Starting phenix.real_space_refine on Sun Aug 24 06:53:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o7h_0641/08_2025/6o7h_0641.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o7h_0641/08_2025/6o7h_0641.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6o7h_0641/08_2025/6o7h_0641.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o7h_0641/08_2025/6o7h_0641.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o7h_0641/08_2025/6o7h_0641.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o7h_0641/08_2025/6o7h_0641.map" } resolution = 2.9 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= 0.005 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 50 5.49 5 S 49 5.16 5 C 11014 2.51 5 N 3083 2.21 5 O 3377 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 71 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17576 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 6152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 771, 6152 Classifications: {'peptide': 771} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 35, 'TRANS': 735} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "B" Number of atoms: 1047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1047 Classifications: {'peptide': 150} Incomplete info: {'truncation_to_alanine': 42} Link IDs: {'PTRANS': 5, 'TRANS': 144} Chain breaks: 3 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 166 Unresolved non-hydrogen angles: 212 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ASP:plan': 3, 'ARG:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'GLN:plan1': 2, 'TRP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 96 Chain: "C" Number of atoms: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2214 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 12, 'TRANS': 265} Chain breaks: 1 Chain: "D" Number of atoms: 2265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2265 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 12, 'TRANS': 272} Chain breaks: 1 Chain: "E" Number of atoms: 2261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2261 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 20, 'TRANS': 265} Chain: "G" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 589 Classifications: {'RNA': 27} Modifications used: {'5*END': 1, 'rna2p_pur': 9, 'rna2p_pyr': 5, 'rna3p_pur': 10, 'rna3p_pyr': 3} Link IDs: {'rna2p': 13, 'rna3p': 13} Chain: "H" Number of atoms: 398 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 398 Classifications: {'RNA': 19} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 4, 'rna3p_pur': 6, 'rna3p_pyr': 8} Link IDs: {'rna2p': 5, 'rna3p': 13} Chain: "F" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 313 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 3, 'TRANS': 35} Chain: "F" Number of atoms: 2223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 322, 2223 Classifications: {'peptide': 322} Incomplete info: {'backbone_only': 7, 'truncation_to_alanine': 106} Link IDs: {'PTRANS': 12, 'TRANS': 309} Chain breaks: 10 Unresolved non-hydrogen bonds: 287 Unresolved non-hydrogen angles: 409 Unresolved non-hydrogen dihedrals: 179 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'UNK:plan-1': 93, 'GLN:plan1': 1, 'PHE:plan': 2, 'TYR:plan': 1, 'TRP:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 146 Chain: "K" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Classifications: {'RNA': 4} Modifications used: {'rna2p_pur': 3, 'rna3p_pur': 1} Link IDs: {'rna2p': 2, 'rna3p': 1} 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} Chain: "H" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Classifications: {'RNA': 1} Modifications used: {'rna2p_pur': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3079 SG CYS A 389 57.900 85.339 89.908 1.00 26.12 S ATOM 3099 SG CYS A 392 53.925 83.414 90.176 1.00 20.38 S ATOM 3254 SG CYS A 413 55.553 86.020 92.716 1.00 30.17 S ATOM 3274 SG CYS A 416 56.496 82.553 92.693 1.00 30.70 S ATOM 8026 SG CYS C 113 73.888 99.035 65.322 1.00 24.94 S ATOM 8093 SG CYS C 122 74.316 98.299 61.726 1.00 18.20 S ATOM 8113 SG CYS C 125 71.610 95.804 64.201 1.00 17.21 S ATOM 10291 SG CYS D 113 93.830 71.709 67.401 1.00 32.50 S ATOM 10358 SG CYS D 122 96.213 71.721 64.605 1.00 31.10 S ATOM 10378 SG CYS D 125 91.608 70.721 64.658 1.00 23.12 S Time building chain proxies: 4.09, per 1000 atoms: 0.23 Number of scatterers: 17576 At special positions: 0 Unit cell: (127.413, 119.79, 150.282, 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 50 15.00 O 3377 8.00 N 3083 7.00 C 11014 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 Links applied TRANS " UNK F 40 " - " ARG F 39 " Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 737.4 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " 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 125 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " pdb=" ZN D 301 " pdb="ZN ZN D 301 " - pdb=" NE2 HIS D 111 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 122 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 113 " pdb="ZN ZN D 301 " - pdb=" SG CYS D 125 " Number of angles added : 12 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3882 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 29 sheets defined 42.3% alpha, 15.8% beta 10 base pairs and 17 stacking pairs defined. Time for finding SS restraints: 2.25 Creating SS restraints... Processing helix chain 'A' and resid 2 through 13 removed outlier: 3.557A pdb=" N ALA A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 17 through 22 Processing helix chain 'A' and resid 29 through 42 removed outlier: 3.893A pdb=" N GLN A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.778A pdb=" N LEU A 52 " --> pdb=" O ALA A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.591A pdb=" N ARG A 73 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LEU A 78 " --> pdb=" O ARG A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 84 removed outlier: 3.764A pdb=" N PHE A 83 " --> pdb=" O SER A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 105 removed outlier: 3.507A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASN A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N SER A 105 " --> pdb=" O ASP A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 167 Processing helix chain 'A' and resid 171 through 184 Proline residue: A 177 - end of helix removed outlier: 3.730A 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 218 through 224 Processing helix chain 'A' and resid 243 through 248 Processing helix chain 'A' and resid 255 through 282 removed outlier: 3.557A pdb=" N ALA A 264 " --> pdb=" O ARG A 260 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N GLU A 267 " --> pdb=" O SER A 263 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N SER A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 286 No H-bonds generated for 'chain 'A' and resid 284 through 286' Processing helix chain 'A' and resid 303 through 325 removed outlier: 3.697A pdb=" N GLU A 312 " --> pdb=" O LYS A 308 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 343 Processing helix chain 'A' and resid 351 through 369 removed outlier: 3.572A pdb=" N LYS A 357 " --> pdb=" O ALA A 353 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N HIS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 424 removed outlier: 3.733A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.854A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 removed outlier: 3.663A pdb=" N PHE A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) 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: 3.664A pdb=" N THR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N MET A 545 " --> pdb=" O ALA A 541 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 558 removed outlier: 3.737A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 558 " --> pdb=" O GLY A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 596 through 614 removed outlier: 3.877A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 651 removed outlier: 3.897A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 651 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.839A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA A 685 " --> pdb=" O TRP A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 702 through 719 removed outlier: 4.526A pdb=" N LYS A 708 " --> pdb=" O GLY A 704 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 715 " --> pdb=" O GLU A 711 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N TYR A 716 " --> pdb=" O ILE A 712 " (cutoff:3.500A) Processing helix chain 'A' and resid 723 through 736 removed outlier: 4.355A pdb=" N TYR A 727 " --> pdb=" O VAL A 723 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ALA A 730 " --> pdb=" O ALA A 726 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS A 736 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 755 Processing helix chain 'A' and resid 764 through 775 removed outlier: 4.309A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 28 Processing helix chain 'B' and resid 37 through 42 removed outlier: 3.835A pdb=" N MET B 41 " --> pdb=" O GLY B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 48 through 62 removed outlier: 4.203A pdb=" N ILE B 52 " --> pdb=" O GLN B 48 " (cutoff:3.500A) Proline residue: B 54 - end of helix Processing helix chain 'B' and resid 72 through 86 removed outlier: 3.555A pdb=" N VAL B 79 " --> pdb=" O LEU B 75 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TYR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 108 Processing helix chain 'B' and resid 117 through 132 removed outlier: 3.861A pdb=" N VAL B 121 " --> pdb=" O LYS B 117 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N LYS B 122 " --> pdb=" O ASP B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 156 removed outlier: 3.616A pdb=" N LEU B 142 " --> pdb=" O SER B 138 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ILE B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU B 149 " --> pdb=" O PHE B 145 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) Proline residue: B 151 - end of helix removed outlier: 4.019A pdb=" N VAL B 155 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LEU B 156 " --> pdb=" O MET B 152 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 182 removed outlier: 3.787A pdb=" N PHE B 171 " --> pdb=" O LYS B 167 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 70 removed outlier: 3.609A pdb=" N ARG C 70 " --> pdb=" O LEU C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 Processing helix chain 'C' and resid 123 through 129 removed outlier: 3.967A pdb=" N LEU C 127 " --> pdb=" O PRO C 123 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 158 removed outlier: 3.509A pdb=" N TRP C 156 " --> pdb=" O TRP C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 223 removed outlier: 3.919A pdb=" N ASP C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.585A pdb=" N TYR C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR C 253 " --> pdb=" O ASP C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 274 Processing helix chain 'C' and resid 282 through 287 removed outlier: 3.617A pdb=" N LYS C 286 " --> pdb=" O GLU C 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 70 removed outlier: 3.799A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG D 70 " --> pdb=" O LEU D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 Processing helix chain 'D' and resid 124 through 129 Processing helix chain 'D' and resid 151 through 159 removed outlier: 3.641A pdb=" N TRP D 156 " --> pdb=" O TRP D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 221 Processing helix chain 'D' and resid 247 through 254 removed outlier: 4.032A pdb=" N TYR D 251 " --> pdb=" O PRO D 247 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ARG D 252 " --> pdb=" O LEU D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 272 removed outlier: 3.905A 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 280 through 285 removed outlier: 3.865A pdb=" N GLU D 284 " --> pdb=" O PHE D 280 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLY D 285 " --> pdb=" O SER D 281 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 280 through 285' Processing helix chain 'E' and resid 20 through 36 Processing helix chain 'E' and resid 37 through 50 removed outlier: 3.888A pdb=" N VAL E 41 " --> pdb=" O GLY E 37 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU E 42 " --> pdb=" O GLN E 38 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.919A pdb=" N LEU E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 99 removed outlier: 3.569A pdb=" N ARG E 95 " --> pdb=" O THR E 91 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 111 removed outlier: 3.845A pdb=" N GLU E 108 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU E 109 " --> pdb=" O LYS E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 169 removed outlier: 3.554A pdb=" N PHE E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 182 removed outlier: 3.755A pdb=" N ARG E 177 " --> pdb=" O ALA E 173 " (cutoff:3.500A) removed outlier: 4.017A 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 43 through 47 removed outlier: 3.591A pdb=" N UNK F 46 " --> pdb=" O UNK F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 60 removed outlier: 4.304A pdb=" N UNK F 58 " --> pdb=" O UNK F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 132 removed outlier: 3.572A pdb=" N LEU F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA F 120 " --> pdb=" O SER F 116 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 142 removed outlier: 3.815A pdb=" N UNK F 141 " --> pdb=" O UNK F 137 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N UNK F 142 " --> pdb=" O UNK F 138 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 137 through 142' Processing helix chain 'F' and resid 151 through 155 removed outlier: 4.183A pdb=" N UNK F 155 " --> pdb=" O UNK F 151 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 151 through 155' Processing helix chain 'F' and resid 160 through 169 removed outlier: 4.251A pdb=" N UNK F 166 " --> pdb=" O UNK F 162 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N UNK F 169 " --> pdb=" O UNK F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 187 Processing helix chain 'F' and resid 204 through 207 Processing helix chain 'F' and resid 218 through 220 No H-bonds generated for 'chain 'F' and resid 218 through 220' Processing helix chain 'F' and resid 256 through 263 removed outlier: 3.935A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 271 through 276 removed outlier: 3.677A pdb=" N LYS F 276 " --> pdb=" O TRP F 272 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.564A pdb=" N TRP F 290 " --> pdb=" O GLU F 286 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLU F 291 " --> pdb=" O ASP F 287 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 317 through 323 Processing helix chain 'F' and resid 340 through 344 removed outlier: 3.837A pdb=" N MET F 344 " --> pdb=" O TRP F 341 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 349 removed outlier: 4.113A pdb=" N LEU F 348 " --> pdb=" O THR F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 removed outlier: 4.313A pdb=" N VAL F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LYS F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) removed outlier: 3.742A 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: 4.224A 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: 6.708A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 6.495A 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: 4.265A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 430 " --> pdb=" O LYS A 468 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 580 through 586 removed outlier: 7.044A pdb=" N ILE A 580 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N ALA A 595 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL A 582 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL A 593 " --> pdb=" O VAL A 582 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP A 589 " --> pdb=" O GLY A 586 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LEU A 620 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N PHE A 656 " --> pdb=" O LEU A 620 " (cutoff:3.500A) removed outlier: 6.906A 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: 6.675A 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: 3.887A 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: 3.792A pdb=" N GLY C 13 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY C 7 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.138A pdb=" N VAL C 10 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE C 243 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LYS C 12 " --> pdb=" O ASP C 241 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 85 through 88 removed outlier: 4.706A pdb=" N SER C 85 " --> pdb=" O LYS C 99 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N PHE C 101 " --> pdb=" O SER C 85 " (cutoff:3.500A) removed outlier: 7.602A 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: 3.726A 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: 3.612A pdb=" N PHE D 194 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N GLY D 13 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL D 10 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE D 243 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N LYS D 12 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 3.525A 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: 7.392A pdb=" N SER D 85 " --> pdb=" O PHE D 100 " (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 169 Processing sheet with id=AC1, first strand: chain 'D' and resid 231 through 232 removed outlier: 7.294A pdb=" N GLY D 232 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL F 211 " --> pdb=" O GLY D 232 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 58 through 61 removed outlier: 8.252A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 67 through 68 Processing sheet with id=AC4, first strand: chain 'E' and resid 124 through 134 removed outlier: 3.646A pdb=" N VAL E 127 " --> pdb=" O GLU E 148 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 252 through 254 removed outlier: 4.608A pdb=" N TYR E 211 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 229 through 232 removed outlier: 3.535A pdb=" N LEU E 230 " --> pdb=" O PHE E 246 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC8, first strand: chain 'E' and resid 261 through 263 Processing sheet with id=AC9, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AD1, first strand: chain 'F' and resid 15 through 20 removed outlier: 5.565A pdb=" N ASN F 18 " --> pdb=" O GLU F 102 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 236 through 243 removed outlier: 3.718A pdb=" N ILE F 236 " --> pdb=" O VAL F 229 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N LEU F 385 " --> pdb=" O GLU F 228 " (cutoff:3.500A) 620 hydrogen bonds defined for protein. 1770 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 24 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 17 stacking parallelities Total time for adding SS restraints: 3.31 Time building geometry restraints manager: 2.15 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: 4576 1.33 - 1.45: 3643 1.45 - 1.57: 9655 1.57 - 1.69: 97 1.69 - 1.81: 80 Bond restraints: 18051 Sorted by residual: bond pdb=" C5 A K 3 " pdb=" C6 A K 3 " ideal model delta sigma weight residual 1.406 1.324 0.082 2.00e-02 2.50e+03 1.70e+01 bond pdb=" C5 A K 1 " pdb=" C6 A K 1 " ideal model delta sigma weight residual 1.406 1.328 0.078 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C5 A K 4 " pdb=" C6 A K 4 " ideal model delta sigma weight residual 1.406 1.329 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" P A K 3 " pdb=" O5' A K 3 " ideal model delta sigma weight residual 1.593 1.649 -0.056 1.50e-02 4.44e+03 1.37e+01 bond pdb=" C5 A K 2 " pdb=" C6 A K 2 " ideal model delta sigma weight residual 1.406 1.337 0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 18046 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.90: 24507 4.90 - 9.80: 117 9.80 - 14.70: 7 14.70 - 19.60: 2 19.60 - 24.50: 3 Bond angle restraints: 24636 Sorted by residual: angle pdb=" O3' A K 2 " pdb=" P A K 3 " pdb=" O5' A K 3 " ideal model delta sigma weight residual 104.00 85.62 18.38 1.50e+00 4.44e-01 1.50e+02 angle pdb=" OP2 A K 3 " pdb=" P A K 3 " pdb=" O5' A K 3 " ideal model delta sigma weight residual 108.00 83.50 24.50 3.00e+00 1.11e-01 6.67e+01 angle pdb=" OP1 A K 1 " pdb=" P A K 1 " pdb=" O5' A K 1 " ideal model delta sigma weight residual 108.00 87.41 20.59 3.00e+00 1.11e-01 4.71e+01 angle pdb=" N PRO A 113 " pdb=" CA PRO A 113 " pdb=" CB PRO A 113 " ideal model delta sigma weight residual 103.00 110.37 -7.37 1.10e+00 8.26e-01 4.49e+01 angle pdb=" N PRO B 33 " pdb=" CA PRO B 33 " pdb=" CB PRO B 33 " ideal model delta sigma weight residual 103.25 110.20 -6.95 1.05e+00 9.07e-01 4.38e+01 ... (remaining 24631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.35: 10557 34.35 - 68.70: 242 68.70 - 103.05: 26 103.05 - 137.40: 0 137.40 - 171.74: 3 Dihedral angle restraints: 10828 sinusoidal: 4758 harmonic: 6070 Sorted by residual: dihedral pdb=" O4' C G 11 " pdb=" C1' C G 11 " pdb=" N1 C G 11 " pdb=" C2 C G 11 " ideal model delta sinusoidal sigma weight residual -128.00 43.74 -171.74 1 1.70e+01 3.46e-03 6.61e+01 dihedral pdb=" O4' C G 5 " pdb=" C1' C G 5 " pdb=" N1 C G 5 " pdb=" C2 C G 5 " ideal model delta sinusoidal sigma weight residual -128.00 30.12 -158.12 1 1.70e+01 3.46e-03 6.40e+01 dihedral pdb=" C4' A K 2 " pdb=" O4' A K 2 " pdb=" C1' A K 2 " pdb=" C2' A K 2 " ideal model delta sinusoidal sigma weight residual -21.00 26.55 -47.55 1 8.00e+00 1.56e-02 4.88e+01 ... (remaining 10825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 2492 0.116 - 0.231: 216 0.231 - 0.347: 13 0.347 - 0.463: 1 0.463 - 0.579: 2 Chirality restraints: 2724 Sorted by residual: chirality pdb=" P A K 1 " pdb=" OP1 A K 1 " pdb=" OP2 A K 1 " pdb=" O5' A K 1 " both_signs ideal model delta sigma weight residual True 2.41 -2.99 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" P A K 3 " pdb=" OP1 A K 3 " pdb=" OP2 A K 3 " pdb=" O5' A K 3 " both_signs ideal model delta sigma weight residual True 2.41 -2.96 -0.55 2.00e-01 2.50e+01 7.62e+00 chirality pdb=" C1' C G 5 " pdb=" O4' C G 5 " pdb=" C2' C G 5 " pdb=" N1 C G 5 " both_signs ideal model delta sigma weight residual False 2.45 2.10 0.35 2.00e-01 2.50e+01 3.02e+00 ... (remaining 2721 not shown) Planarity restraints: 2993 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 252 " 0.026 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" C GLY A 252 " -0.091 2.00e-02 2.50e+03 pdb=" O GLY A 252 " 0.035 2.00e-02 2.50e+03 pdb=" N LYS A 253 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 71 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.96e+01 pdb=" C MET A 71 " 0.077 2.00e-02 2.50e+03 pdb=" O MET A 71 " -0.029 2.00e-02 2.50e+03 pdb=" N ILE A 72 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA E 47 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.93e+01 pdb=" C ALA E 47 " 0.076 2.00e-02 2.50e+03 pdb=" O ALA E 47 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE E 48 " -0.025 2.00e-02 2.50e+03 ... (remaining 2990 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 10 2.26 - 2.92: 6851 2.92 - 3.58: 23617 3.58 - 4.24: 42811 4.24 - 4.90: 71232 Nonbonded interactions: 144521 Sorted by model distance: nonbonded pdb=" O3' C H 35 " pdb=" P G H 101 " model vdw 1.596 3.400 nonbonded pdb=" P A K 1 " pdb=" O3' A K 4 " model vdw 1.628 3.400 nonbonded pdb=" O2' A K 1 " pdb=" OP1 A K 2 " model vdw 2.055 3.040 nonbonded pdb=" O5' A K 1 " pdb=" O3' A K 4 " model vdw 2.127 3.040 nonbonded pdb=" OE2 GLU A 180 " pdb=" OH TYR A 547 " model vdw 2.204 3.040 ... (remaining 144516 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' and (resid 4 through 26 or resid 34 through 301)) selection = (chain 'D' and (resid 4 through 26 or resid 34 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: 0.980 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 20.960 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 : 0.007 0.210 18064 Z= 0.398 Angle : 1.159 28.884 24651 Z= 0.658 Chirality : 0.067 0.579 2724 Planarity : 0.007 0.061 2992 Dihedral : 14.233 171.744 6943 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.33 % Favored : 94.57 % Rotamer: Outliers : 1.21 % Allowed : 4.83 % Favored : 93.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.34 (0.15), residues: 2006 helix: -3.61 (0.12), residues: 771 sheet: -1.91 (0.27), residues: 290 loop : -2.44 (0.17), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 212 TYR 0.029 0.003 TYR C 233 PHE 0.029 0.003 PHE A 502 TRP 0.023 0.002 TRP A 320 HIS 0.007 0.002 HIS D 22 Details of bonding type rmsd covalent geometry : bond 0.00643 (18051) covalent geometry : angle 1.10477 (24636) hydrogen bonds : bond 0.28449 ( 640) hydrogen bonds : angle 10.28375 ( 1818) metal coordination : bond 0.13674 ( 12) metal coordination : angle 15.96816 ( 12) link_TRANS : bond 0.00937 ( 1) link_TRANS : angle 1.24286 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 445 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 MET cc_start: 0.8305 (mtm) cc_final: 0.7894 (mtt) REVERT: A 158 VAL cc_start: 0.8439 (t) cc_final: 0.8144 (t) REVERT: A 159 LYS cc_start: 0.8553 (tmmt) cc_final: 0.8194 (tppt) REVERT: A 162 TRP cc_start: 0.8459 (t-100) cc_final: 0.8073 (t-100) REVERT: A 167 LYS cc_start: 0.7779 (mtmt) cc_final: 0.7552 (mtmt) REVERT: A 170 LEU cc_start: 0.8991 (tp) cc_final: 0.8660 (tp) REVERT: A 297 MET cc_start: 0.8933 (ttt) cc_final: 0.8663 (ttt) REVERT: A 757 GLU cc_start: 0.7493 (pt0) cc_final: 0.6770 (pt0) outliers start: 20 outliers final: 5 residues processed: 460 average time/residue: 0.7366 time to fit residues: 370.9105 Evaluate side-chains 272 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 267 time to evaluate : 0.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain A residue 147 PHE Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 597 ASP Chi-restraints excluded: chain C residue 273 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.0770 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.9942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 456 GLN A 668 HIS B 72 ASN C 37 ASN C 179 ASN D 22 HIS D 83 ASN D 106 ASN D 179 ASN D 183 ASN F 18 ASN F 33 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.176739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.130171 restraints weight = 19264.702| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.02 r_work: 0.3087 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18064 Z= 0.164 Angle : 0.674 14.311 24651 Z= 0.347 Chirality : 0.046 0.244 2724 Planarity : 0.006 0.066 2992 Dihedral : 15.722 178.571 3133 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 3.26 % Allowed : 15.99 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.92 (0.16), residues: 2006 helix: -1.77 (0.16), residues: 784 sheet: -1.51 (0.27), residues: 283 loop : -2.15 (0.18), residues: 939 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 157 TYR 0.019 0.002 TYR A 265 PHE 0.019 0.002 PHE E 15 TRP 0.017 0.001 TRP A 131 HIS 0.005 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00365 (18051) covalent geometry : angle 0.66930 (24636) hydrogen bonds : bond 0.05235 ( 640) hydrogen bonds : angle 5.66691 ( 1818) metal coordination : bond 0.00774 ( 12) metal coordination : angle 3.55487 ( 12) link_TRANS : bond 0.00051 ( 1) link_TRANS : angle 0.36244 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 298 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: A 6 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8675 (tp) REVERT: A 21 GLN cc_start: 0.8210 (tm130) cc_final: 0.7899 (tm-30) REVERT: A 65 MET cc_start: 0.4247 (ptm) cc_final: 0.3818 (ptm) REVERT: A 71 MET cc_start: 0.8036 (mtm) cc_final: 0.7714 (mtt) REVERT: A 155 ARG cc_start: 0.8442 (ttm110) cc_final: 0.8084 (mtm-85) REVERT: A 159 LYS cc_start: 0.8583 (tmmt) cc_final: 0.7930 (tppt) REVERT: A 249 ARG cc_start: 0.8965 (ttp-170) cc_final: 0.8621 (ttp80) REVERT: A 316 LYS cc_start: 0.8557 (OUTLIER) cc_final: 0.8185 (tttt) REVERT: A 375 LYS cc_start: 0.8189 (OUTLIER) cc_final: 0.7915 (ptmt) REVERT: A 501 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8253 (p) REVERT: A 507 MET cc_start: 0.7982 (mtp) cc_final: 0.7700 (mmt) REVERT: A 633 ILE cc_start: 0.7844 (OUTLIER) cc_final: 0.7494 (mt) REVERT: A 667 LYS cc_start: 0.8438 (mtmt) cc_final: 0.8238 (mtmt) REVERT: A 755 ARG cc_start: 0.7593 (mtp85) cc_final: 0.6908 (mtp85) REVERT: A 757 GLU cc_start: 0.7781 (pt0) cc_final: 0.7223 (pt0) REVERT: B 122 LYS cc_start: 0.8258 (mttt) cc_final: 0.7948 (mttt) REVERT: B 123 MET cc_start: 0.7566 (ttt) cc_final: 0.7237 (ttm) REVERT: C 237 LYS cc_start: 0.8793 (ttpp) cc_final: 0.8379 (tptp) REVERT: D 1 MET cc_start: 0.7596 (tmt) cc_final: 0.7339 (tmt) REVERT: D 267 LYS cc_start: 0.7774 (ptmt) cc_final: 0.7573 (pttp) REVERT: E 104 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8479 (tp) REVERT: E 140 ASP cc_start: 0.8439 (m-30) cc_final: 0.8238 (m-30) REVERT: E 176 MET cc_start: 0.9031 (mmm) cc_final: 0.8383 (mmt) REVERT: E 264 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7405 (tp30) REVERT: F 1 MET cc_start: 0.4329 (ttt) cc_final: 0.4063 (ttt) REVERT: F 7 LYS cc_start: 0.7475 (OUTLIER) cc_final: 0.6839 (mmtp) REVERT: F 128 LYS cc_start: 0.5736 (tptt) cc_final: 0.5482 (tttt) REVERT: F 131 LYS cc_start: 0.5856 (mmmm) cc_final: 0.5354 (mtpp) REVERT: F 276 LYS cc_start: 0.5468 (mtpp) cc_final: 0.4891 (mmmm) outliers start: 54 outliers final: 14 residues processed: 330 average time/residue: 0.7430 time to fit residues: 269.8980 Evaluate side-chains 279 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 257 time to evaluate : 0.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 247 ILE Chi-restraints excluded: chain A residue 316 LYS Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 103 ARG Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 104 LEU Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 243 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 128 optimal weight: 0.9980 chunk 127 optimal weight: 9.9990 chunk 71 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 157 optimal weight: 2.9990 chunk 167 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.171093 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.123040 restraints weight = 19440.631| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.01 r_work: 0.2954 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18064 Z= 0.211 Angle : 0.676 14.461 24651 Z= 0.346 Chirality : 0.047 0.235 2724 Planarity : 0.006 0.063 2992 Dihedral : 15.553 176.786 3126 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.71 % Allowed : 16.29 % 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 aren not related in a simple way. whole: -2.11 (0.17), residues: 2006 helix: -0.81 (0.18), residues: 794 sheet: -1.18 (0.28), residues: 301 loop : -1.95 (0.19), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 157 TYR 0.023 0.002 TYR A 265 PHE 0.030 0.002 PHE E 15 TRP 0.016 0.002 TRP A 131 HIS 0.008 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00497 (18051) covalent geometry : angle 0.67235 (24636) hydrogen bonds : bond 0.04870 ( 640) hydrogen bonds : angle 5.29525 ( 1818) metal coordination : bond 0.01607 ( 12) metal coordination : angle 3.17225 ( 12) link_TRANS : bond 0.00045 ( 1) link_TRANS : angle 0.20386 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 265 time to evaluate : 0.476 Fit side-chains revert: symmetry clash REVERT: A 65 MET cc_start: 0.4550 (ptm) cc_final: 0.4166 (ptp) REVERT: A 71 MET cc_start: 0.8055 (mtm) cc_final: 0.7737 (mtt) REVERT: A 157 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8255 (tp) REVERT: A 158 VAL cc_start: 0.8137 (t) cc_final: 0.7836 (t) REVERT: A 159 LYS cc_start: 0.8530 (tmmt) cc_final: 0.7934 (tppt) REVERT: A 375 LYS cc_start: 0.8237 (OUTLIER) cc_final: 0.7929 (ptmt) REVERT: A 409 GLU cc_start: 0.7370 (mp0) cc_final: 0.7168 (mp0) REVERT: A 501 THR cc_start: 0.8520 (OUTLIER) cc_final: 0.8107 (p) REVERT: A 503 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: A 513 ARG cc_start: 0.8089 (mpt180) cc_final: 0.7836 (mpt180) REVERT: A 630 ARG cc_start: 0.8510 (mmt180) cc_final: 0.7696 (mpt180) REVERT: A 633 ILE cc_start: 0.8104 (OUTLIER) cc_final: 0.7790 (mt) REVERT: A 718 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7759 (mtp180) REVERT: A 755 ARG cc_start: 0.7537 (mtp85) cc_final: 0.6941 (mtp85) REVERT: A 757 GLU cc_start: 0.7754 (pt0) cc_final: 0.7234 (pt0) REVERT: A 773 MET cc_start: 0.8649 (mtp) cc_final: 0.8431 (mtp) REVERT: B 122 LYS cc_start: 0.8260 (mttt) cc_final: 0.7960 (mttt) REVERT: B 123 MET cc_start: 0.7731 (ttt) cc_final: 0.7428 (ttm) REVERT: C 164 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8216 (pt0) REVERT: C 168 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8365 (mt-10) REVERT: C 237 LYS cc_start: 0.8874 (ttpp) cc_final: 0.8443 (tptp) REVERT: D 1 MET cc_start: 0.7744 (tmt) cc_final: 0.7496 (tmt) REVERT: D 153 GLU cc_start: 0.8278 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: D 185 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7766 (ptp-170) REVERT: D 267 LYS cc_start: 0.7899 (ptmt) cc_final: 0.7691 (pttp) REVERT: E 89 ARG cc_start: 0.7011 (ttm-80) cc_final: 0.6656 (ttm-80) REVERT: E 96 LEU cc_start: 0.8821 (mt) cc_final: 0.8619 (mt) REVERT: E 129 VAL cc_start: 0.9244 (OUTLIER) cc_final: 0.8821 (t) REVERT: E 139 GLN cc_start: 0.8858 (mm-40) cc_final: 0.8403 (mt0) REVERT: E 147 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7806 (tm-30) REVERT: E 176 MET cc_start: 0.9096 (mmm) cc_final: 0.8322 (mmp) REVERT: E 262 ARG cc_start: 0.8691 (ttm110) cc_final: 0.8470 (ttm110) REVERT: E 264 GLU cc_start: 0.7639 (OUTLIER) cc_final: 0.7327 (tp30) REVERT: F 1 MET cc_start: 0.3747 (ttt) cc_final: 0.3362 (ttt) REVERT: F 3 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7120 (tp30) REVERT: F 215 LYS cc_start: 0.8578 (mptm) cc_final: 0.8117 (mmtp) REVERT: F 244 GLU cc_start: 0.7548 (pt0) cc_final: 0.7035 (pm20) outliers start: 78 outliers final: 22 residues processed: 318 average time/residue: 0.6820 time to fit residues: 239.2348 Evaluate side-chains 282 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 718 ARG Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 164 GLU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain F residue 3 GLU Chi-restraints excluded: chain F residue 7 LYS Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 332 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 2 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 173 optimal weight: 0.0070 chunk 150 optimal weight: 0.8980 chunk 108 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 65 optimal weight: 0.0980 chunk 102 optimal weight: 0.9980 chunk 119 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.176428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.129391 restraints weight = 19515.190| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.01 r_work: 0.3063 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2924 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 18064 Z= 0.115 Angle : 0.561 13.510 24651 Z= 0.286 Chirality : 0.042 0.197 2724 Planarity : 0.004 0.048 2992 Dihedral : 15.397 177.254 3125 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 3.26 % Allowed : 17.86 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.47 (0.18), residues: 2006 helix: -0.13 (0.18), residues: 802 sheet: -0.95 (0.29), residues: 291 loop : -1.70 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 74 TYR 0.014 0.001 TYR A 552 PHE 0.019 0.001 PHE B 181 TRP 0.018 0.001 TRP A 131 HIS 0.003 0.001 HIS F 254 Details of bonding type rmsd covalent geometry : bond 0.00255 (18051) covalent geometry : angle 0.55916 (24636) hydrogen bonds : bond 0.03705 ( 640) hydrogen bonds : angle 4.83132 ( 1818) metal coordination : bond 0.00423 ( 12) metal coordination : angle 2.20590 ( 12) link_TRANS : bond 0.00000 ( 1) link_TRANS : angle 0.20196 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 254 time to evaluate : 0.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.4600 (ptm) cc_final: 0.4132 (ptp) REVERT: A 71 MET cc_start: 0.8174 (mtm) cc_final: 0.7730 (mtt) REVERT: A 157 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8286 (tp) REVERT: A 158 VAL cc_start: 0.8236 (t) cc_final: 0.7960 (t) REVERT: A 159 LYS cc_start: 0.8555 (tmmt) cc_final: 0.7976 (tppt) REVERT: A 375 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7852 (ptmt) REVERT: A 501 THR cc_start: 0.8410 (OUTLIER) cc_final: 0.8027 (p) REVERT: A 503 GLU cc_start: 0.8401 (OUTLIER) cc_final: 0.7669 (mp0) REVERT: A 507 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.8187 (mmt) REVERT: A 552 TYR cc_start: 0.7888 (m-80) cc_final: 0.7610 (m-80) REVERT: A 629 GLU cc_start: 0.7670 (OUTLIER) cc_final: 0.7435 (mt-10) REVERT: A 630 ARG cc_start: 0.8456 (mmt180) cc_final: 0.7649 (mpt180) REVERT: A 633 ILE cc_start: 0.7999 (OUTLIER) cc_final: 0.7670 (mt) REVERT: A 755 ARG cc_start: 0.7515 (mtp85) cc_final: 0.6893 (mtp85) REVERT: A 757 GLU cc_start: 0.7695 (pt0) cc_final: 0.7190 (pt0) REVERT: B 122 LYS cc_start: 0.8293 (mttt) cc_final: 0.7891 (mttt) REVERT: B 123 MET cc_start: 0.7791 (ttt) cc_final: 0.7487 (ttm) REVERT: C 168 GLU cc_start: 0.9128 (OUTLIER) cc_final: 0.7848 (mp0) REVERT: C 236 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8307 (m) REVERT: C 237 LYS cc_start: 0.8773 (ttpp) cc_final: 0.8357 (tptp) REVERT: C 267 LYS cc_start: 0.8364 (pttt) cc_final: 0.7395 (ptmm) REVERT: D 107 ARG cc_start: 0.8000 (mpt-90) cc_final: 0.7684 (mpt-90) REVERT: D 153 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7975 (tt0) REVERT: E 3 LYS cc_start: 0.8923 (mtpm) cc_final: 0.8709 (ttpp) REVERT: E 139 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8477 (mt0) REVERT: E 140 ASP cc_start: 0.8458 (m-30) cc_final: 0.8236 (m-30) REVERT: E 147 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7804 (tm-30) REVERT: E 264 GLU cc_start: 0.7530 (OUTLIER) cc_final: 0.7252 (tp30) REVERT: F 4 ARG cc_start: 0.7087 (mtm-85) cc_final: 0.6599 (mtt180) REVERT: F 98 MET cc_start: 0.5510 (ptp) cc_final: 0.5197 (ptp) REVERT: F 244 GLU cc_start: 0.7643 (pt0) cc_final: 0.7233 (pm20) REVERT: F 301 MET cc_start: 0.6325 (ttm) cc_final: 0.5499 (tpp) outliers start: 54 outliers final: 17 residues processed: 291 average time/residue: 0.6611 time to fit residues: 212.4456 Evaluate side-chains 259 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 230 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 507 MET Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 264 GLU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 68 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 166 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 174 optimal weight: 2.9990 chunk 161 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 chunk 16 optimal weight: 9.9990 chunk 172 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 179 HIS C 177 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.172967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.125085 restraints weight = 19233.089| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.06 r_work: 0.2968 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 18064 Z= 0.212 Angle : 0.652 13.423 24651 Z= 0.331 Chirality : 0.047 0.228 2724 Planarity : 0.005 0.067 2992 Dihedral : 15.450 177.097 3125 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 4.16 % Allowed : 18.35 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.40 (0.18), residues: 2006 helix: -0.07 (0.18), residues: 807 sheet: -1.04 (0.28), residues: 314 loop : -1.64 (0.19), residues: 885 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 74 TYR 0.018 0.002 TYR A 265 PHE 0.020 0.002 PHE B 181 TRP 0.015 0.002 TRP C 152 HIS 0.008 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00503 (18051) covalent geometry : angle 0.64883 (24636) hydrogen bonds : bond 0.04422 ( 640) hydrogen bonds : angle 5.00835 ( 1818) metal coordination : bond 0.01723 ( 12) metal coordination : angle 2.83404 ( 12) link_TRANS : bond 0.00057 ( 1) link_TRANS : angle 0.15036 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 240 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.4732 (ptm) cc_final: 0.4450 (ptp) REVERT: A 71 MET cc_start: 0.8115 (mtm) cc_final: 0.7718 (mtt) REVERT: A 91 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8830 (tt) REVERT: A 153 ASP cc_start: 0.8062 (t0) cc_final: 0.7838 (t0) REVERT: A 158 VAL cc_start: 0.8276 (t) cc_final: 0.8012 (t) REVERT: A 159 LYS cc_start: 0.8566 (tmmt) cc_final: 0.7965 (tppt) REVERT: A 375 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7896 (ptmt) REVERT: A 501 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8240 (p) REVERT: A 503 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: A 630 ARG cc_start: 0.8583 (mmt180) cc_final: 0.7793 (mpt180) REVERT: A 633 ILE cc_start: 0.8119 (OUTLIER) cc_final: 0.7752 (mt) REVERT: A 708 LYS cc_start: 0.7115 (mmtp) cc_final: 0.6507 (mmmt) REVERT: A 718 ARG cc_start: 0.8175 (ttt180) cc_final: 0.7841 (ttt90) REVERT: A 755 ARG cc_start: 0.7452 (mtp85) cc_final: 0.6830 (mtp85) REVERT: A 757 GLU cc_start: 0.7691 (pt0) cc_final: 0.7088 (pt0) REVERT: B 122 LYS cc_start: 0.8297 (mttt) cc_final: 0.7904 (mttt) REVERT: B 123 MET cc_start: 0.7815 (ttt) cc_final: 0.7504 (ttm) REVERT: C 168 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8413 (mt-10) REVERT: C 236 VAL cc_start: 0.8920 (OUTLIER) cc_final: 0.8550 (m) REVERT: C 237 LYS cc_start: 0.8854 (ttpp) cc_final: 0.8447 (tptp) REVERT: C 263 ASP cc_start: 0.7882 (p0) cc_final: 0.7644 (p0) REVERT: C 267 LYS cc_start: 0.8409 (pttt) cc_final: 0.7439 (ptmm) REVERT: D 94 GLN cc_start: 0.7332 (tp40) cc_final: 0.6925 (tp-100) REVERT: D 107 ARG cc_start: 0.8001 (mpt-90) cc_final: 0.7548 (mtt90) REVERT: D 153 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8019 (tt0) REVERT: D 185 ARG cc_start: 0.8779 (OUTLIER) cc_final: 0.7945 (ptp-170) REVERT: E 3 LYS cc_start: 0.8952 (OUTLIER) cc_final: 0.8678 (ttpp) REVERT: E 129 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.8855 (t) REVERT: E 139 GLN cc_start: 0.8780 (mm-40) cc_final: 0.8515 (mt0) REVERT: E 147 GLU cc_start: 0.8402 (OUTLIER) cc_final: 0.7921 (tm-30) REVERT: F 1 MET cc_start: 0.3924 (OUTLIER) cc_final: 0.3342 (ttt) REVERT: F 391 MET cc_start: 0.7799 (OUTLIER) cc_final: 0.7542 (ptm) outliers start: 69 outliers final: 26 residues processed: 285 average time/residue: 0.6731 time to fit residues: 211.7287 Evaluate side-chains 269 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 229 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 563 TYR Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 14 LYS Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 269 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 3 LYS Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 98 LYS Chi-restraints excluded: chain E residue 121 GLU Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 332 VAL Chi-restraints excluded: chain F residue 345 THR Chi-restraints excluded: chain F residue 391 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 1 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 43 optimal weight: 0.0470 chunk 17 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 2 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.176633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.128945 restraints weight = 19276.292| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.06 r_work: 0.3027 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 4.44 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18064 Z= 0.117 Angle : 0.567 12.466 24651 Z= 0.287 Chirality : 0.043 0.196 2724 Planarity : 0.004 0.051 2992 Dihedral : 15.267 177.215 3125 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.32 % Allowed : 19.31 % Favored : 77.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.02 (0.18), residues: 2006 helix: 0.33 (0.19), residues: 804 sheet: -0.89 (0.28), residues: 303 loop : -1.49 (0.20), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 74 TYR 0.013 0.001 TYR A 552 PHE 0.012 0.001 PHE E 159 TRP 0.018 0.001 TRP F 393 HIS 0.004 0.001 HIS D 205 Details of bonding type rmsd covalent geometry : bond 0.00262 (18051) covalent geometry : angle 0.56530 (24636) hydrogen bonds : bond 0.03570 ( 640) hydrogen bonds : angle 4.70239 ( 1818) metal coordination : bond 0.00431 ( 12) metal coordination : angle 2.27492 ( 12) link_TRANS : bond 0.00000 ( 1) link_TRANS : angle 0.18758 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 244 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.4676 (ptm) cc_final: 0.4388 (ptp) REVERT: A 71 MET cc_start: 0.8106 (mtm) cc_final: 0.7658 (mtt) REVERT: A 91 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8806 (tp) REVERT: A 159 LYS cc_start: 0.8603 (tmmt) cc_final: 0.7973 (tppt) REVERT: A 375 LYS cc_start: 0.8205 (OUTLIER) cc_final: 0.7878 (ptmt) REVERT: A 407 ASP cc_start: 0.7498 (OUTLIER) cc_final: 0.7285 (m-30) REVERT: A 443 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8280 (tt) REVERT: A 501 THR cc_start: 0.8394 (OUTLIER) cc_final: 0.8049 (p) REVERT: A 503 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.7722 (mp0) REVERT: A 552 TYR cc_start: 0.8022 (m-80) cc_final: 0.7726 (m-80) REVERT: A 629 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7322 (mt-10) REVERT: A 630 ARG cc_start: 0.8524 (mmt180) cc_final: 0.7702 (mpt180) REVERT: A 633 ILE cc_start: 0.7915 (OUTLIER) cc_final: 0.7514 (mt) REVERT: A 755 ARG cc_start: 0.7431 (mtp85) cc_final: 0.6780 (mtp85) REVERT: A 757 GLU cc_start: 0.7593 (pt0) cc_final: 0.7059 (pt0) REVERT: A 775 VAL cc_start: 0.6604 (OUTLIER) cc_final: 0.6145 (m) REVERT: B 122 LYS cc_start: 0.8295 (mttt) cc_final: 0.7886 (mttt) REVERT: B 123 MET cc_start: 0.7749 (ttt) cc_final: 0.7522 (ttm) REVERT: C 168 GLU cc_start: 0.9149 (OUTLIER) cc_final: 0.7900 (mp0) REVERT: C 236 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8305 (m) REVERT: C 237 LYS cc_start: 0.8792 (ttpp) cc_final: 0.8364 (tptp) REVERT: C 263 ASP cc_start: 0.7736 (p0) cc_final: 0.7431 (p0) REVERT: C 267 LYS cc_start: 0.8314 (pttt) cc_final: 0.7386 (ptmm) REVERT: D 94 GLN cc_start: 0.7285 (tp40) cc_final: 0.6917 (tp-100) REVERT: D 107 ARG cc_start: 0.8040 (mpt-90) cc_final: 0.7558 (mtt90) REVERT: D 153 GLU cc_start: 0.8193 (OUTLIER) cc_final: 0.7980 (tt0) REVERT: D 185 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7940 (ptp-170) REVERT: E 3 LYS cc_start: 0.8898 (mtpm) cc_final: 0.8607 (ttpp) REVERT: E 139 GLN cc_start: 0.8722 (mm-40) cc_final: 0.8497 (mt0) REVERT: E 147 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7944 (tm-30) REVERT: E 262 ARG cc_start: 0.8566 (ttm-80) cc_final: 0.8024 (ttm-80) REVERT: F 244 GLU cc_start: 0.7732 (pt0) cc_final: 0.7214 (pm20) REVERT: F 301 MET cc_start: 0.6413 (ttm) cc_final: 0.5495 (tpp) outliers start: 55 outliers final: 21 residues processed: 279 average time/residue: 0.7079 time to fit residues: 217.7069 Evaluate side-chains 267 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 232 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 407 ASP Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 629 GLU Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 153 GLU Chi-restraints excluded: chain D residue 185 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 220 LYS Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 3 optimal weight: 0.9980 chunk 180 optimal weight: 7.9990 chunk 172 optimal weight: 0.0370 chunk 18 optimal weight: 0.6980 chunk 146 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 152 optimal weight: 0.4980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 86 optimal weight: 3.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.176978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.129981 restraints weight = 19424.514| |-----------------------------------------------------------------------------| r_work (start): 0.3315 rms_B_bonded: 2.05 r_work: 0.3038 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8207 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 18064 Z= 0.105 Angle : 0.546 10.392 24651 Z= 0.276 Chirality : 0.042 0.210 2724 Planarity : 0.004 0.046 2992 Dihedral : 15.148 177.878 3125 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.72 % Allowed : 19.61 % Favored : 77.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.74 (0.19), residues: 2006 helix: 0.73 (0.19), residues: 788 sheet: -0.93 (0.27), residues: 315 loop : -1.39 (0.20), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 694 TYR 0.012 0.001 TYR E 90 PHE 0.013 0.001 PHE E 159 TRP 0.024 0.001 TRP F 393 HIS 0.004 0.001 HIS F 254 Details of bonding type rmsd covalent geometry : bond 0.00232 (18051) covalent geometry : angle 0.54458 (24636) hydrogen bonds : bond 0.03382 ( 640) hydrogen bonds : angle 4.49388 ( 1818) metal coordination : bond 0.00498 ( 12) metal coordination : angle 2.10113 ( 12) link_TRANS : bond 0.00001 ( 1) link_TRANS : angle 0.18558 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 247 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 2 GLU cc_start: 0.5765 (pm20) cc_final: 0.5426 (pm20) REVERT: A 39 ARG cc_start: 0.7894 (mpt180) cc_final: 0.7597 (mpt180) REVERT: A 65 MET cc_start: 0.4456 (ptm) cc_final: 0.4118 (ptp) REVERT: A 71 MET cc_start: 0.8054 (mtm) cc_final: 0.7595 (mtt) REVERT: A 91 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8815 (tp) REVERT: A 159 LYS cc_start: 0.8573 (tmmt) cc_final: 0.7938 (tppt) REVERT: A 375 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7882 (ptmt) REVERT: A 443 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8004 (tt) REVERT: A 501 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.8005 (p) REVERT: A 503 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7689 (mp0) REVERT: A 552 TYR cc_start: 0.8073 (m-80) cc_final: 0.7770 (m-80) REVERT: A 577 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7771 (tt0) REVERT: A 630 ARG cc_start: 0.8468 (mmt180) cc_final: 0.7623 (mpt180) REVERT: A 735 ARG cc_start: 0.8199 (mtm-85) cc_final: 0.7824 (mtp180) REVERT: A 755 ARG cc_start: 0.7427 (mtp85) cc_final: 0.6803 (mtp85) REVERT: A 757 GLU cc_start: 0.7618 (pt0) cc_final: 0.7028 (pt0) REVERT: A 775 VAL cc_start: 0.6592 (OUTLIER) cc_final: 0.6176 (m) REVERT: B 122 LYS cc_start: 0.8306 (mttt) cc_final: 0.7960 (mttt) REVERT: B 123 MET cc_start: 0.7710 (ttt) cc_final: 0.7291 (ttm) REVERT: C 168 GLU cc_start: 0.9103 (OUTLIER) cc_final: 0.7828 (mp0) REVERT: C 236 VAL cc_start: 0.8554 (OUTLIER) cc_final: 0.8263 (m) REVERT: C 237 LYS cc_start: 0.8791 (ttpp) cc_final: 0.8347 (tptp) REVERT: C 263 ASP cc_start: 0.7731 (p0) cc_final: 0.7400 (p0) REVERT: C 267 LYS cc_start: 0.8387 (pttt) cc_final: 0.7412 (ptmm) REVERT: D 85 SER cc_start: 0.8724 (t) cc_final: 0.8486 (p) REVERT: D 94 GLN cc_start: 0.7262 (tp40) cc_final: 0.6873 (tp-100) REVERT: D 107 ARG cc_start: 0.8050 (mpt-90) cc_final: 0.7540 (mtt90) REVERT: E 3 LYS cc_start: 0.8881 (mtpm) cc_final: 0.8586 (ttpp) REVERT: E 17 ASP cc_start: 0.8495 (t0) cc_final: 0.8264 (t0) REVERT: E 35 ILE cc_start: 0.8920 (pt) cc_final: 0.8621 (mt) REVERT: E 129 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.8830 (t) REVERT: E 147 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.7871 (tm-30) REVERT: E 176 MET cc_start: 0.8945 (mmm) cc_final: 0.8299 (mmp) REVERT: F 1 MET cc_start: 0.3847 (ttt) cc_final: 0.3297 (ttt) REVERT: F 215 LYS cc_start: 0.8600 (mptm) cc_final: 0.8058 (mmtp) REVERT: F 301 MET cc_start: 0.6348 (ttm) cc_final: 0.5320 (tpp) outliers start: 45 outliers final: 22 residues processed: 280 average time/residue: 0.7084 time to fit residues: 219.2120 Evaluate side-chains 267 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 235 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 573 ASP Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 160 optimal weight: 0.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.0270 chunk 173 optimal weight: 0.0370 chunk 122 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 66 optimal weight: 0.6980 chunk 58 optimal weight: 3.9990 chunk 111 optimal weight: 0.4980 chunk 139 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 overall best weight: 0.4518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.176230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.128920 restraints weight = 19347.089| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.99 r_work: 0.3100 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18064 Z= 0.105 Angle : 0.546 10.283 24651 Z= 0.276 Chirality : 0.042 0.196 2724 Planarity : 0.004 0.068 2992 Dihedral : 15.110 177.756 3125 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.60 % Allowed : 20.58 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.54 (0.19), residues: 2006 helix: 0.94 (0.19), residues: 783 sheet: -0.88 (0.27), residues: 315 loop : -1.31 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 74 TYR 0.013 0.001 TYR E 90 PHE 0.013 0.001 PHE E 159 TRP 0.025 0.001 TRP F 393 HIS 0.006 0.001 HIS F 254 Details of bonding type rmsd covalent geometry : bond 0.00232 (18051) covalent geometry : angle 0.54422 (24636) hydrogen bonds : bond 0.03275 ( 640) hydrogen bonds : angle 4.43704 ( 1818) metal coordination : bond 0.00453 ( 12) metal coordination : angle 2.02287 ( 12) link_TRANS : bond 0.00001 ( 1) link_TRANS : angle 0.17092 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 244 time to evaluate : 0.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.4374 (ptm) cc_final: 0.4038 (ptp) REVERT: A 71 MET cc_start: 0.8087 (mtm) cc_final: 0.7675 (mtt) REVERT: A 87 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7268 (tpp) REVERT: A 91 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8844 (tp) REVERT: A 159 LYS cc_start: 0.8591 (tmmt) cc_final: 0.7936 (tppt) REVERT: A 160 ARG cc_start: 0.7184 (mmm-85) cc_final: 0.6947 (mtm180) REVERT: A 375 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7837 (ptpt) REVERT: A 443 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8190 (tt) REVERT: A 456 GLN cc_start: 0.6934 (pm20) cc_final: 0.6715 (pm20) REVERT: A 501 THR cc_start: 0.8336 (OUTLIER) cc_final: 0.8025 (p) REVERT: A 503 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7693 (mp0) REVERT: A 552 TYR cc_start: 0.8122 (m-80) cc_final: 0.7822 (m-80) REVERT: A 577 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7791 (tt0) REVERT: A 630 ARG cc_start: 0.8433 (mmt180) cc_final: 0.7630 (mpt180) REVERT: A 755 ARG cc_start: 0.7425 (mtp85) cc_final: 0.6781 (mtp85) REVERT: A 757 GLU cc_start: 0.7633 (pt0) cc_final: 0.7032 (pt0) REVERT: A 775 VAL cc_start: 0.6704 (OUTLIER) cc_final: 0.6290 (m) REVERT: B 123 MET cc_start: 0.7778 (ttt) cc_final: 0.7385 (ttm) REVERT: C 168 GLU cc_start: 0.9111 (OUTLIER) cc_final: 0.7850 (mp0) REVERT: C 236 VAL cc_start: 0.8558 (OUTLIER) cc_final: 0.8274 (m) REVERT: C 237 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8362 (tptp) REVERT: C 263 ASP cc_start: 0.7673 (p0) cc_final: 0.7287 (p0) REVERT: C 267 LYS cc_start: 0.8388 (pttt) cc_final: 0.7407 (ptmm) REVERT: D 85 SER cc_start: 0.8696 (t) cc_final: 0.8465 (p) REVERT: D 94 GLN cc_start: 0.7276 (tp40) cc_final: 0.6912 (tp-100) REVERT: D 107 ARG cc_start: 0.7967 (mpt-90) cc_final: 0.7553 (mtt180) REVERT: E 3 LYS cc_start: 0.8894 (mtpm) cc_final: 0.8602 (ttpp) REVERT: E 17 ASP cc_start: 0.8583 (t0) cc_final: 0.8356 (t0) REVERT: E 35 ILE cc_start: 0.8902 (pt) cc_final: 0.8644 (mt) REVERT: E 129 VAL cc_start: 0.9259 (OUTLIER) cc_final: 0.8830 (t) REVERT: E 147 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7843 (tm-30) REVERT: E 176 MET cc_start: 0.8941 (mmm) cc_final: 0.8361 (mmp) REVERT: F 301 MET cc_start: 0.6347 (ttm) cc_final: 0.5390 (tpp) outliers start: 43 outliers final: 22 residues processed: 279 average time/residue: 0.7024 time to fit residues: 216.1412 Evaluate side-chains 262 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 229 time to evaluate : 0.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain A residue 775 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 142 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 chunk 113 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 119 optimal weight: 4.9990 chunk 40 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 4 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 194 ASN ** C 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.174213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.125943 restraints weight = 19258.898| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.05 r_work: 0.3039 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2898 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18064 Z= 0.156 Angle : 0.593 10.163 24651 Z= 0.300 Chirality : 0.044 0.208 2724 Planarity : 0.004 0.049 2992 Dihedral : 15.140 177.456 3125 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.69 % Favored : 95.26 % Rotamer: Outliers : 2.35 % Allowed : 21.30 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.58 (0.19), residues: 2006 helix: 0.85 (0.19), residues: 795 sheet: -0.82 (0.28), residues: 313 loop : -1.33 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 74 TYR 0.014 0.001 TYR E 90 PHE 0.016 0.002 PHE E 159 TRP 0.026 0.001 TRP F 393 HIS 0.007 0.001 HIS F 254 Details of bonding type rmsd covalent geometry : bond 0.00365 (18051) covalent geometry : angle 0.59073 (24636) hydrogen bonds : bond 0.03764 ( 640) hydrogen bonds : angle 4.61318 ( 1818) metal coordination : bond 0.01037 ( 12) metal coordination : angle 2.36837 ( 12) link_TRANS : bond 0.00027 ( 1) link_TRANS : angle 0.14375 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 236 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 MET cc_start: 0.4473 (ptm) cc_final: 0.4134 (ptp) REVERT: A 71 MET cc_start: 0.8096 (mtm) cc_final: 0.7657 (mtt) REVERT: A 91 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8789 (tp) REVERT: A 159 LYS cc_start: 0.8557 (tmmt) cc_final: 0.7907 (tppt) REVERT: A 375 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7864 (ptpt) REVERT: A 443 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8222 (tt) REVERT: A 501 THR cc_start: 0.8339 (OUTLIER) cc_final: 0.8018 (p) REVERT: A 503 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: A 577 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7906 (tt0) REVERT: A 630 ARG cc_start: 0.8455 (mmt180) cc_final: 0.7629 (mpt180) REVERT: A 633 ILE cc_start: 0.7836 (tp) cc_final: 0.7394 (mt) REVERT: A 755 ARG cc_start: 0.7424 (mtp85) cc_final: 0.6767 (mtp85) REVERT: A 757 GLU cc_start: 0.7653 (pt0) cc_final: 0.7020 (pt0) REVERT: B 123 MET cc_start: 0.7826 (ttt) cc_final: 0.7474 (ttm) REVERT: C 168 GLU cc_start: 0.9181 (OUTLIER) cc_final: 0.8349 (mt-10) REVERT: C 236 VAL cc_start: 0.8764 (OUTLIER) cc_final: 0.8467 (m) REVERT: C 237 LYS cc_start: 0.8817 (ttpp) cc_final: 0.8383 (tptp) REVERT: C 263 ASP cc_start: 0.7767 (p0) cc_final: 0.7392 (p0) REVERT: C 267 LYS cc_start: 0.8423 (pttt) cc_final: 0.7470 (ptmm) REVERT: D 75 ARG cc_start: 0.7598 (ppp80) cc_final: 0.7290 (ttm170) REVERT: D 85 SER cc_start: 0.8721 (t) cc_final: 0.8481 (p) REVERT: D 94 GLN cc_start: 0.7320 (tp40) cc_final: 0.6921 (tp-100) REVERT: D 107 ARG cc_start: 0.7974 (mpt-90) cc_final: 0.7498 (mtt180) REVERT: D 267 LYS cc_start: 0.8384 (pttm) cc_final: 0.8110 (pttp) REVERT: E 17 ASP cc_start: 0.8529 (t0) cc_final: 0.8275 (t0) REVERT: E 129 VAL cc_start: 0.9214 (OUTLIER) cc_final: 0.8833 (t) REVERT: E 147 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7901 (tm-30) REVERT: E 176 MET cc_start: 0.9065 (mmm) cc_final: 0.8376 (mmp) REVERT: F 215 LYS cc_start: 0.8647 (mptm) cc_final: 0.8160 (mmtp) REVERT: F 301 MET cc_start: 0.6326 (ttm) cc_final: 0.5335 (tpp) outliers start: 39 outliers final: 23 residues processed: 264 average time/residue: 0.7034 time to fit residues: 204.7739 Evaluate side-chains 260 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 228 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 ASP Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 49 GLU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 142 VAL Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 115 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 88 optimal weight: 0.0970 chunk 32 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 100 optimal weight: 0.0570 chunk 111 optimal weight: 0.9990 chunk 162 optimal weight: 0.9980 chunk 94 optimal weight: 1.9990 chunk 113 optimal weight: 0.7980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.175804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.129006 restraints weight = 19270.668| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.92 r_work: 0.3054 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 18064 Z= 0.109 Angle : 0.553 10.243 24651 Z= 0.280 Chirality : 0.042 0.192 2724 Planarity : 0.004 0.054 2992 Dihedral : 15.045 177.679 3125 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 2.29 % Allowed : 21.30 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.43 (0.19), residues: 2006 helix: 1.08 (0.19), residues: 784 sheet: -0.80 (0.28), residues: 311 loop : -1.30 (0.20), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 74 TYR 0.015 0.001 TYR A 552 PHE 0.012 0.001 PHE E 159 TRP 0.027 0.001 TRP F 393 HIS 0.007 0.001 HIS F 254 Details of bonding type rmsd covalent geometry : bond 0.00244 (18051) covalent geometry : angle 0.55163 (24636) hydrogen bonds : bond 0.03283 ( 640) hydrogen bonds : angle 4.45101 ( 1818) metal coordination : bond 0.00461 ( 12) metal coordination : angle 2.10013 ( 12) link_TRANS : bond 0.00002 ( 1) link_TRANS : angle 0.16614 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4012 Ramachandran restraints generated. 2006 Oldfield, 0 Emsley, 2006 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 232 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 33 GLN cc_start: 0.8225 (mm-40) cc_final: 0.7907 (mm110) REVERT: A 65 MET cc_start: 0.4505 (ptm) cc_final: 0.4190 (ptp) REVERT: A 71 MET cc_start: 0.8096 (mtm) cc_final: 0.7682 (mtt) REVERT: A 87 MET cc_start: 0.8006 (OUTLIER) cc_final: 0.7377 (tpp) REVERT: A 91 LEU cc_start: 0.9063 (OUTLIER) cc_final: 0.8788 (tp) REVERT: A 159 LYS cc_start: 0.8567 (tmmt) cc_final: 0.7928 (tppt) REVERT: A 375 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7835 (ptmt) REVERT: A 501 THR cc_start: 0.8276 (OUTLIER) cc_final: 0.7971 (p) REVERT: A 503 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7641 (mp0) REVERT: A 552 TYR cc_start: 0.8003 (m-80) cc_final: 0.7727 (m-10) REVERT: A 577 GLU cc_start: 0.8213 (mt-10) cc_final: 0.7811 (tt0) REVERT: A 630 ARG cc_start: 0.8410 (mmt180) cc_final: 0.7587 (mpt180) REVERT: A 755 ARG cc_start: 0.7410 (mtp85) cc_final: 0.6748 (mtp85) REVERT: A 757 GLU cc_start: 0.7614 (pt0) cc_final: 0.6996 (pt0) REVERT: B 108 LYS cc_start: 0.7105 (mtpt) cc_final: 0.6899 (mtmt) REVERT: B 123 MET cc_start: 0.7875 (ttt) cc_final: 0.7586 (ttm) REVERT: C 168 GLU cc_start: 0.9108 (OUTLIER) cc_final: 0.7811 (mp0) REVERT: C 236 VAL cc_start: 0.8586 (OUTLIER) cc_final: 0.8307 (m) REVERT: C 237 LYS cc_start: 0.8798 (ttpp) cc_final: 0.8364 (tptp) REVERT: C 263 ASP cc_start: 0.7743 (p0) cc_final: 0.7298 (p0) REVERT: C 267 LYS cc_start: 0.8354 (pttt) cc_final: 0.7361 (ptmm) REVERT: D 85 SER cc_start: 0.8660 (t) cc_final: 0.8404 (p) REVERT: D 94 GLN cc_start: 0.7440 (tp40) cc_final: 0.7044 (tp-100) REVERT: D 107 ARG cc_start: 0.7907 (mpt-90) cc_final: 0.7434 (mtt180) REVERT: E 17 ASP cc_start: 0.8588 (t0) cc_final: 0.8323 (t0) REVERT: E 35 ILE cc_start: 0.8878 (pt) cc_final: 0.8655 (mt) REVERT: E 129 VAL cc_start: 0.9255 (OUTLIER) cc_final: 0.8820 (t) REVERT: E 147 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7905 (tm-30) REVERT: E 176 MET cc_start: 0.8956 (mmm) cc_final: 0.8389 (mmp) REVERT: F 215 LYS cc_start: 0.8655 (mptm) cc_final: 0.8189 (mmtp) REVERT: F 301 MET cc_start: 0.6307 (ttm) cc_final: 0.5420 (tpp) REVERT: F 302 LYS cc_start: 0.6233 (mmmt) cc_final: 0.5735 (mmtt) outliers start: 38 outliers final: 21 residues processed: 258 average time/residue: 0.6560 time to fit residues: 187.4084 Evaluate side-chains 257 residues out of total 1723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 87 MET Chi-restraints excluded: chain A residue 91 LEU Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 375 LYS Chi-restraints excluded: chain A residue 487 VAL Chi-restraints excluded: chain A residue 501 THR Chi-restraints excluded: chain A residue 503 GLU Chi-restraints excluded: chain A residue 638 ASP Chi-restraints excluded: chain A residue 642 GLU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 168 GLU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain C residue 236 VAL Chi-restraints excluded: chain C residue 270 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 70 ARG Chi-restraints excluded: chain D residue 260 VAL Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 129 VAL Chi-restraints excluded: chain E residue 147 GLU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 34 VAL Chi-restraints excluded: chain F residue 227 VAL Chi-restraints excluded: chain F residue 243 ILE Chi-restraints excluded: chain F residue 345 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 181 random chunks: chunk 52 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 151 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 132 optimal weight: 0.0980 chunk 144 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 53 optimal weight: 0.8980 chunk 159 optimal weight: 0.2980 chunk 101 optimal weight: 0.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 456 GLN D 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.176838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.129398 restraints weight = 19360.801| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.02 r_work: 0.3058 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2918 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.4291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 18064 Z= 0.115 Angle : 0.562 10.293 24651 Z= 0.283 Chirality : 0.043 0.450 2724 Planarity : 0.004 0.054 2992 Dihedral : 15.017 177.731 3125 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.34 % Favored : 95.61 % Rotamer: Outliers : 2.05 % Allowed : 21.54 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.19), residues: 2006 helix: 1.13 (0.19), residues: 784 sheet: -0.78 (0.28), residues: 314 loop : -1.27 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 74 TYR 0.014 0.001 TYR A 552 PHE 0.013 0.001 PHE E 159 TRP 0.030 0.001 TRP F 393 HIS 0.007 0.001 HIS F 254 Details of bonding type rmsd covalent geometry : bond 0.00263 (18051) covalent geometry : angle 0.56020 (24636) hydrogen bonds : bond 0.03322 ( 640) hydrogen bonds : angle 4.46860 ( 1818) metal coordination : bond 0.00545 ( 12) metal coordination : angle 2.02484 ( 12) link_TRANS : bond 0.00005 ( 1) link_TRANS : angle 0.16038 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7158.84 seconds wall clock time: 122 minutes 18.70 seconds (7338.70 seconds total)