints weight = 21869.816| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.67 r_work: 0.3184 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17134 Z= 0.127 Angle : 0.603 11.870 23268 Z= 0.301 Chirality : 0.044 0.227 2548 Planarity : 0.005 0.068 2909 Dihedral : 11.706 174.907 2681 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.36 % Favored : 94.59 % Rotamer: Outliers : 4.10 % Allowed : 17.51 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.18), residues: 2035 helix: 0.11 (0.18), residues: 838 sheet: -0.49 (0.29), residues: 293 loop : -1.60 (0.19), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 53 TYR 0.021 0.001 TYR E 124 PHE 0.015 0.001 PHE A 59 TRP 0.011 0.001 TRP A 131 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (17123) covalent geometry : angle 0.60211 / 0.30 (23262) hydrogen bonds : bond 0.03827 / 2.61 ( 609) hydrogen bonds : angle 4.79023 / 3.29 ( 1752) metal coordination : bond 0.00835 / 0.43 ( 11) metal coordination : angle 2.37389 / 1.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 257 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ASP cc_start: 0.8584 (OUTLIER) cc_final: 0.8331 (p0) REVERT: A 21 GLN cc_start: 0.7811 (tp40) cc_final: 0.7207 (tm-30) REVERT: A 71 MET cc_start: 0.8050 (mmp) cc_final: 0.7731 (mtt) REVERT: A 89 ASP cc_start: 0.8246 (m-30) cc_final: 0.8028 (m-30) REVERT: A 308 LYS cc_start: 0.8748 (tttt) cc_final: 0.8191 (mttt) REVERT: A 411 LYS cc_start: 0.8810 (mptt) cc_final: 0.8404 (mmmm) REVERT: A 577 GLU cc_start: 0.7601 (pp20) cc_final: 0.7353 (pp20) REVERT: A 584 TYR cc_start: 0.8438 (t80) cc_final: 0.8062 (t80) REVERT: A 644 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8452 (tp) REVERT: B 73 LYS cc_start: 0.6432 (ptpp) cc_final: 0.6228 (ptpp) REVERT: B 180 LYS cc_start: 0.6186 (ttpt) cc_final: 0.5783 (ttpp) REVERT: C 90 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7681 (ttp-110) REVERT: C 257 GLU cc_start: 0.7366 (tm-30) cc_final: 0.7125 (tm-30) REVERT: C 282 GLU cc_start: 0.6983 (tp30) cc_final: 0.6557 (tp30) REVERT: D 2 ASP cc_start: 0.7846 (t0) cc_final: 0.7009 (t70) REVERT: D 92 ASP cc_start: 0.7108 (OUTLIER) cc_final: 0.6122 (p0) REVERT: D 94 GLN cc_start: 0.6257 (OUTLIER) cc_final: 0.5982 (mp10) REVERT: D 244 GLU cc_start: 0.8059 (tt0) cc_final: 0.7584 (tp30) REVERT: E 89 ARG cc_start: 0.7120 (OUTLIER) cc_final: 0.6822 (mtt-85) REVERT: E 140 ASP cc_start: 0.8751 (m-30) cc_final: 0.8484 (m-30) REVERT: E 255 ASN cc_start: 0.8801 (t0) cc_final: 0.8249 (p0) REVERT: F 215 LYS cc_start: 0.6919 (pttt) cc_final: 0.6628 (pttp) REVERT: F 287 ASP cc_start: 0.6564 (t70) cc_final: 0.6003 (m-30) REVERT: F 346 ILE cc_start: 0.6607 (OUTLIER) cc_final: 0.6338 (pp) outliers start: 67 outliers final: 36 residues processed: 305 average time/residue: 0.5942 time to fit residues: 202.5585 Evaluate side-chains 283 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 241 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 94 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 23 VAL Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 45 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 20.0000 chunk 23 optimal weight: 0.9990 chunk 195 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 160 optimal weight: 0.8980 chunk 191 optimal weight: 5.9990 chunk 99 optimal weight: 0.0870 chunk 189 optimal weight: 7.9990 overall best weight: 0.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.164386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.125946 restraints weight = 21859.839| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 2.66 r_work: 0.3179 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17134 Z= 0.143 Angle : 0.621 11.102 23268 Z= 0.307 Chirality : 0.045 0.244 2548 Planarity : 0.004 0.060 2909 Dihedral : 11.670 174.759 2680 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.55 % Favored : 94.40 % Rotamer: Outliers : 3.80 % Allowed : 18.31 % Favored : 77.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.98 (0.18), residues: 2035 helix: 0.25 (0.18), residues: 837 sheet: -0.45 (0.29), residues: 293 loop : -1.55 (0.19), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 53 TYR 0.021 0.001 TYR E 124 PHE 0.021 0.001 PHE A 59 TRP 0.012 0.001 TRP A 335 HIS 0.005 0.001 HIS A 380 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (17123) covalent geometry : angle 0.61986 / 0.31 (23262) hydrogen bonds : bond 0.03850 / 2.62 ( 609) hydrogen bonds : angle 4.77653 / 3.28 ( 1752) metal coordination : bond 0.00985 / 0.50 ( 11) metal coordination : angle 2.38307 / 1.22 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 246 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4 ASP cc_start: 0.8569 (OUTLIER) cc_final: 0.8296 (p0) REVERT: A 21 GLN cc_start: 0.7862 (tp40) cc_final: 0.7437 (tp40) REVERT: A 59 PHE cc_start: 0.7482 (m-10) cc_final: 0.7140 (m-80) REVERT: A 71 MET cc_start: 0.8108 (mmp) cc_final: 0.7818 (mtt) REVERT: A 89 ASP cc_start: 0.8248 (m-30) cc_final: 0.8026 (m-30) REVERT: A 308 LYS cc_start: 0.8713 (tttt) cc_final: 0.8417 (mtpp) REVERT: A 411 LYS cc_start: 0.8828 (mptt) cc_final: 0.8407 (mmmm) REVERT: A 577 GLU cc_start: 0.7670 (pp20) cc_final: 0.7339 (pp20) REVERT: A 584 TYR cc_start: 0.8412 (t80) cc_final: 0.8052 (t80) REVERT: A 644 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8477 (tp) REVERT: B 180 LYS cc_start: 0.6034 (ttpt) cc_final: 0.5720 (ttpp) REVERT: C 257 GLU cc_start: 0.7410 (tm-30) cc_final: 0.7112 (tm-30) REVERT: C 282 GLU cc_start: 0.7028 (tp30) cc_final: 0.6518 (tp30) REVERT: D 92 ASP cc_start: 0.7039 (OUTLIER) cc_final: 0.6035 (p0) REVERT: D 244 GLU cc_start: 0.8044 (tt0) cc_final: 0.7544 (tp30) REVERT: E 89 ARG cc_start: 0.7150 (OUTLIER) cc_final: 0.6803 (mtt-85) REVERT: E 140 ASP cc_start: 0.8808 (m-30) cc_final: 0.8492 (m-30) REVERT: E 255 ASN cc_start: 0.8763 (t0) cc_final: 0.8235 (p0) REVERT: F 215 LYS cc_start: 0.6876 (pttt) cc_final: 0.6583 (pttp) REVERT: F 287 ASP cc_start: 0.6569 (t70) cc_final: 0.6000 (m-30) REVERT: F 346 ILE cc_start: 0.6606 (OUTLIER) cc_final: 0.6298 (pp) outliers start: 62 outliers final: 43 residues processed: 289 average time/residue: 0.5994 time to fit residues: 193.7544 Evaluate side-chains 291 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 155 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 259 ILE Chi-restraints excluded: chain D residue 268 SER Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 11 optimal weight: 30.0000 chunk 106 optimal weight: 2.9990 chunk 203 optimal weight: 20.0000 chunk 121 optimal weight: 0.7980 chunk 199 optimal weight: 4.9990 chunk 176 optimal weight: 7.9990 chunk 53 optimal weight: 0.4980 chunk 118 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 chunk 174 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.163721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.125073 restraints weight = 22023.902| |-----------------------------------------------------------------------------| r_work (start): 0.3443 rms_B_bonded: 2.73 r_work: 0.3168 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17134 Z= 0.150 Angle : 0.635 14.281 23268 Z= 0.314 Chirality : 0.045 0.213 2548 Planarity : 0.004 0.053 2909 Dihedral : 11.671 174.689 2680 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.41 % Favored : 94.55 % Rotamer: Outliers : 3.74 % Allowed : 18.92 % Favored : 77.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.88 (0.18), residues: 2035 helix: 0.38 (0.18), residues: 836 sheet: -0.44 (0.29), residues: 288 loop : -1.53 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 53 TYR 0.022 0.001 TYR E 124 PHE 0.011 0.001 PHE A 296 TRP 0.017 0.001 TRP F 393 HIS 0.005 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (17123) covalent geometry : angle 0.63346 / 0.31 (23262) hydrogen bonds : bond 0.03872 / 2.64 ( 609) hydrogen bonds : angle 4.75571 / 3.26 ( 1752) metal coordination : bond 0.01094 / 0.56 ( 11) metal coordination : angle 2.45284 / 1.27 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 243 time to evaluate : 0.577 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8316 (p0) REVERT: A 21 GLN cc_start: 0.7871 (tp40) cc_final: 0.7477 (tp40) REVERT: A 89 ASP cc_start: 0.8226 (m-30) cc_final: 0.8010 (m-30) REVERT: A 308 LYS cc_start: 0.8740 (tttt) cc_final: 0.8401 (mtpp) REVERT: A 385 ARG cc_start: 0.7325 (mmp-170) cc_final: 0.7111 (mmm160) REVERT: A 409 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7128 (mm-30) REVERT: A 411 LYS cc_start: 0.8871 (mptt) cc_final: 0.8447 (mmmm) REVERT: A 577 GLU cc_start: 0.7709 (pp20) cc_final: 0.7400 (pp20) REVERT: A 584 TYR cc_start: 0.8417 (t80) cc_final: 0.8066 (t80) REVERT: A 644 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8491 (tp) REVERT: A 773 MET cc_start: 0.7995 (mtm) cc_final: 0.7606 (ptp) REVERT: C 75 ARG cc_start: 0.8475 (OUTLIER) cc_final: 0.7412 (mtt90) REVERT: C 282 GLU cc_start: 0.7091 (tp30) cc_final: 0.6372 (tp30) REVERT: D 92 ASP cc_start: 0.7060 (OUTLIER) cc_final: 0.6055 (p0) REVERT: D 244 GLU cc_start: 0.7991 (tt0) cc_final: 0.7488 (tp30) REVERT: E 89 ARG cc_start: 0.7031 (OUTLIER) cc_final: 0.6749 (mtt-85) REVERT: E 255 ASN cc_start: 0.8779 (t0) cc_final: 0.8261 (p0) REVERT: F 215 LYS cc_start: 0.6809 (pttt) cc_final: 0.6468 (pttp) REVERT: F 287 ASP cc_start: 0.6571 (t70) cc_final: 0.5994 (m-30) REVERT: F 346 ILE cc_start: 0.6590 (OUTLIER) cc_final: 0.6280 (pp) outliers start: 61 outliers final: 40 residues processed: 287 average time/residue: 0.6128 time to fit residues: 196.4767 Evaluate side-chains 282 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 236 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain A residue 709 LEU Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 75 ARG Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 239 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 210 ILE Chi-restraints excluded: chain F residue 257 THR Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 190 optimal weight: 0.3980 chunk 128 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 200 optimal weight: 9.9990 chunk 47 optimal weight: 0.4980 chunk 126 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 81 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.164993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.127354 restraints weight = 21954.120| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.89 r_work: 0.3183 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 17134 Z= 0.124 Angle : 0.626 12.687 23268 Z= 0.310 Chirality : 0.044 0.219 2548 Planarity : 0.004 0.051 2909 Dihedral : 11.682 175.283 2680 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.55 % Favored : 94.40 % Rotamer: Outliers : 3.61 % Allowed : 19.47 % Favored : 76.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.18), residues: 2035 helix: 0.54 (0.18), residues: 839 sheet: -0.54 (0.29), residues: 293 loop : -1.50 (0.19), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 53 TYR 0.024 0.001 TYR E 124 PHE 0.013 0.001 PHE E 159 TRP 0.021 0.001 TRP F 393 HIS 0.005 0.001 HIS A 295 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (17123) covalent geometry : angle 0.62468 / 0.31 (23262) hydrogen bonds : bond 0.03689 / 2.52 ( 609) hydrogen bonds : angle 4.67645 / 3.21 ( 1752) metal coordination : bond 0.00786 / 0.41 ( 11) metal coordination : angle 2.37134 / 1.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 247 time to evaluate : 0.638 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4 ASP cc_start: 0.8543 (OUTLIER) cc_final: 0.8301 (p0) REVERT: A 21 GLN cc_start: 0.7891 (tp40) cc_final: 0.7553 (tp40) REVERT: A 66 LYS cc_start: 0.7017 (mmpt) cc_final: 0.6768 (mmpt) REVERT: A 89 ASP cc_start: 0.8211 (m-30) cc_final: 0.7990 (m-30) REVERT: A 99 GLU cc_start: 0.8387 (tp30) cc_final: 0.7701 (tp30) REVERT: A 167 LYS cc_start: 0.8506 (mtpp) cc_final: 0.8161 (ttpp) REVERT: A 228 ARG cc_start: 0.7785 (mtp-110) cc_final: 0.6955 (mpp-170) REVERT: A 308 LYS cc_start: 0.8737 (tttt) cc_final: 0.8405 (mtpp) REVERT: A 385 ARG cc_start: 0.7313 (mmp-170) cc_final: 0.7107 (mmm160) REVERT: A 409 GLU cc_start: 0.7338 (mm-30) cc_final: 0.7133 (mm-30) REVERT: A 411 LYS cc_start: 0.8871 (mptt) cc_final: 0.8449 (mmmm) REVERT: A 572 ARG cc_start: 0.8516 (OUTLIER) cc_final: 0.7505 (ppp80) REVERT: A 577 GLU cc_start: 0.7634 (pp20) cc_final: 0.7347 (pp20) REVERT: A 584 TYR cc_start: 0.8404 (t80) cc_final: 0.8093 (t80) REVERT: A 630 ARG cc_start: 0.8558 (ptt90) cc_final: 0.8256 (ptt90) REVERT: A 644 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8501 (tp) REVERT: A 773 MET cc_start: 0.7963 (mtm) cc_final: 0.7594 (ptp) REVERT: C 90 ARG cc_start: 0.7918 (ttp80) cc_final: 0.7489 (ttp-110) REVERT: C 160 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7306 (mp0) REVERT: C 256 ASP cc_start: 0.7245 (m-30) cc_final: 0.7007 (m-30) REVERT: C 282 GLU cc_start: 0.7011 (tp30) cc_final: 0.6441 (tp30) REVERT: D 92 ASP cc_start: 0.7180 (OUTLIER) cc_final: 0.6179 (p0) REVERT: D 164 GLU cc_start: 0.7596 (OUTLIER) cc_final: 0.7342 (tm-30) REVERT: D 244 GLU cc_start: 0.7994 (tt0) cc_final: 0.7503 (tp30) REVERT: E 89 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.6774 (mtt-85) REVERT: E 143 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.8990 (tt) REVERT: E 223 THR cc_start: 0.9380 (t) cc_final: 0.9037 (m) REVERT: E 255 ASN cc_start: 0.8779 (t0) cc_final: 0.8264 (p0) REVERT: F 287 ASP cc_start: 0.6566 (t70) cc_final: 0.6008 (m-30) REVERT: F 346 ILE cc_start: 0.6599 (OUTLIER) cc_final: 0.6280 (pp) outliers start: 59 outliers final: 35 residues processed: 290 average time/residue: 0.6079 time to fit residues: 196.9091 Evaluate side-chains 291 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 248 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 36 ARG Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 145 ASP Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 572 ARG Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 654 ARG Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain C residue 272 ILE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 245 THR Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 115 SER Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 19 optimal weight: 0.4980 chunk 169 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 179 optimal weight: 0.3980 chunk 199 optimal weight: 5.9990 chunk 160 optimal weight: 0.6980 chunk 170 optimal weight: 0.0770 chunk 177 optimal weight: 4.9990 chunk 171 optimal weight: 2.9990 chunk 18 optimal weight: 0.0770 chunk 86 optimal weight: 6.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.166045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.128649 restraints weight = 21904.352| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.86 r_work: 0.3205 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17134 Z= 0.111 Angle : 0.621 13.270 23268 Z= 0.307 Chirality : 0.044 0.243 2548 Planarity : 0.004 0.047 2909 Dihedral : 11.664 176.080 2680 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.06 % Favored : 94.89 % Rotamer: Outliers : 2.45 % Allowed : 21.25 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2035 helix: 0.70 (0.19), residues: 835 sheet: -0.54 (0.29), residues: 293 loop : -1.39 (0.20), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 53 TYR 0.034 0.001 TYR A 26 PHE 0.012 0.001 PHE E 159 TRP 0.028 0.001 TRP F 393 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.11 (17123) covalent geometry : angle 0.61997 / 0.31 (23262) hydrogen bonds : bond 0.03510 / 2.40 ( 609) hydrogen bonds : angle 4.62238 / 3.19 ( 1752) metal coordination : bond 0.00727 / 0.38 ( 11) metal coordination : angle 2.26001 / 1.17 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4070 Ramachandran restraints generated. 2035 Oldfield, 0 Emsley, 2035 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 4 ASP cc_start: 0.8518 (OUTLIER) cc_final: 0.8287 (p0) REVERT: A 21 GLN cc_start: 0.7857 (tp40) cc_final: 0.7507 (tp40) REVERT: A 89 ASP cc_start: 0.8157 (m-30) cc_final: 0.7926 (m-30) REVERT: A 167 LYS cc_start: 0.8514 (mtpp) cc_final: 0.8179 (ttpp) REVERT: A 308 LYS cc_start: 0.8762 (tttt) cc_final: 0.8436 (mtpp) REVERT: A 411 LYS cc_start: 0.8874 (mptt) cc_final: 0.8456 (mmmm) REVERT: A 577 GLU cc_start: 0.7623 (pp20) cc_final: 0.7331 (pp20) REVERT: A 584 TYR cc_start: 0.8376 (t80) cc_final: 0.8077 (t80) REVERT: A 644 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8478 (tp) REVERT: A 773 MET cc_start: 0.7931 (mtm) cc_final: 0.7574 (ptp) REVERT: C 90 ARG cc_start: 0.7887 (ttp80) cc_final: 0.7491 (ttp-110) REVERT: C 160 GLU cc_start: 0.7590 (mt-10) cc_final: 0.7305 (mp0) REVERT: C 282 GLU cc_start: 0.7080 (tp30) cc_final: 0.6702 (tp30) REVERT: D 92 ASP cc_start: 0.7258 (OUTLIER) cc_final: 0.6306 (p0) REVERT: D 164 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7280 (tm-30) REVERT: D 202 ASN cc_start: 0.8799 (t160) cc_final: 0.8532 (t0) REVERT: D 244 GLU cc_start: 0.7914 (tt0) cc_final: 0.7444 (tp30) REVERT: E 89 ARG cc_start: 0.7092 (OUTLIER) cc_final: 0.6838 (mtt-85) REVERT: E 223 THR cc_start: 0.9367 (t) cc_final: 0.9032 (m) REVERT: E 255 ASN cc_start: 0.8771 (t0) cc_final: 0.8293 (p0) REVERT: F 287 ASP cc_start: 0.6461 (t70) cc_final: 0.5943 (m-30) REVERT: F 346 ILE cc_start: 0.6583 (OUTLIER) cc_final: 0.6268 (pp) outliers start: 40 outliers final: 25 residues processed: 276 average time/residue: 0.6191 time to fit residues: 190.6656 Evaluate side-chains 276 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 245 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 148 SER Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 250 VAL Chi-restraints excluded: chain A residue 444 VAL Chi-restraints excluded: chain A residue 455 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 696 LYS Chi-restraints excluded: chain B residue 109 VAL Chi-restraints excluded: chain B residue 156 LEU Chi-restraints excluded: chain B residue 172 LEU Chi-restraints excluded: chain C residue 120 LEU Chi-restraints excluded: chain C residue 148 LEU Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 92 ASP Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 164 GLU Chi-restraints excluded: chain D residue 181 ARG Chi-restraints excluded: chain D residue 269 VAL Chi-restraints excluded: chain D residue 272 ILE Chi-restraints excluded: chain E residue 89 ARG Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 277 THR Chi-restraints excluded: chain F residue 5 THR Chi-restraints excluded: chain F residue 8 VAL Chi-restraints excluded: chain F residue 10 SER Chi-restraints excluded: chain F residue 324 SER Chi-restraints excluded: chain F residue 333 LEU Chi-restraints excluded: chain F residue 346 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 208 random chunks: chunk 70 optimal weight: 0.0980 chunk 111 optimal weight: 0.8980 chunk 1 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 184 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 177 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 61 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 382 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.165068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.127138 restraints weight = 21851.289| |-----------------------------------------------------------------------------| r_work (start): 0.3469 rms_B_bonded: 2.85 r_work: 0.3195 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3055 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 17134 Z= 0.134 Angle : 0.637 12.980 23268 Z= 0.315 Chirality : 0.046 0.589 2548 Planarity : 0.004 0.046 2909 Dihedral : 11.631 174.920 2680 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.01 % Favored : 94.94 % Rotamer: Outliers : 2.94 % Allowed : 20.94 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.61 (0.18), residues: 2035 helix: 0.71 (0.18), residues: 837 sheet: -0.57 (0.29), residues: 290 loop : -1.40 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 53 TYR 0.041 0.001 TYR A 26 PHE 0.012 0.001 PHE E 159 TRP 0.030 0.001 TRP F 393 HIS 0.004 0.001 HIS A 382 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.13 (17123) covalent geometry : angle 0.63597 / 0.31 (23262) hydrogen bonds : bond 0.03672 / 2.51 ( 609) hydrogen bonds : angle 4.64956 / 3.22 ( 1752) metal coordination : bond 0.00814 / 0.42 ( 11) metal coordination : angle 2.10894 / 1.08 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6839.64 seconds wall clock time: 116 minutes 56.11 seconds (7016.11 seconds total)