Starting phenix.real_space_refine on Sun Sep 13 03:17:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o7i_0642/09_2026/6o7i_0642_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o7i_0642/09_2026/6o7i_0642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6o7i_0642/09_2026/6o7i_0642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o7i_0642/09_2026/6o7i_0642.map" model { file = "/net/cci-nas-00/data/ceres_data/6o7i_0642/09_2026/6o7i_0642_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o7i_0642/09_2026/6o7i_0642_neut.cif" } resolution = 3.2 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= 0.004 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 4 6.06 5 P 48 5.49 5 S 60 5.16 5 C 12749 2.51 5 N 3555 2.21 5 O 3860 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20276 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 5935 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 33, 'TRANS': 707} Chain breaks: 6 Chain: "B" Number of atoms: 1065 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1065 Classifications: {'peptide': 146} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 4, 'TRANS': 141} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 115 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 2, 'TRP:plan': 2, 'TYR:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 75 Chain: "C" Number of atoms: 2191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2191 Classifications: {'peptide': 275} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "D" Number of atoms: 2178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2178 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 12, 'TRANS': 259} Chain breaks: 2 Chain: "E" Number of atoms: 2207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 279, 2207 Classifications: {'peptide': 279} Link IDs: {'PTRANS': 20, 'TRANS': 258} Chain breaks: 1 Chain: "J" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 907 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 4, 'TRANS': 116} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'TRP:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'TYR:plan': 1, 'PHE:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 67 Chain: "G" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 569 Classifications: {'RNA': 26} Modifications used: {'5*END': 1, 'rna2p_pur': 10, 'rna2p_pyr': 3, 'rna3p_pur': 9, 'rna3p_pyr': 4} Link IDs: {'rna2p': 12, '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': 3, 'rna3p_pur': 6, 'rna3p_pyr': 9} Link IDs: {'rna2p': 3, 'rna3p': 15} Chain: "K" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2198 Classifications: {'peptide': 275} Link IDs: {'PTRANS': 12, 'TRANS': 262} Chain breaks: 1 Chain: "I" 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: "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: "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: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3000 SG CYS A 389 61.945 108.426 107.521 1.00 26.96 S ATOM 3020 SG CYS A 392 57.962 106.580 107.991 1.00 25.58 S ATOM 3175 SG CYS A 413 59.672 108.840 110.942 1.00 33.04 S ATOM 3195 SG CYS A 416 60.786 105.552 110.270 1.00 32.70 S ATOM 7804 SG CYS C 113 78.649 118.893 83.547 1.00 26.80 S ATOM 7871 SG CYS C 122 80.218 118.407 80.144 1.00 17.37 S ATOM 7891 SG CYS C 125 76.481 116.361 82.122 1.00 21.96 S ATOM 10000 SG CYS D 113 95.191 89.112 86.916 1.00 29.12 S ATOM 10067 SG CYS D 122 97.096 88.689 83.714 1.00 23.66 S ATOM 10087 SG CYS D 125 93.080 88.859 83.641 1.00 23.54 S ATOM 16261 SG CYS K 113 95.575 55.229 83.185 1.00 56.33 S ATOM 16328 SG CYS K 122 98.462 54.545 81.147 1.00 52.56 S ATOM 16348 SG CYS K 125 94.722 56.298 79.316 1.00 44.05 S Time building chain proxies: 4.48, per 1000 atoms: 0.22 Number of scatterers: 20276 At special positions: 0 Unit cell: (129.591, 143.748, 168.795, 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 4 29.99 S 60 16.00 P 48 15.00 O 3860 8.00 N 3555 7.00 C 12749 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: 1.52 Conformation dependent library (CDL) restraints added in 818.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 801 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 413 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 392 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 389 " pdb="ZN ZN A 801 " - pdb=" SG CYS A 416 " pdb=" ZN C 301 " pdb="ZN ZN C 301 " - pdb=" SG CYS C 113 " 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=" NE2 HIS C 111 " 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 " pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" NE2 HIS K 111 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 122 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 125 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 113 " Number of angles added : 15 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4524 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 32 sheets defined 39.0% alpha, 14.9% beta 10 base pairs and 14 stacking pairs defined. Time for finding SS restraints: 2.44 Creating SS restraints... Processing helix chain 'A' and resid 2 through 11 removed outlier: 4.378A pdb=" N ALA A 8 " --> pdb=" O ASP A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 Processing helix chain 'A' and resid 31 through 44 removed outlier: 5.210A pdb=" N PHE A 37 " --> pdb=" O GLN A 33 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU A 38 " --> pdb=" O GLY A 34 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASN A 44 " --> pdb=" O ASP A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 53 removed outlier: 3.793A pdb=" N LEU A 53 " --> pdb=" O GLU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 69 through 78 removed outlier: 3.823A pdb=" N ARG A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 106 removed outlier: 3.779A pdb=" N LEU A 91 " --> pdb=" O MET A 87 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N TRP A 95 " --> pdb=" O LEU A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 168 Processing helix chain 'A' and resid 175 through 183 removed outlier: 3.675A pdb=" N GLU A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS A 181 " --> pdb=" O PRO A 177 " (cutoff:3.500A) removed outlier: 3.587A 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 263 removed outlier: 3.511A pdb=" N LEU A 259 " --> pdb=" O THR A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 282 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: 3.715A pdb=" N LYS A 308 " --> pdb=" O PRO A 304 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLU A 309 " --> pdb=" O ASP A 305 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 343 No H-bonds generated for 'chain 'A' and resid 341 through 343' Processing helix chain 'A' and resid 351 through 356 Processing helix chain 'A' and resid 356 through 367 removed outlier: 3.564A pdb=" N HIS A 361 " --> pdb=" O LYS A 357 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS A 362 " --> pdb=" O ARG A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 425 removed outlier: 3.619A pdb=" N ASN A 417 " --> pdb=" O CYS A 413 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N LEU A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU A 422 " --> pdb=" O ARG A 418 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN A 425 " --> pdb=" O SER A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 508 removed outlier: 3.951A pdb=" N ALA A 508 " --> pdb=" O GLU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 530 removed outlier: 3.874A pdb=" N PHE A 528 " --> pdb=" O ARG A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 551 removed outlier: 3.653A pdb=" N THR A 540 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE A 549 " --> pdb=" O MET A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 553 through 559 removed outlier: 3.517A pdb=" N ILE A 557 " --> pdb=" O ILE A 553 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLY A 559 " --> pdb=" O ALA A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 561 through 566 Processing helix chain 'A' and resid 598 through 614 removed outlier: 3.848A pdb=" N PHE A 604 " --> pdb=" O PHE A 600 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA A 612 " --> pdb=" O ARG A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 650 removed outlier: 3.996A pdb=" N VAL A 640 " --> pdb=" O MET A 636 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU A 642 " --> pdb=" O ASP A 638 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP A 645 " --> pdb=" O SER A 641 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 650 " --> pdb=" O THR A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 674 through 684 removed outlier: 3.772A pdb=" N ARG A 682 " --> pdb=" O GLU A 678 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N THR A 683 " --> pdb=" O GLU A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 703 through 713 removed outlier: 3.524A pdb=" N TRP A 707 " --> pdb=" O LYS A 703 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N LEU A 709 " --> pdb=" O LEU A 705 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N LEU A 710 " --> pdb=" O LEU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 719 removed outlier: 3.934A pdb=" N VAL A 717 " --> pdb=" O ARG A 713 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG A 718 " --> pdb=" O GLU A 714 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASP A 719 " --> pdb=" O LEU A 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 713 through 719' Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.547A pdb=" N LEU A 728 " --> pdb=" O ARG A 724 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 729 " --> pdb=" O TRP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 774 removed outlier: 4.421A pdb=" N ILE A 770 " --> pdb=" O GLY A 766 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL A 771 " --> pdb=" O VAL A 767 " (cutoff:3.500A) Processing helix chain 'B' and resid 45 through 49 removed outlier: 4.373A pdb=" N TRP B 49 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 63 Processing helix chain 'B' and resid 72 through 84 removed outlier: 3.736A pdb=" N THR B 80 " --> pdb=" O ALA B 76 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA B 82 " --> pdb=" O ALA B 78 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N TYR B 84 " --> pdb=" O THR B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 110 removed outlier: 3.695A pdb=" N LEU B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 126 removed outlier: 4.056A pdb=" N ARG B 124 " --> pdb=" O LEU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 147 removed outlier: 3.990A pdb=" N ARG B 147 " --> pdb=" O ASP B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 183 removed outlier: 3.863A pdb=" N GLN B 173 " --> pdb=" O TYR B 169 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL B 175 " --> pdb=" O PHE B 171 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N VAL B 176 " --> pdb=" O LEU B 172 " (cutoff:3.500A) Processing helix chain 'C' and resid 51 through 70 removed outlier: 3.595A pdb=" N LEU C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ARG C 58 " --> pdb=" O SER C 54 " (cutoff:3.500A) Processing helix chain 'C' and resid 115 through 120 removed outlier: 3.631A pdb=" N ALA C 119 " --> pdb=" O ASP C 115 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 129 Processing helix chain 'C' and resid 149 through 155 Processing helix chain 'C' and resid 205 through 220 removed outlier: 3.532A pdb=" N LEU C 220 " --> pdb=" O ALA C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 247 through 254 removed outlier: 3.792A pdb=" N TYR C 251 " --> pdb=" O PRO C 247 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 285 removed outlier: 3.614A pdb=" N GLY C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 70 removed outlier: 4.052A pdb=" N ARG D 58 " --> pdb=" O SER D 54 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER D 61 " --> pdb=" O GLY D 57 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 62 " --> pdb=" O ARG D 58 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ILE D 65 " --> pdb=" O SER D 61 " (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 149 through 158 removed outlier: 3.714A pdb=" N GLU D 154 " --> pdb=" O LYS D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 223 Processing helix chain 'D' and resid 249 through 254 Processing helix chain 'D' and resid 280 through 287 Processing helix chain 'E' and resid 20 through 36 removed outlier: 3.728A pdb=" N ALA E 27 " --> pdb=" O THR E 23 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ALA E 34 " --> pdb=" O ASN E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 51 Processing helix chain 'E' and resid 70 through 74 removed outlier: 3.895A pdb=" N VAL E 73 " --> pdb=" O PRO E 70 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLU E 74 " --> pdb=" O LEU E 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 70 through 74' Processing helix chain 'E' and resid 76 through 81 removed outlier: 3.602A pdb=" N ILE E 80 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU E 81 " --> pdb=" O LEU E 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 76 through 81' Processing helix chain 'E' and resid 90 through 99 removed outlier: 3.599A pdb=" N ALA E 99 " --> pdb=" O ARG E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 111 Processing helix chain 'E' and resid 164 through 171 removed outlier: 4.003A pdb=" N PHE E 168 " --> pdb=" O PRO E 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 179 Processing helix chain 'J' and resid 51 through 63 Processing helix chain 'J' and resid 72 through 83 removed outlier: 3.676A pdb=" N THR J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) Processing helix chain 'J' and resid 95 through 100 Processing helix chain 'J' and resid 100 through 108 removed outlier: 3.822A pdb=" N THR J 104 " --> pdb=" O ASP J 100 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR J 105 " --> pdb=" O MET J 101 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N GLU J 106 " --> pdb=" O ALA J 102 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU J 107 " --> pdb=" O ARG J 103 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LYS J 108 " --> pdb=" O THR J 104 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 100 through 108' Processing helix chain 'J' and resid 117 through 132 removed outlier: 4.311A pdb=" N VAL J 121 " --> pdb=" O LYS J 117 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N THR J 130 " --> pdb=" O LEU J 126 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N VAL J 131 " --> pdb=" O LEU J 127 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 155 removed outlier: 4.257A pdb=" N VAL J 155 " --> pdb=" O PRO J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 165 through 178 removed outlier: 3.874A pdb=" N VAL J 176 " --> pdb=" O LEU J 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 62 removed outlier: 3.702A pdb=" N ARG K 58 " --> pdb=" O SER K 54 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 69 Processing helix chain 'K' and resid 115 through 120 Processing helix chain 'K' and resid 149 through 157 removed outlier: 4.197A pdb=" N LYS K 155 " --> pdb=" O GLU K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 206 through 223 Processing helix chain 'K' and resid 249 through 254 Processing helix chain 'K' and resid 267 through 272 removed outlier: 3.572A pdb=" N ILE K 272 " --> pdb=" O SER K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 275 through 280 Processing helix chain 'K' and resid 280 through 287 Processing helix chain 'F' and resid 36 through 44 No H-bonds generated for 'chain 'F' and resid 36 through 44' Processing helix chain 'F' and resid 51 through 60 removed outlier: 3.572A pdb=" N UNK F 55 " --> pdb=" O UNK F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 133 removed outlier: 3.785A pdb=" N LEU F 117 " --> pdb=" O PRO F 113 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ALA F 124 " --> pdb=" O ALA F 120 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N CYS F 133 " --> pdb=" O ALA F 129 " (cutoff:3.500A) Processing helix chain 'F' and resid 160 through 169 removed outlier: 3.716A pdb=" N UNK F 166 " --> pdb=" O UNK F 162 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 185 removed outlier: 3.785A pdb=" N UNK F 183 " --> pdb=" O UNK F 179 " (cutoff:3.500A) 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 262 removed outlier: 3.505A pdb=" N LEU F 260 " --> pdb=" O ASP F 256 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG F 261 " --> pdb=" O THR F 257 " (cutoff:3.500A) Processing helix chain 'F' and resid 284 through 297 removed outlier: 3.654A pdb=" N ALA F 292 " --> pdb=" O PHE F 288 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR F 297 " --> pdb=" O VAL F 293 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 304 Processing helix chain 'F' and resid 317 through 324 Processing helix chain 'F' and resid 340 through 344 removed outlier: 3.666A pdb=" N ALA F 343 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N MET F 344 " --> pdb=" O TRP F 341 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 340 through 344' Processing helix chain 'F' and resid 345 through 352 removed outlier: 4.099A pdb=" N LEU F 348 " --> pdb=" O THR F 345 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N VAL F 351 " --> pdb=" O LEU F 348 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU F 352 " --> pdb=" O LEU F 349 " (cutoff:3.500A) Processing helix chain 'F' and resid 354 through 365 removed outlier: 4.025A pdb=" N VAL F 360 " --> pdb=" O LYS F 356 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LYS F 362 " --> pdb=" O GLU F 358 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LYS F 363 " --> pdb=" O ASN F 359 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.622A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N HIS A 295 " --> pdb=" O ASN A 291 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 291 removed outlier: 6.622A pdb=" N MET A 297 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASN A 291 " --> pdb=" O HIS A 295 " (cutoff:3.500A) removed outlier: 5.481A 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 402 through 403 Processing sheet with id=AA5, first strand: chain 'A' and resid 444 through 445 removed outlier: 3.639A pdb=" N VAL A 444 " --> pdb=" O PHE A 451 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 464 " --> pdb=" O ARG A 434 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 580 through 585 removed outlier: 6.585A pdb=" N PHE A 591 " --> pdb=" O VAL A 583 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 594 " --> pdb=" O GLY A 516 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 654 through 655 Processing sheet with id=AA8, first strand: chain 'C' and resid 49 through 50 removed outlier: 4.398A pdb=" N GLU C 195 " --> pdb=" O ARG C 144 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ALA C 146 " --> pdb=" O GLU C 193 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N GLU C 193 " --> pdb=" O ALA C 146 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU C 148 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N GLU C 191 " --> pdb=" O LEU C 148 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 190 " --> pdb=" O ALA C 17 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL C 10 " --> pdb=" O PHE C 243 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N PHE C 243 " --> pdb=" O VAL C 10 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N LYS C 12 " --> pdb=" O ASP C 241 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE C 243 " --> pdb=" O SER C 261 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 261 " --> pdb=" O PHE C 243 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 85 through 88 removed outlier: 7.316A pdb=" N SER C 85 " --> pdb=" O PHE C 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 103 through 104 Processing sheet with id=AB2, first strand: chain 'C' and resid 166 through 171 Processing sheet with id=AB3, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.702A pdb=" N PHE D 147 " --> pdb=" O GLU D 193 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 141 through 143 removed outlier: 3.589A pdb=" N PHE D 194 " --> pdb=" O GLY D 13 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N GLY D 13 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLY D 7 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL D 10 " --> pdb=" O PHE D 243 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N PHE D 243 " --> pdb=" O VAL D 10 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LYS D 12 " --> pdb=" O ASP D 241 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N PHE D 243 " --> pdb=" O SER D 261 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 85 through 88 removed outlier: 5.247A pdb=" N SER D 85 " --> pdb=" O LYS D 99 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N PHE D 101 " --> pdb=" O SER D 85 " (cutoff:3.500A) removed outlier: 7.573A pdb=" N GLY D 87 " --> pdb=" O PHE D 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 103 through 104 Processing sheet with id=AB7, first strand: chain 'D' and resid 163 through 168 Processing sheet with id=AB8, first strand: chain 'E' and resid 58 through 61 removed outlier: 8.185A pdb=" N SER E 155 " --> pdb=" O PRO E 11 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL E 157 " --> pdb=" O LEU E 9 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 66 through 68 Processing sheet with id=AC1, first strand: chain 'E' and resid 124 through 132 Processing sheet with id=AC2, first strand: chain 'E' and resid 251 through 254 removed outlier: 4.022A pdb=" N SER E 251 " --> pdb=" O THR E 214 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR E 211 " --> pdb=" O VAL E 282 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 229 through 232 Processing sheet with id=AC4, first strand: chain 'E' and resid 235 through 236 Processing sheet with id=AC5, first strand: chain 'E' and resid 261 through 263 removed outlier: 3.806A pdb=" N VAL E 271 " --> pdb=" O LEU E 263 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'K' and resid 141 through 143 removed outlier: 3.963A pdb=" N GLY K 7 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE K 147 " --> pdb=" O GLU K 193 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'K' and resid 141 through 143 removed outlier: 3.963A pdb=" N GLY K 7 " --> pdb=" O VAL K 200 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL K 10 " --> pdb=" O PHE K 243 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N PHE K 243 " --> pdb=" O VAL K 10 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N LYS K 12 " --> pdb=" O ASP K 241 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ASP K 241 " --> pdb=" O LYS K 12 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N PHE K 243 " --> pdb=" O SER K 261 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 85 through 88 removed outlier: 7.057A pdb=" N SER K 85 " --> pdb=" O PHE K 100 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'K' and resid 103 through 104 Processing sheet with id=AD1, first strand: chain 'K' and resid 163 through 168 removed outlier: 3.721A pdb=" N ARG K 181 " --> pdb=" O GLU K 168 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 248 through 251 Processing sheet with id=AD3, first strand: chain 'F' and resid 19 through 20 removed outlier: 3.668A pdb=" N ILE F 100 " --> pdb=" O LEU F 20 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'F' and resid 209 through 211 Processing sheet with id=AD5, first strand: chain 'F' and resid 237 through 243 removed outlier: 3.723A pdb=" N LEU F 385 " --> pdb=" O GLU F 228 " (cutoff:3.500A) 653 hydrogen bonds defined for protein. 1890 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 26 hydrogen bonds 48 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 14 stacking parallelities Total time for adding SS restraints: 3.55 Time building geometry restraints manager: 2.12 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: 4689 1.33 - 1.45: 4928 1.45 - 1.57: 10990 1.57 - 1.69: 93 1.69 - 1.82: 97 Bond restraints: 20797 Sorted by residual: bond pdb=" C5 A G 6 " pdb=" C4 A G 6 " ideal model delta sigma weight residual 1.383 1.348 0.035 7.00e-03 2.04e+04 2.44e+01 bond pdb=" N9 A G 5 " pdb=" C4 A G 5 " ideal model delta sigma weight residual 1.374 1.346 0.028 6.00e-03 2.78e+04 2.11e+01 bond pdb=" N ILE C 23 " pdb=" CA ILE C 23 " ideal model delta sigma weight residual 1.458 1.496 -0.038 9.00e-03 1.23e+04 1.82e+01 bond pdb=" N7 A G 6 " pdb=" C5 A G 6 " ideal model delta sigma weight residual 1.388 1.363 0.025 6.00e-03 2.78e+04 1.75e+01 bond pdb=" C5 A G 7 " pdb=" C4 A G 7 " ideal model delta sigma weight residual 1.383 1.355 0.028 7.00e-03 2.04e+04 1.56e+01 ... (remaining 20792 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 26235 2.10 - 4.20: 1730 4.20 - 6.30: 261 6.30 - 8.39: 72 8.39 - 10.49: 15 Bond angle restraints: 28313 Sorted by residual: angle pdb=" N1 C H 33 " pdb=" C6 C H 33 " pdb=" C5 C H 33 " ideal model delta sigma weight residual 121.00 124.77 -3.77 5.00e-01 4.00e+00 5.68e+01 angle pdb=" C3' C H 33 " pdb=" O3' C H 33 " pdb=" P G H 34 " ideal model delta sigma weight residual 119.70 126.93 -7.23 1.20e+00 6.94e-01 3.63e+01 angle pdb=" N ASP D 2 " pdb=" CA ASP D 2 " pdb=" C ASP D 2 " ideal model delta sigma weight residual 110.91 117.26 -6.35 1.17e+00 7.31e-01 2.94e+01 angle pdb=" C2 C H 33 " pdb=" N1 C H 33 " pdb=" C6 C H 33 " ideal model delta sigma weight residual 120.30 118.14 2.16 4.00e-01 6.25e+00 2.91e+01 angle pdb=" O4' A I 3 " pdb=" C1' A I 3 " pdb=" N9 A I 3 " ideal model delta sigma weight residual 108.50 112.15 -3.65 7.00e-01 2.04e+00 2.72e+01 ... (remaining 28308 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.33: 12200 33.33 - 66.65: 258 66.65 - 99.98: 28 99.98 - 133.31: 0 133.31 - 166.64: 1 Dihedral angle restraints: 12487 sinusoidal: 5431 harmonic: 7056 Sorted by residual: dihedral pdb=" O4' C G 14 " pdb=" C1' C G 14 " pdb=" N1 C G 14 " pdb=" C2 C G 14 " ideal model delta sinusoidal sigma weight residual -128.00 38.64 -166.64 1 1.70e+01 3.46e-03 6.55e+01 dihedral pdb=" O4' U H 29 " pdb=" C1' U H 29 " pdb=" N1 U H 29 " pdb=" C2 U H 29 " ideal model delta sinusoidal sigma weight residual -160.00 -79.30 -80.70 1 1.50e+01 4.44e-03 3.58e+01 dihedral pdb=" CA LYS A 369 " pdb=" C LYS A 369 " pdb=" N ARG A 370 " pdb=" CA ARG A 370 " ideal model delta harmonic sigma weight residual -180.00 -150.95 -29.05 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 12484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2313 0.073 - 0.147: 655 0.147 - 0.220: 123 0.220 - 0.293: 22 0.293 - 0.367: 8 Chirality restraints: 3121 Sorted by residual: chirality pdb=" CB VAL E 157 " pdb=" CA VAL E 157 " pdb=" CG1 VAL E 157 " pdb=" CG2 VAL E 157 " both_signs ideal model delta sigma weight residual False -2.63 -2.26 -0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB VAL E 132 " pdb=" CA VAL E 132 " pdb=" CG1 VAL E 132 " pdb=" CG2 VAL E 132 " both_signs ideal model delta sigma weight residual False -2.63 -2.27 -0.36 2.00e-01 2.50e+01 3.24e+00 chirality pdb=" CB VAL C 236 " pdb=" CA VAL C 236 " pdb=" CG1 VAL C 236 " pdb=" CG2 VAL C 236 " both_signs ideal model delta sigma weight residual False -2.63 -2.28 -0.35 2.00e-01 2.50e+01 3.09e+00 ... (remaining 3118 not shown) Planarity restraints: 3463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G G 13 " -0.048 2.00e-02 2.50e+03 2.01e-02 1.21e+01 pdb=" N9 G G 13 " 0.045 2.00e-02 2.50e+03 pdb=" C8 G G 13 " 0.005 2.00e-02 2.50e+03 pdb=" N7 G G 13 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G G 13 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G G 13 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G G 13 " -0.019 2.00e-02 2.50e+03 pdb=" N1 G G 13 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G G 13 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G G 13 " 0.000 2.00e-02 2.50e+03 pdb=" N3 G G 13 " 0.007 2.00e-02 2.50e+03 pdb=" C4 G G 13 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS A 389 " -0.057 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 390 " 0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 390 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 390 " -0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 13 " -0.055 5.00e-02 4.00e+02 8.28e-02 1.10e+01 pdb=" N PRO E 14 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO E 14 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 14 " -0.045 5.00e-02 4.00e+02 ... (remaining 3460 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 701 2.68 - 3.24: 18184 3.24 - 3.79: 31840 3.79 - 4.35: 42398 4.35 - 4.90: 71151 Nonbonded interactions: 164274 Sorted by model distance: nonbonded pdb=" O2' G G 9 " pdb=" C5 C G 10 " model vdw 2.131 3.340 nonbonded pdb=" O2' C G 10 " pdb=" O5' G G 11 " model vdw 2.203 3.040 nonbonded pdb=" O THR A 435 " pdb=" OG SER A 449 " model vdw 2.244 3.040 nonbonded pdb=" OE2 GLU C 168 " pdb=" OH TYR C 233 " model vdw 2.244 3.040 nonbonded pdb=" O ARG B 124 " pdb=" OH TYR J 178 " model vdw 2.251 3.040 ... (remaining 164269 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 24 or resid 38 through 272 or resid 276 through \ 301)) selection = (chain 'D' and (resid 4 through 24 or resid 38 through 301)) selection = (chain 'K' and (resid 4 through 24 or resid 38 through 272 or resid 276 through \ 301)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.380 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 23.160 Find NCS groups from input model: 0.240 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:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 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 : 0.013 0.636 20814 Z= 0.563 Angle : 1.233 43.218 28331 Z= 0.699 Chirality : 0.072 0.367 3121 Planarity : 0.008 0.087 3462 Dihedral : 13.656 166.637 7960 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.04 % Allowed : 8.17 % Favored : 91.78 % Rotamer: Outliers : 1.03 % Allowed : 5.28 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.51 (0.14), residues: 2325 helix: -3.32 (0.12), residues: 803 sheet: -2.61 (0.24), residues: 348 loop : -2.84 (0.15), residues: 1174 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.002 ARG E 177 TYR 0.044 0.004 TYR A 265 PHE 0.043 0.005 PHE A 502 TRP 0.037 0.005 TRP A 131 HIS 0.015 0.003 HIS A 14 Details of bonding type rmsd/Z covalent geometry : bond 0.01192 / 0.55 (20797) covalent geometry : angle 1.17881 / 0.69 (28313) hydrogen bonds : bond 0.17065 / 11.01 ( 663) hydrogen bonds : angle 8.37625 / 5.87 ( 1938) metal coordination : bond 0.19429 / 14.56 ( 16) metal coordination : angle 15.75742 / 8.91 ( 15) link_TRANS : bond 0.00202 / 0.11 ( 1) link_TRANS : angle 0.23009 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 422 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 PHE cc_start: 0.8136 (m-80) cc_final: 0.7924 (m-10) REVERT: A 159 LYS cc_start: 0.8263 (tmmt) cc_final: 0.7932 (mmmm) REVERT: A 493 LYS cc_start: 0.7926 (ptpp) cc_final: 0.7669 (mtmm) REVERT: A 600 PHE cc_start: 0.7789 (t80) cc_final: 0.7468 (t80) REVERT: A 711 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6807 (mm-30) REVERT: B 152 MET cc_start: 0.6926 (mtm) cc_final: 0.5890 (mmt) REVERT: E 128 ASP cc_start: 0.8059 (p0) cc_final: 0.7698 (p0) REVERT: J 101 MET cc_start: 0.3046 (tpt) cc_final: 0.2532 (tpt) REVERT: K 181 ARG cc_start: 0.7003 (pmt170) cc_final: 0.4809 (pmt170) REVERT: F 262 LEU cc_start: 0.7431 (mt) cc_final: 0.6450 (tp) REVERT: F 283 GLU cc_start: 0.4352 (tm-30) cc_final: 0.4146 (mm-30) REVERT: F 344 MET cc_start: 0.4155 (mmm) cc_final: 0.2337 (tmm) REVERT: F 391 MET cc_start: -0.0444 (ptm) cc_final: -0.1081 (ptm) outliers start: 20 outliers final: 7 residues processed: 434 average time/residue: 0.1885 time to fit residues: 116.7689 Evaluate side-chains 288 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 281 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain E residue 132 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 98 optimal weight: 4.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.4980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 20.0000 chunk 77 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN B 72 ASN C 22 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS E 139 GLN E 200 HIS K 22 HIS K 179 ASN F 18 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.199922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.153568 restraints weight = 25522.350| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.56 r_work: 0.3149 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3149 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.1959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 20814 Z= 0.168 Angle : 0.685 11.925 28331 Z= 0.357 Chirality : 0.046 0.244 3121 Planarity : 0.006 0.063 3462 Dihedral : 14.324 170.469 3472 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Rotamer: Outliers : 2.41 % Allowed : 8.41 % Favored : 89.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.61 (0.15), residues: 2325 helix: -2.14 (0.15), residues: 869 sheet: -2.19 (0.26), residues: 326 loop : -2.63 (0.16), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 126 TYR 0.018 0.002 TYR B 125 PHE 0.025 0.002 PHE A 561 TRP 0.022 0.002 TRP A 131 HIS 0.005 0.001 HIS E 200 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 (20797) covalent geometry : angle 0.67683 / 0.36 (28313) hydrogen bonds : bond 0.05144 / 3.42 ( 663) hydrogen bonds : angle 5.82534 / 4.16 ( 1938) metal coordination : bond 0.00744 / 0.39 ( 16) metal coordination : angle 4.77291 / 2.52 ( 15) link_TRANS : bond 0.00003 / 0.00 ( 1) link_TRANS : angle 0.22824 / 0.12 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 313 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LEU cc_start: 0.7910 (mt) cc_final: 0.7698 (mp) REVERT: A 124 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7495 (t0) REVERT: A 155 ARG cc_start: 0.7566 (ttp-110) cc_final: 0.7203 (mtm110) REVERT: A 156 GLU cc_start: 0.7171 (tp30) cc_final: 0.6871 (tp30) REVERT: A 159 LYS cc_start: 0.8390 (tmmt) cc_final: 0.8009 (mmtm) REVERT: A 298 ILE cc_start: 0.9055 (pt) cc_final: 0.8795 (mt) REVERT: A 326 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7957 (pt0) REVERT: A 385 ARG cc_start: 0.7802 (tpp80) cc_final: 0.7591 (mmm160) REVERT: A 438 ASN cc_start: 0.7797 (p0) cc_final: 0.7445 (p0) REVERT: A 493 LYS cc_start: 0.8023 (ptpp) cc_final: 0.7714 (mtmm) REVERT: A 532 MET cc_start: 0.8960 (mpp) cc_final: 0.8499 (mpp) REVERT: A 533 ASP cc_start: 0.8234 (p0) cc_final: 0.7958 (p0) REVERT: A 545 MET cc_start: 0.8807 (tpt) cc_final: 0.8588 (tpp) REVERT: A 600 PHE cc_start: 0.7810 (t80) cc_final: 0.7548 (t80) REVERT: A 729 THR cc_start: 0.8103 (m) cc_final: 0.7803 (t) REVERT: A 733 LEU cc_start: 0.8497 (mt) cc_final: 0.8205 (tt) REVERT: B 152 MET cc_start: 0.6516 (mtm) cc_final: 0.5346 (mmt) REVERT: B 157 MET cc_start: 0.4550 (tpp) cc_final: 0.4252 (tpp) REVERT: C 172 ASP cc_start: 0.8614 (t70) cc_final: 0.8338 (t0) REVERT: E 128 ASP cc_start: 0.8389 (p0) cc_final: 0.8154 (p0) REVERT: E 205 ASP cc_start: 0.8087 (t0) cc_final: 0.7270 (p0) REVERT: K 62 LEU cc_start: 0.8522 (mp) cc_final: 0.8309 (mp) REVERT: K 181 ARG cc_start: 0.7372 (pmt170) cc_final: 0.5808 (pmt170) REVERT: K 236 VAL cc_start: 0.8798 (OUTLIER) cc_final: 0.8294 (m) REVERT: K 250 TYR cc_start: 0.8830 (t80) cc_final: 0.8530 (t80) REVERT: K 263 ASP cc_start: 0.6613 (p0) cc_final: 0.6286 (p0) REVERT: K 265 ARG cc_start: 0.7987 (mtm180) cc_final: 0.7737 (tpt90) REVERT: F 262 LEU cc_start: 0.7296 (mt) cc_final: 0.6550 (tp) REVERT: F 280 GLU cc_start: 0.3706 (tt0) cc_final: 0.1884 (pt0) REVERT: F 284 VAL cc_start: 0.3825 (OUTLIER) cc_final: 0.3595 (p) REVERT: F 286 GLU cc_start: 0.5941 (tm-30) cc_final: 0.5239 (pm20) REVERT: F 289 LEU cc_start: 0.7835 (tp) cc_final: 0.7336 (mt) REVERT: F 344 MET cc_start: 0.2948 (mmm) cc_final: 0.0524 (tmm) REVERT: F 391 MET cc_start: -0.1126 (ptm) cc_final: -0.1688 (ptm) outliers start: 47 outliers final: 24 residues processed: 341 average time/residue: 0.1818 time to fit residues: 90.6681 Evaluate side-chains 279 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 252 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain A residue 773 MET Chi-restraints excluded: chain C residue 23 ILE Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain K residue 236 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 284 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 61 optimal weight: 1.9990 chunk 178 optimal weight: 40.0000 chunk 99 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 141 optimal weight: 3.9990 chunk 200 optimal weight: 0.6980 chunk 176 optimal weight: 30.0000 chunk 186 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN C 205 HIS J 173 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.198378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.152844 restraints weight = 25597.218| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 3.59 r_work: 0.3104 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 20814 Z= 0.195 Angle : 0.650 11.499 28331 Z= 0.335 Chirality : 0.046 0.284 3121 Planarity : 0.005 0.056 3462 Dihedral : 14.151 169.032 3470 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.98 % Allowed : 10.67 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.99 (0.16), residues: 2325 helix: -1.47 (0.16), residues: 870 sheet: -1.96 (0.26), residues: 333 loop : -2.39 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 75 TYR 0.019 0.002 TYR A 98 PHE 0.035 0.002 PHE A 561 TRP 0.015 0.001 TRP C 156 HIS 0.007 0.001 HIS C 205 Details of bonding type rmsd/Z covalent geometry : bond 0.00457 / 0.19 (20797) covalent geometry : angle 0.64436 / 0.33 (28313) hydrogen bonds : bond 0.04586 / 3.08 ( 663) hydrogen bonds : angle 5.37256 / 3.84 ( 1938) metal coordination : bond 0.00821 / 0.59 ( 16) metal coordination : angle 3.82650 / 2.08 ( 15) link_TRANS : bond 0.00007 / 0.00 ( 1) link_TRANS : angle 0.20770 / 0.10 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 266 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.8003 (tm-30) REVERT: A 78 LEU cc_start: 0.7950 (mt) cc_final: 0.7706 (mp) REVERT: A 124 ASN cc_start: 0.7902 (OUTLIER) cc_final: 0.7619 (t0) REVERT: A 155 ARG cc_start: 0.7454 (ttp-110) cc_final: 0.6999 (ttm110) REVERT: A 159 LYS cc_start: 0.8401 (tmmt) cc_final: 0.7980 (mmtm) REVERT: A 160 ARG cc_start: 0.7576 (ttp-170) cc_final: 0.7361 (mtm-85) REVERT: A 298 ILE cc_start: 0.9086 (pt) cc_final: 0.8870 (mt) REVERT: A 326 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7959 (pt0) REVERT: A 493 LYS cc_start: 0.7963 (ptpp) cc_final: 0.7678 (mtmm) REVERT: A 533 ASP cc_start: 0.8272 (p0) cc_final: 0.7920 (p0) REVERT: A 558 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 600 PHE cc_start: 0.7886 (t80) cc_final: 0.7591 (t80) REVERT: B 152 MET cc_start: 0.6405 (mtm) cc_final: 0.5329 (mmt) REVERT: B 153 LEU cc_start: 0.6055 (mm) cc_final: 0.5797 (mt) REVERT: D 115 ASP cc_start: 0.8178 (m-30) cc_final: 0.7942 (m-30) REVERT: E 22 ASP cc_start: 0.8151 (OUTLIER) cc_final: 0.7892 (m-30) REVERT: E 205 ASP cc_start: 0.8055 (t0) cc_final: 0.7264 (p0) REVERT: J 101 MET cc_start: 0.3691 (tpt) cc_final: 0.3216 (tpt) REVERT: K 62 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8356 (mp) REVERT: K 153 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.6896 (mm-30) REVERT: K 236 VAL cc_start: 0.8885 (m) cc_final: 0.8477 (m) REVERT: K 250 TYR cc_start: 0.8880 (t80) cc_final: 0.8608 (t80) REVERT: K 263 ASP cc_start: 0.6823 (p0) cc_final: 0.6467 (p0) REVERT: K 265 ARG cc_start: 0.8022 (mtm180) cc_final: 0.7745 (tpt90) REVERT: F 262 LEU cc_start: 0.7176 (mt) cc_final: 0.6407 (tp) REVERT: F 284 VAL cc_start: 0.3888 (OUTLIER) cc_final: 0.3416 (p) REVERT: F 286 GLU cc_start: 0.6274 (tm-30) cc_final: 0.5513 (pm20) REVERT: F 289 LEU cc_start: 0.7881 (tp) cc_final: 0.7324 (mt) REVERT: F 301 MET cc_start: -0.1369 (ttm) cc_final: -0.2160 (ttm) REVERT: F 344 MET cc_start: 0.3024 (mmm) cc_final: 0.0631 (tmm) outliers start: 58 outliers final: 31 residues processed: 304 average time/residue: 0.1711 time to fit residues: 77.4885 Evaluate side-chains 277 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 240 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 204 THR Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 62 LEU Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 284 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 91 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 196 optimal weight: 0.6980 chunk 207 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 179 optimal weight: 10.0000 chunk 178 optimal weight: 0.7980 chunk 144 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 382 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.200519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.157789 restraints weight = 25766.958| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 3.54 r_work: 0.3140 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.2646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 20814 Z= 0.126 Angle : 0.585 14.363 28331 Z= 0.300 Chirality : 0.044 0.256 3121 Planarity : 0.005 0.049 3462 Dihedral : 14.040 173.682 3468 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.87 % Allowed : 11.49 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.55 (0.16), residues: 2325 helix: -1.02 (0.17), residues: 870 sheet: -1.77 (0.27), residues: 337 loop : -2.18 (0.17), residues: 1118 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 207 TYR 0.027 0.001 TYR A 26 PHE 0.021 0.001 PHE A 561 TRP 0.012 0.001 TRP A 162 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (20797) covalent geometry : angle 0.58004 / 0.30 (28313) hydrogen bonds : bond 0.04060 / 2.75 ( 663) hydrogen bonds : angle 5.01666 / 3.58 ( 1938) metal coordination : bond 0.00986 / 0.67 ( 16) metal coordination : angle 3.43841 / 1.83 ( 15) link_TRANS : bond 0.00007 / 0.00 ( 1) link_TRANS : angle 0.18895 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 277 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8249 (OUTLIER) cc_final: 0.7998 (tm-30) REVERT: A 36 ARG cc_start: 0.7460 (mtp-110) cc_final: 0.7218 (ttt-90) REVERT: A 124 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7484 (t0) REVERT: A 155 ARG cc_start: 0.7464 (ttp-110) cc_final: 0.7166 (mtm110) REVERT: A 159 LYS cc_start: 0.8401 (tmmt) cc_final: 0.8013 (mmtm) REVERT: A 326 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7914 (pt0) REVERT: A 493 LYS cc_start: 0.7922 (ptpp) cc_final: 0.7661 (mtmm) REVERT: A 510 THR cc_start: 0.7912 (OUTLIER) cc_final: 0.7641 (p) REVERT: A 533 ASP cc_start: 0.8182 (p0) cc_final: 0.7967 (p0) REVERT: A 600 PHE cc_start: 0.7818 (t80) cc_final: 0.7486 (t80) REVERT: B 152 MET cc_start: 0.6331 (mtm) cc_final: 0.5433 (mmt) REVERT: D 115 ASP cc_start: 0.8264 (m-30) cc_final: 0.8057 (m-30) REVERT: E 22 ASP cc_start: 0.8049 (OUTLIER) cc_final: 0.7796 (m-30) REVERT: E 205 ASP cc_start: 0.8044 (t0) cc_final: 0.7192 (p0) REVERT: J 101 MET cc_start: 0.3737 (tpt) cc_final: 0.3432 (tpt) REVERT: J 123 MET cc_start: 0.2912 (OUTLIER) cc_final: 0.2492 (ttt) REVERT: K 153 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.7041 (mm-30) REVERT: K 181 ARG cc_start: 0.7379 (pmt170) cc_final: 0.6051 (ptt180) REVERT: K 187 VAL cc_start: 0.8342 (p) cc_final: 0.7950 (m) REVERT: K 236 VAL cc_start: 0.8711 (m) cc_final: 0.8475 (m) REVERT: K 250 TYR cc_start: 0.8852 (t80) cc_final: 0.8592 (t80) REVERT: K 263 ASP cc_start: 0.6638 (p0) cc_final: 0.6335 (p0) REVERT: K 265 ARG cc_start: 0.7860 (mtm180) cc_final: 0.7657 (tpt90) REVERT: F 3 GLU cc_start: 0.5450 (tm-30) cc_final: 0.4087 (mp0) REVERT: F 206 MET cc_start: 0.6084 (mmt) cc_final: 0.5569 (mmt) REVERT: F 262 LEU cc_start: 0.7194 (mt) cc_final: 0.6351 (tp) REVERT: F 284 VAL cc_start: 0.3888 (OUTLIER) cc_final: 0.3468 (p) REVERT: F 286 GLU cc_start: 0.6251 (tm-30) cc_final: 0.5518 (pm20) REVERT: F 289 LEU cc_start: 0.7909 (tp) cc_final: 0.7397 (mt) REVERT: F 301 MET cc_start: -0.1443 (ttm) cc_final: -0.2225 (ttm) REVERT: F 344 MET cc_start: 0.2908 (mmm) cc_final: 0.0913 (tmm) outliers start: 56 outliers final: 30 residues processed: 308 average time/residue: 0.1790 time to fit residues: 81.7100 Evaluate side-chains 290 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 253 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 510 THR Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain C residue 26 GLN Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain J residue 123 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 284 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 133 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 87 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 150 optimal weight: 0.8980 chunk 6 optimal weight: 8.9990 chunk 159 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.198752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.153790 restraints weight = 25421.991| |-----------------------------------------------------------------------------| r_work (start): 0.3720 rms_B_bonded: 3.56 r_work: 0.3109 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 20814 Z= 0.177 Angle : 0.611 15.650 28331 Z= 0.312 Chirality : 0.045 0.251 3121 Planarity : 0.005 0.052 3462 Dihedral : 13.968 170.880 3468 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 3.08 % Allowed : 12.21 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.38 (0.16), residues: 2325 helix: -0.87 (0.17), residues: 887 sheet: -1.64 (0.27), residues: 333 loop : -2.13 (0.17), residues: 1105 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 58 TYR 0.021 0.002 TYR K 224 PHE 0.032 0.002 PHE A 59 TRP 0.014 0.001 TRP A 596 HIS 0.005 0.001 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 (20797) covalent geometry : angle 0.60740 / 0.31 (28313) hydrogen bonds : bond 0.04115 / 2.79 ( 663) hydrogen bonds : angle 4.93567 / 3.51 ( 1938) metal coordination : bond 0.00721 / 0.51 ( 16) metal coordination : angle 3.02140 / 1.64 ( 15) link_TRANS : bond 0.00008 / 0.00 ( 1) link_TRANS : angle 0.17733 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 257 time to evaluate : 0.761 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7639 (tm-30) REVERT: A 124 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7536 (t0) REVERT: A 155 ARG cc_start: 0.7473 (ttp-110) cc_final: 0.7118 (ttm110) REVERT: A 156 GLU cc_start: 0.7224 (tp30) cc_final: 0.6803 (tp30) REVERT: A 159 LYS cc_start: 0.8406 (tmmt) cc_final: 0.8007 (mmtm) REVERT: A 326 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7967 (pt0) REVERT: A 493 LYS cc_start: 0.7943 (ptpp) cc_final: 0.7666 (mtmm) REVERT: A 600 PHE cc_start: 0.7882 (t80) cc_final: 0.7565 (t80) REVERT: A 629 GLU cc_start: 0.5154 (pm20) cc_final: 0.4865 (pm20) REVERT: B 152 MET cc_start: 0.6435 (mtm) cc_final: 0.5584 (mmt) REVERT: C 276 PHE cc_start: 0.7524 (OUTLIER) cc_final: 0.6783 (m-80) REVERT: D 115 ASP cc_start: 0.8458 (m-30) cc_final: 0.8249 (m-30) REVERT: D 184 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7871 (tt0) REVERT: E 22 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7860 (m-30) REVERT: E 205 ASP cc_start: 0.8019 (t0) cc_final: 0.7244 (p0) REVERT: J 101 MET cc_start: 0.3743 (tpt) cc_final: 0.2986 (tpt) REVERT: K 66 LEU cc_start: 0.8465 (OUTLIER) cc_final: 0.8232 (tt) REVERT: K 105 ILE cc_start: 0.7568 (mm) cc_final: 0.7084 (tt) REVERT: K 153 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.7048 (mm-30) REVERT: K 181 ARG cc_start: 0.7385 (pmt170) cc_final: 0.6122 (ptt180) REVERT: K 187 VAL cc_start: 0.8320 (p) cc_final: 0.7904 (m) REVERT: K 250 TYR cc_start: 0.8900 (t80) cc_final: 0.8632 (t80) REVERT: K 263 ASP cc_start: 0.6766 (p0) cc_final: 0.6355 (p0) REVERT: K 265 ARG cc_start: 0.7856 (mtm180) cc_final: 0.7623 (tpt90) REVERT: F 262 LEU cc_start: 0.7157 (mt) cc_final: 0.6576 (mt) REVERT: F 284 VAL cc_start: 0.3948 (OUTLIER) cc_final: 0.3505 (p) REVERT: F 286 GLU cc_start: 0.6065 (tm-30) cc_final: 0.5380 (pm20) REVERT: F 289 LEU cc_start: 0.7976 (tp) cc_final: 0.7465 (mt) REVERT: F 344 MET cc_start: 0.3094 (mmm) cc_final: 0.0636 (tmm) outliers start: 60 outliers final: 41 residues processed: 295 average time/residue: 0.1670 time to fit residues: 73.7872 Evaluate side-chains 296 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 247 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 96 ASN Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 110 ILE Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 230 ILE Chi-restraints excluded: chain F residue 284 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 114 optimal weight: 1.9990 chunk 59 optimal weight: 0.0980 chunk 157 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 108 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 112 optimal weight: 0.8980 chunk 167 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.201038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.156272 restraints weight = 25401.114| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 3.69 r_work: 0.3141 rms_B_bonded: 4.69 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.2979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 20814 Z= 0.113 Angle : 0.563 14.170 28331 Z= 0.286 Chirality : 0.043 0.246 3121 Planarity : 0.004 0.048 3462 Dihedral : 13.903 175.040 3468 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 3.03 % Allowed : 12.88 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.17), residues: 2325 helix: -0.58 (0.17), residues: 883 sheet: -1.53 (0.27), residues: 335 loop : -1.99 (0.17), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 160 TYR 0.021 0.001 TYR K 224 PHE 0.019 0.001 PHE A 59 TRP 0.012 0.001 TRP C 156 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (20797) covalent geometry : angle 0.55878 / 0.29 (28313) hydrogen bonds : bond 0.03729 / 2.54 ( 663) hydrogen bonds : angle 4.71113 / 3.35 ( 1938) metal coordination : bond 0.00956 / 0.65 ( 16) metal coordination : angle 3.06493 / 1.64 ( 15) link_TRANS : bond 0.00011 / 0.01 ( 1) link_TRANS : angle 0.17143 / 0.09 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 266 time to evaluate : 0.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7896 (tm-30) REVERT: A 124 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7449 (t0) REVERT: A 155 ARG cc_start: 0.7286 (ttp-110) cc_final: 0.6980 (ttm110) REVERT: A 159 LYS cc_start: 0.8287 (tmmt) cc_final: 0.8036 (mmtm) REVERT: A 326 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7937 (pt0) REVERT: A 493 LYS cc_start: 0.7916 (ptpp) cc_final: 0.7682 (mtmm) REVERT: A 600 PHE cc_start: 0.7865 (t80) cc_final: 0.7645 (t80) REVERT: B 149 LEU cc_start: 0.7091 (mt) cc_final: 0.6834 (mt) REVERT: B 152 MET cc_start: 0.6330 (mtm) cc_final: 0.5642 (mmt) REVERT: C 276 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6894 (m-80) REVERT: D 184 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: E 65 TYR cc_start: 0.8860 (m-10) cc_final: 0.8539 (m-10) REVERT: E 205 ASP cc_start: 0.8070 (t0) cc_final: 0.7166 (p0) REVERT: J 101 MET cc_start: 0.3625 (tpt) cc_final: 0.2845 (tpt) REVERT: K 66 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8245 (tt) REVERT: K 105 ILE cc_start: 0.7573 (mm) cc_final: 0.7126 (tt) REVERT: K 153 GLU cc_start: 0.7599 (OUTLIER) cc_final: 0.7215 (tm-30) REVERT: K 181 ARG cc_start: 0.7445 (pmt170) cc_final: 0.6298 (ptt180) REVERT: K 187 VAL cc_start: 0.8353 (p) cc_final: 0.8004 (m) REVERT: K 250 TYR cc_start: 0.8885 (t80) cc_final: 0.8643 (t80) REVERT: K 263 ASP cc_start: 0.6545 (p0) cc_final: 0.6243 (p0) REVERT: F 3 GLU cc_start: 0.5612 (tm-30) cc_final: 0.4217 (mp0) REVERT: F 252 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7353 (mt-10) REVERT: F 262 LEU cc_start: 0.7166 (mt) cc_final: 0.6323 (tp) REVERT: F 280 GLU cc_start: 0.3489 (tt0) cc_final: 0.1950 (pt0) REVERT: F 284 VAL cc_start: 0.4098 (OUTLIER) cc_final: 0.3777 (p) REVERT: F 286 GLU cc_start: 0.6020 (tm-30) cc_final: 0.5391 (pm20) REVERT: F 289 LEU cc_start: 0.7929 (tp) cc_final: 0.7532 (mt) REVERT: F 301 MET cc_start: -0.1406 (ttm) cc_final: -0.2271 (ttm) REVERT: F 344 MET cc_start: 0.2968 (mmm) cc_final: 0.0988 (tmm) outliers start: 59 outliers final: 35 residues processed: 305 average time/residue: 0.1643 time to fit residues: 75.2780 Evaluate side-chains 297 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 255 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 153 GLU Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 284 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 10 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 200 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 71 optimal weight: 0.0050 chunk 175 optimal weight: 7.9990 chunk 194 optimal weight: 4.9990 chunk 46 optimal weight: 0.2980 chunk 4 optimal weight: 7.9990 chunk 75 optimal weight: 8.9990 overall best weight: 1.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN K 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.198284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.150651 restraints weight = 25612.046| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 3.85 r_work: 0.3087 rms_B_bonded: 4.65 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 20814 Z= 0.185 Angle : 0.612 14.312 28331 Z= 0.310 Chirality : 0.045 0.236 3121 Planarity : 0.005 0.050 3462 Dihedral : 13.853 170.209 3468 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 3.03 % Allowed : 13.34 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.17), residues: 2325 helix: -0.47 (0.17), residues: 892 sheet: -1.40 (0.27), residues: 345 loop : -1.99 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 173 TYR 0.019 0.002 TYR K 224 PHE 0.026 0.002 PHE A 561 TRP 0.016 0.001 TRP E 227 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00438 / 0.18 (20797) covalent geometry : angle 0.60941 / 0.31 (28313) hydrogen bonds : bond 0.03988 / 2.71 ( 663) hydrogen bonds : angle 4.75865 / 3.38 ( 1938) metal coordination : bond 0.00553 / 0.36 ( 16) metal coordination : angle 2.72488 / 1.49 ( 15) link_TRANS : bond 0.00010 / 0.01 ( 1) link_TRANS : angle 0.15892 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 264 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7976 (tm-30) REVERT: A 124 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7576 (t0) REVERT: A 155 ARG cc_start: 0.7319 (ttp-110) cc_final: 0.6963 (ttm110) REVERT: A 159 LYS cc_start: 0.8494 (tmmt) cc_final: 0.7832 (mmmm) REVERT: A 192 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7006 (mp0) REVERT: A 493 LYS cc_start: 0.7912 (ptpp) cc_final: 0.7642 (mtmm) REVERT: A 600 PHE cc_start: 0.7941 (t80) cc_final: 0.7605 (t80) REVERT: B 149 LEU cc_start: 0.7097 (mt) cc_final: 0.6816 (mt) REVERT: B 152 MET cc_start: 0.6275 (mtm) cc_final: 0.5588 (mmt) REVERT: C 276 PHE cc_start: 0.7588 (OUTLIER) cc_final: 0.6925 (m-80) REVERT: D 184 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.7899 (tt0) REVERT: E 22 ASP cc_start: 0.8100 (OUTLIER) cc_final: 0.7859 (m-30) REVERT: E 205 ASP cc_start: 0.7991 (t0) cc_final: 0.7181 (p0) REVERT: J 101 MET cc_start: 0.3589 (tpt) cc_final: 0.3332 (tpt) REVERT: K 66 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8208 (tt) REVERT: K 105 ILE cc_start: 0.7636 (mm) cc_final: 0.7177 (tt) REVERT: K 181 ARG cc_start: 0.7472 (pmt170) cc_final: 0.6249 (ptt180) REVERT: K 187 VAL cc_start: 0.8300 (p) cc_final: 0.7892 (m) REVERT: K 250 TYR cc_start: 0.8914 (t80) cc_final: 0.8713 (t80) REVERT: K 263 ASP cc_start: 0.6823 (p0) cc_final: 0.6461 (p0) REVERT: F 3 GLU cc_start: 0.5402 (tm-30) cc_final: 0.4160 (mp0) REVERT: F 132 GLU cc_start: 0.1882 (tm-30) cc_final: 0.1487 (mt-10) REVERT: F 283 GLU cc_start: 0.6651 (tp30) cc_final: 0.4918 (mm-30) REVERT: F 284 VAL cc_start: 0.4334 (OUTLIER) cc_final: 0.3580 (p) REVERT: F 289 LEU cc_start: 0.7850 (tp) cc_final: 0.7527 (mt) REVERT: F 301 MET cc_start: -0.1470 (ttm) cc_final: -0.2304 (ttm) REVERT: F 344 MET cc_start: 0.3198 (mmm) cc_final: 0.0701 (tmm) outliers start: 59 outliers final: 43 residues processed: 300 average time/residue: 0.1711 time to fit residues: 76.6938 Evaluate side-chains 297 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 247 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 561 PHE Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 284 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 111 optimal weight: 1.9990 chunk 203 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 210 optimal weight: 9.9990 chunk 164 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 chunk 66 optimal weight: 0.8980 chunk 206 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.198360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.152407 restraints weight = 25617.876| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.75 r_work: 0.3094 rms_B_bonded: 4.70 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 20814 Z= 0.174 Angle : 0.602 14.206 28331 Z= 0.306 Chirality : 0.045 0.227 3121 Planarity : 0.005 0.052 3462 Dihedral : 13.835 170.497 3466 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 3.23 % Allowed : 13.75 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.17), residues: 2325 helix: -0.34 (0.18), residues: 882 sheet: -1.38 (0.27), residues: 345 loop : -1.94 (0.18), residues: 1098 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 181 TYR 0.023 0.001 TYR K 224 PHE 0.024 0.001 PHE A 561 TRP 0.016 0.001 TRP C 156 HIS 0.005 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.17 (20797) covalent geometry : angle 0.59918 / 0.31 (28313) hydrogen bonds : bond 0.03881 / 2.64 ( 663) hydrogen bonds : angle 4.72271 / 3.35 ( 1938) metal coordination : bond 0.00628 / 0.41 ( 16) metal coordination : angle 2.79625 / 1.52 ( 15) link_TRANS : bond 0.00011 / 0.01 ( 1) link_TRANS : angle 0.15039 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 260 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: A 36 ARG cc_start: 0.6974 (ttt-90) cc_final: 0.6367 (ttp80) REVERT: A 124 ASN cc_start: 0.8033 (OUTLIER) cc_final: 0.7598 (t0) REVERT: A 155 ARG cc_start: 0.7329 (ttp-110) cc_final: 0.7004 (ttm110) REVERT: A 159 LYS cc_start: 0.8484 (tmmt) cc_final: 0.7875 (mmmm) REVERT: A 192 GLU cc_start: 0.7554 (mm-30) cc_final: 0.7016 (mp0) REVERT: A 493 LYS cc_start: 0.7878 (ptpp) cc_final: 0.7593 (mtmm) REVERT: A 558 GLU cc_start: 0.7726 (tm-30) cc_final: 0.7448 (tm-30) REVERT: A 600 PHE cc_start: 0.8051 (t80) cc_final: 0.7720 (t80) REVERT: A 692 ASN cc_start: 0.8198 (OUTLIER) cc_final: 0.7605 (t0) REVERT: B 149 LEU cc_start: 0.7155 (mt) cc_final: 0.6926 (mt) REVERT: B 152 MET cc_start: 0.6164 (mtm) cc_final: 0.5496 (mmt) REVERT: C 276 PHE cc_start: 0.7665 (OUTLIER) cc_final: 0.6999 (m-80) REVERT: D 184 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.7874 (tt0) REVERT: E 22 ASP cc_start: 0.8104 (OUTLIER) cc_final: 0.7863 (m-30) REVERT: E 205 ASP cc_start: 0.7982 (t0) cc_final: 0.7140 (p0) REVERT: J 101 MET cc_start: 0.3604 (tpt) cc_final: 0.2850 (tpt) REVERT: K 66 LEU cc_start: 0.8504 (OUTLIER) cc_final: 0.8267 (tt) REVERT: K 105 ILE cc_start: 0.7556 (mm) cc_final: 0.7060 (tt) REVERT: K 135 SER cc_start: 0.7886 (OUTLIER) cc_final: 0.7508 (t) REVERT: K 187 VAL cc_start: 0.8432 (p) cc_final: 0.8112 (m) REVERT: K 263 ASP cc_start: 0.6716 (p0) cc_final: 0.6413 (p0) REVERT: F 3 GLU cc_start: 0.5410 (tm-30) cc_final: 0.4177 (mp0) REVERT: F 132 GLU cc_start: 0.1885 (tm-30) cc_final: 0.1445 (mt-10) REVERT: F 252 GLU cc_start: 0.7767 (mt-10) cc_final: 0.7328 (mt-10) REVERT: F 283 GLU cc_start: 0.6644 (tp30) cc_final: 0.4912 (mm-30) REVERT: F 284 VAL cc_start: 0.4363 (OUTLIER) cc_final: 0.3596 (p) REVERT: F 289 LEU cc_start: 0.7870 (tp) cc_final: 0.7557 (mt) REVERT: F 301 MET cc_start: -0.1493 (ttm) cc_final: -0.2254 (ttm) REVERT: F 344 MET cc_start: 0.3200 (mmm) cc_final: 0.0675 (tmm) outliers start: 63 outliers final: 46 residues processed: 299 average time/residue: 0.1725 time to fit residues: 76.8283 Evaluate side-chains 304 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 249 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 135 SER Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 284 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 83 optimal weight: 0.5980 chunk 170 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 160 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 116 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 174 optimal weight: 7.9990 chunk 112 optimal weight: 6.9990 chunk 82 optimal weight: 5.9990 chunk 205 optimal weight: 3.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 199 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.196646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.149704 restraints weight = 25268.299| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 3.66 r_work: 0.3073 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 20814 Z= 0.237 Angle : 0.658 14.013 28331 Z= 0.332 Chirality : 0.047 0.235 3121 Planarity : 0.005 0.059 3462 Dihedral : 13.850 167.378 3466 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 3.18 % Allowed : 13.80 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.89 (0.17), residues: 2325 helix: -0.35 (0.18), residues: 885 sheet: -1.39 (0.27), residues: 349 loop : -1.94 (0.18), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 160 TYR 0.023 0.002 TYR K 224 PHE 0.033 0.002 PHE A 561 TRP 0.019 0.002 TRP C 156 HIS 0.006 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00571 / 0.24 (20797) covalent geometry : angle 0.65444 / 0.33 (28313) hydrogen bonds : bond 0.04122 / 2.80 ( 663) hydrogen bonds : angle 4.81183 / 3.41 ( 1938) metal coordination : bond 0.00580 / 0.35 ( 16) metal coordination : angle 2.88860 / 1.57 ( 15) link_TRANS : bond 0.00011 / 0.01 ( 1) link_TRANS : angle 0.15269 / 0.08 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 251 time to evaluate : 1.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8360 (OUTLIER) cc_final: 0.8011 (tm-30) REVERT: A 36 ARG cc_start: 0.7052 (ttt-90) cc_final: 0.6834 (ttp80) REVERT: A 124 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7663 (t0) REVERT: A 155 ARG cc_start: 0.7299 (ttp-110) cc_final: 0.7047 (ttm110) REVERT: A 159 LYS cc_start: 0.8469 (tmmt) cc_final: 0.7954 (mmmm) REVERT: A 192 GLU cc_start: 0.7604 (mm-30) cc_final: 0.7060 (mp0) REVERT: A 493 LYS cc_start: 0.7951 (ptpp) cc_final: 0.7662 (mtmm) REVERT: A 558 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7535 (tm-30) REVERT: A 600 PHE cc_start: 0.8086 (t80) cc_final: 0.7751 (t80) REVERT: A 692 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7573 (t0) REVERT: B 152 MET cc_start: 0.6482 (mtm) cc_final: 0.5532 (mmt) REVERT: C 276 PHE cc_start: 0.7791 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: D 184 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: E 22 ASP cc_start: 0.8140 (OUTLIER) cc_final: 0.7875 (m-30) REVERT: E 205 ASP cc_start: 0.7999 (t0) cc_final: 0.7227 (p0) REVERT: K 66 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8273 (tt) REVERT: K 103 ARG cc_start: 0.7959 (ttm-80) cc_final: 0.7605 (ttm170) REVERT: K 135 SER cc_start: 0.7924 (OUTLIER) cc_final: 0.7616 (t) REVERT: K 187 VAL cc_start: 0.8451 (p) cc_final: 0.8112 (m) REVERT: K 263 ASP cc_start: 0.6828 (p0) cc_final: 0.6516 (p0) REVERT: F 3 GLU cc_start: 0.5307 (tm-30) cc_final: 0.4317 (mp0) REVERT: F 283 GLU cc_start: 0.6641 (tp30) cc_final: 0.5054 (mm-30) REVERT: F 284 VAL cc_start: 0.4354 (OUTLIER) cc_final: 0.3698 (p) REVERT: F 289 LEU cc_start: 0.7855 (tp) cc_final: 0.7568 (mt) REVERT: F 344 MET cc_start: 0.3466 (mmm) cc_final: 0.0819 (tmm) outliers start: 62 outliers final: 48 residues processed: 290 average time/residue: 0.1637 time to fit residues: 71.0918 Evaluate side-chains 306 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 249 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 166 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 342 GLU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 171 ILE Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 128 ASP Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain E residue 260 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 135 SER Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 169 VAL Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 89 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 140 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 96 optimal weight: 0.3980 chunk 45 optimal weight: 0.7980 chunk 30 optimal weight: 2.9990 chunk 160 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.200169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.154240 restraints weight = 25543.407| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 3.59 r_work: 0.3114 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 20814 Z= 0.117 Angle : 0.575 14.384 28331 Z= 0.290 Chirality : 0.043 0.224 3121 Planarity : 0.004 0.048 3462 Dihedral : 13.789 174.265 3466 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 2.62 % Allowed : 14.52 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.64 (0.17), residues: 2325 helix: -0.08 (0.18), residues: 878 sheet: -1.34 (0.27), residues: 345 loop : -1.82 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 160 TYR 0.023 0.001 TYR K 224 PHE 0.035 0.001 PHE A 561 TRP 0.014 0.001 TRP C 156 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 (20797) covalent geometry : angle 0.57121 / 0.29 (28313) hydrogen bonds : bond 0.03630 / 2.48 ( 663) hydrogen bonds : angle 4.60246 / 3.27 ( 1938) metal coordination : bond 0.00908 / 0.61 ( 16) metal coordination : angle 2.96291 / 1.60 ( 15) link_TRANS : bond 0.00014 / 0.01 ( 1) link_TRANS : angle 0.15190 / 0.08 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4650 Ramachandran restraints generated. 2325 Oldfield, 0 Emsley, 2325 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 263 time to evaluate : 0.819 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7960 (tm-30) REVERT: A 78 LEU cc_start: 0.8129 (mt) cc_final: 0.7839 (mp) REVERT: A 124 ASN cc_start: 0.7956 (OUTLIER) cc_final: 0.7512 (t0) REVERT: A 155 ARG cc_start: 0.7239 (ttp-110) cc_final: 0.6999 (ttm110) REVERT: A 159 LYS cc_start: 0.8444 (tmmt) cc_final: 0.7940 (mmmm) REVERT: A 192 GLU cc_start: 0.7537 (mm-30) cc_final: 0.7312 (mp0) REVERT: A 326 GLU cc_start: 0.8276 (mm-30) cc_final: 0.7879 (pt0) REVERT: A 445 GLU cc_start: 0.7459 (mp0) cc_final: 0.7213 (pm20) REVERT: A 493 LYS cc_start: 0.7951 (ptpp) cc_final: 0.7503 (mtmm) REVERT: A 558 GLU cc_start: 0.7783 (tm-30) cc_final: 0.7536 (tm-30) REVERT: A 600 PHE cc_start: 0.8009 (t80) cc_final: 0.7672 (t80) REVERT: A 629 GLU cc_start: 0.5216 (pm20) cc_final: 0.4857 (mp0) REVERT: A 692 ASN cc_start: 0.8192 (OUTLIER) cc_final: 0.7594 (t0) REVERT: B 149 LEU cc_start: 0.7115 (mt) cc_final: 0.6865 (mt) REVERT: B 152 MET cc_start: 0.6404 (mtm) cc_final: 0.5464 (mmt) REVERT: C 276 PHE cc_start: 0.7606 (OUTLIER) cc_final: 0.6979 (m-80) REVERT: D 172 ASP cc_start: 0.7073 (t0) cc_final: 0.6873 (t0) REVERT: D 184 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7847 (tt0) REVERT: E 205 ASP cc_start: 0.7894 (t0) cc_final: 0.7082 (p0) REVERT: K 66 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8231 (tt) REVERT: K 76 GLU cc_start: 0.6642 (pp20) cc_final: 0.6358 (tp30) REVERT: K 105 ILE cc_start: 0.7538 (mm) cc_final: 0.6993 (tt) REVERT: K 135 SER cc_start: 0.7843 (OUTLIER) cc_final: 0.7437 (t) REVERT: K 187 VAL cc_start: 0.8414 (p) cc_final: 0.8100 (m) REVERT: F 3 GLU cc_start: 0.5175 (tm-30) cc_final: 0.4191 (mp0) REVERT: F 14 ILE cc_start: 0.6842 (mm) cc_final: 0.6543 (mm) REVERT: F 132 GLU cc_start: 0.1445 (tm-30) cc_final: 0.1202 (mt-10) REVERT: F 283 GLU cc_start: 0.6345 (tp30) cc_final: 0.4831 (mm-30) REVERT: F 284 VAL cc_start: 0.4373 (OUTLIER) cc_final: 0.3625 (p) REVERT: F 289 LEU cc_start: 0.7851 (tp) cc_final: 0.7551 (mt) REVERT: F 301 MET cc_start: -0.1531 (ttm) cc_final: -0.2280 (ttm) REVERT: F 344 MET cc_start: 0.3252 (mmm) cc_final: 0.0522 (tmm) outliers start: 51 outliers final: 36 residues processed: 294 average time/residue: 0.1747 time to fit residues: 76.1503 Evaluate side-chains 297 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 253 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 452 VAL Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 568 VAL Chi-restraints excluded: chain A residue 580 ILE Chi-restraints excluded: chain A residue 630 ARG Chi-restraints excluded: chain A residue 672 TYR Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 127 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 169 VAL Chi-restraints excluded: chain C residue 276 PHE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 151 GLU Chi-restraints excluded: chain D residue 169 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 69 LYS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 169 ASP Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 236 SER Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 65 ILE Chi-restraints excluded: chain K residue 66 LEU Chi-restraints excluded: chain K residue 69 SER Chi-restraints excluded: chain K residue 135 SER Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain K residue 191 GLU Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 249 THR Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain F residue 284 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 214 random chunks: chunk 200 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 134 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 0.5980 chunk 86 optimal weight: 0.9980 chunk 192 optimal weight: 5.9990 chunk 156 optimal weight: 3.9990 chunk 202 optimal weight: 0.7980 chunk 128 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 202 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.198817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.151815 restraints weight = 25486.299| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.66 r_work: 0.3103 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.3352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 20814 Z= 0.153 Angle : 0.590 14.085 28331 Z= 0.297 Chirality : 0.044 0.201 3121 Planarity : 0.004 0.050 3462 Dihedral : 13.740 172.284 3466 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.51 % Allowed : 14.73 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2325 helix: -0.11 (0.18), residues: 892 sheet: -1.29 (0.27), residues: 345 loop : -1.78 (0.18), residues: 1088 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 160 TYR 0.023 0.001 TYR K 224 PHE 0.041 0.001 PHE A 561 TRP 0.014 0.001 TRP C 156 HIS 0.005 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.15 (20797) covalent geometry : angle 0.58716 / 0.30 (28313) hydrogen bonds : bond 0.03714 / 2.54 ( 663) hydrogen bonds : angle 4.60194 / 3.26 ( 1938) metal coordination : bond 0.00635 / 0.44 ( 16) metal coordination : angle 2.70032 / 1.49 ( 15) link_TRANS : bond 0.00015 / 0.01 ( 1) link_TRANS : angle 0.14994 / 0.08 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5115.87 seconds wall clock time: 88 minutes 26.20 seconds (5306.20 seconds total)