Starting phenix.real_space_refine on Thu Mar 5 07:39:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6o7i_0642/03_2026/6o7i_0642_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6o7i_0642/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/6o7i_0642/03_2026/6o7i_0642_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6o7i_0642/03_2026/6o7i_0642_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6o7i_0642/03_2026/6o7i_0642.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6o7i_0642/03_2026/6o7i_0642.map" } 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-dev-5986/lib/python3.9/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: 4.10, per 1000 atoms: 0.20 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: 1.38 Conformation dependent library (CDL) restraints added in 955.5 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: 2.29 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: 3.22 Time building geometry restraints manager: 1.91 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=" 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=" CG LEU E 134 " pdb=" CD1 LEU E 134 " ideal model delta sigma weight residual 1.521 1.391 0.130 3.30e-02 9.18e+02 1.56e+01 bond pdb=" CG1 ILE D 40 " pdb=" CD1 ILE D 40 " ideal model delta sigma weight residual 1.513 1.378 0.135 3.90e-02 6.57e+02 1.20e+01 bond pdb=" CB PRO C 51 " pdb=" CG PRO C 51 " ideal model delta sigma weight residual 1.492 1.323 0.169 5.00e-02 4.00e+02 1.15e+01 bond pdb=" CB ILE E 143 " pdb=" CG2 ILE E 143 " ideal model delta sigma weight residual 1.521 1.411 0.110 3.30e-02 9.18e+02 1.12e+01 ... (remaining 20792 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 26295 2.10 - 4.20: 1671 4.20 - 6.30: 260 6.30 - 8.39: 72 8.39 - 10.49: 15 Bond angle restraints: 28313 Sorted by residual: angle pdb=" C4' C G 14 " pdb=" C3' C G 14 " pdb=" O3' C G 14 " ideal model delta sigma weight residual 109.40 100.83 8.57 1.50e+00 4.44e-01 3.26e+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=" C4' G G 9 " pdb=" C3' G G 9 " pdb=" O3' G G 9 " ideal model delta sigma weight residual 109.40 101.48 7.92 1.50e+00 4.44e-01 2.78e+01 angle pdb=" N VAL A 753 " pdb=" CA VAL A 753 " pdb=" C VAL A 753 " ideal model delta sigma weight residual 112.29 107.40 4.89 9.40e-01 1.13e+00 2.70e+01 angle pdb=" C GLY A 376 " pdb=" N LEU A 377 " pdb=" CA LEU A 377 " ideal model delta sigma weight residual 120.28 127.24 -6.96 1.34e+00 5.57e-01 2.70e+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: 2350 0.073 - 0.147: 624 0.147 - 0.220: 116 0.220 - 0.293: 24 0.293 - 0.367: 7 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 20.800 Find NCS groups from input model: 0.220 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 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= 0.527 Angle : 1.225 43.218 28331 Z= 0.655 Chirality : 0.070 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 covalent geometry : bond 0.01191 (20797) covalent geometry : angle 1.17009 (28313) hydrogen bonds : bond 0.17065 ( 663) hydrogen bonds : angle 8.37625 ( 1938) metal coordination : bond 0.19429 ( 16) metal coordination : angle 15.75742 ( 15) link_TRANS : bond 0.00202 ( 1) link_TRANS : angle 0.23009 ( 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 : 0.715 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: 0.1828 time to fit residues: 112.8827 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 : 0.740 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 102 ASN A 382 HIS B 72 ASN C 22 HIS ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 HIS E 200 HIS J 173 GLN K 22 HIS K 179 ASN F 18 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.200557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.154203 restraints weight = 25543.308| |-----------------------------------------------------------------------------| r_work (start): 0.3721 rms_B_bonded: 3.63 r_work: 0.3140 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 20814 Z= 0.151 Angle : 0.636 10.495 28331 Z= 0.326 Chirality : 0.044 0.194 3121 Planarity : 0.006 0.061 3462 Dihedral : 14.199 167.852 3472 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.26 % Allowed : 8.52 % Favored : 89.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.41 (0.15), residues: 2325 helix: -1.93 (0.15), residues: 862 sheet: -2.21 (0.25), residues: 330 loop : -2.51 (0.16), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 207 TYR 0.016 0.002 TYR D 233 PHE 0.029 0.001 PHE A 561 TRP 0.021 0.001 TRP A 131 HIS 0.008 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00344 (20797) covalent geometry : angle 0.62994 (28313) hydrogen bonds : bond 0.04228 ( 663) hydrogen bonds : angle 5.38271 ( 1938) metal coordination : bond 0.00977 ( 16) metal coordination : angle 3.75025 ( 15) link_TRANS : bond 0.00008 ( 1) link_TRANS : angle 0.18467 ( 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 373 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 329 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 TYR cc_start: 0.6944 (m-10) cc_final: 0.6249 (m-10) REVERT: A 36 ARG cc_start: 0.7473 (mtp-110) cc_final: 0.6720 (mtp-110) REVERT: A 39 ARG cc_start: 0.8038 (mtm-85) cc_final: 0.7793 (mtm180) REVERT: A 78 LEU cc_start: 0.7906 (mt) cc_final: 0.7690 (mp) REVERT: A 124 ASN cc_start: 0.7919 (OUTLIER) cc_final: 0.7464 (t0) REVERT: A 155 ARG cc_start: 0.7609 (ttp-110) cc_final: 0.7176 (mtm110) REVERT: A 156 GLU cc_start: 0.7197 (tp30) cc_final: 0.6821 (tp30) REVERT: A 159 LYS cc_start: 0.8434 (tmmt) cc_final: 0.8036 (mmtm) REVERT: A 161 LEU cc_start: 0.8829 (tp) cc_final: 0.8379 (tp) REVERT: A 326 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7939 (pt0) REVERT: A 385 ARG cc_start: 0.7800 (tpp80) cc_final: 0.7595 (mmm160) REVERT: A 402 GLU cc_start: 0.8395 (mp0) cc_final: 0.8172 (mp0) REVERT: A 493 LYS cc_start: 0.7942 (ptpp) cc_final: 0.7688 (mtmm) REVERT: A 501 THR cc_start: 0.7637 (OUTLIER) cc_final: 0.7377 (p) REVERT: A 532 MET cc_start: 0.8992 (mpp) cc_final: 0.8574 (mpp) REVERT: A 533 ASP cc_start: 0.8264 (p0) cc_final: 0.8045 (p0) REVERT: A 600 PHE cc_start: 0.7837 (t80) cc_final: 0.7525 (t80) REVERT: A 694 ARG cc_start: 0.6572 (ttm110) cc_final: 0.6095 (ttp80) REVERT: A 733 LEU cc_start: 0.8291 (mt) cc_final: 0.8041 (tt) REVERT: B 152 MET cc_start: 0.6445 (mtm) cc_final: 0.5293 (mmt) REVERT: C 117 GLU cc_start: 0.8004 (pm20) cc_final: 0.7689 (pm20) REVERT: D 90 ARG cc_start: 0.8043 (ttm-80) cc_final: 0.7434 (ttp-170) REVERT: D 115 ASP cc_start: 0.8193 (m-30) cc_final: 0.7969 (m-30) REVERT: E 128 ASP cc_start: 0.8508 (p0) cc_final: 0.8302 (p0) REVERT: E 205 ASP cc_start: 0.8059 (t0) cc_final: 0.7194 (p0) REVERT: E 264 GLU cc_start: 0.8126 (mp0) cc_final: 0.7923 (pm20) REVERT: J 101 MET cc_start: 0.3480 (tpt) cc_final: 0.2905 (tpt) REVERT: K 187 VAL cc_start: 0.8359 (p) cc_final: 0.7954 (m) REVERT: K 224 TYR cc_start: 0.7586 (p90) cc_final: 0.7360 (p90) REVERT: K 236 VAL cc_start: 0.8849 (m) cc_final: 0.8600 (m) REVERT: K 250 TYR cc_start: 0.8817 (t80) cc_final: 0.8612 (t80) REVERT: K 263 ASP cc_start: 0.6596 (p0) cc_final: 0.6368 (p0) REVERT: K 265 ARG cc_start: 0.7898 (mtm180) cc_final: 0.7664 (tpt90) REVERT: F 258 GLU cc_start: 0.5539 (tp30) cc_final: 0.4303 (mm-30) REVERT: F 262 LEU cc_start: 0.7078 (mt) cc_final: 0.5910 (tp) REVERT: F 283 GLU cc_start: 0.5694 (tm-30) cc_final: 0.4928 (mm-30) REVERT: F 284 VAL cc_start: 0.3656 (OUTLIER) cc_final: 0.2968 (p) REVERT: F 286 GLU cc_start: 0.6067 (tm-30) cc_final: 0.5393 (pm20) REVERT: F 289 LEU cc_start: 0.7799 (tp) cc_final: 0.7339 (mt) REVERT: F 301 MET cc_start: -0.0509 (ttm) cc_final: -0.1598 (ttm) outliers start: 44 outliers final: 21 residues processed: 356 average time/residue: 0.1772 time to fit residues: 92.0919 Evaluate side-chains 285 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 261 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 501 THR 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 633 ILE Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain C residue 15 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 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 260 MET Chi-restraints excluded: chain K residue 228 SER 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: 0.6980 chunk 39 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 132 optimal weight: 5.9990 chunk 141 optimal weight: 5.9990 chunk 200 optimal weight: 3.9990 chunk 176 optimal weight: 30.0000 chunk 186 optimal weight: 8.9990 chunk 199 optimal weight: 1.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.197680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.151554 restraints weight = 25592.769| |-----------------------------------------------------------------------------| r_work (start): 0.3685 rms_B_bonded: 3.66 r_work: 0.3076 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 20814 Z= 0.210 Angle : 0.647 10.474 28331 Z= 0.328 Chirality : 0.045 0.230 3121 Planarity : 0.005 0.061 3462 Dihedral : 14.002 159.929 3468 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.80 % Favored : 93.20 % Rotamer: Outliers : 2.87 % Allowed : 11.29 % Favored : 85.84 % 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: -2.78 (0.16), residues: 2325 helix: -1.23 (0.17), residues: 868 sheet: -1.96 (0.26), residues: 335 loop : -2.27 (0.17), residues: 1122 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 103 TYR 0.019 0.002 TYR A 265 PHE 0.027 0.002 PHE C 276 TRP 0.019 0.002 TRP A 271 HIS 0.007 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00495 (20797) covalent geometry : angle 0.64238 (28313) hydrogen bonds : bond 0.04151 ( 663) hydrogen bonds : angle 5.08266 ( 1938) metal coordination : bond 0.00586 ( 16) metal coordination : angle 3.36069 ( 15) link_TRANS : bond 0.00011 ( 1) link_TRANS : angle 0.13934 ( 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 334 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 278 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7968 (tm-30) REVERT: A 39 ARG cc_start: 0.7990 (mtm-85) cc_final: 0.7694 (mtm180) REVERT: A 51 GLU cc_start: 0.8389 (tp30) cc_final: 0.8185 (tp30) REVERT: A 124 ASN cc_start: 0.7936 (OUTLIER) cc_final: 0.7562 (t0) REVERT: A 155 ARG cc_start: 0.7423 (ttp-110) cc_final: 0.7138 (ttm110) REVERT: A 159 LYS cc_start: 0.8482 (tmmt) cc_final: 0.7860 (mmmm) REVERT: A 336 GLU cc_start: 0.7344 (tm-30) cc_final: 0.7129 (tm-30) REVERT: A 493 LYS cc_start: 0.7906 (ptpp) cc_final: 0.7567 (mtmm) REVERT: A 533 ASP cc_start: 0.8321 (p0) cc_final: 0.7952 (p0) REVERT: A 545 MET cc_start: 0.8957 (tpp) cc_final: 0.8698 (tpt) REVERT: A 558 GLU cc_start: 0.7830 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 600 PHE cc_start: 0.8046 (t80) cc_final: 0.7727 (t80) REVERT: B 152 MET cc_start: 0.6420 (mtm) cc_final: 0.5219 (mmt) REVERT: C 256 ASP cc_start: 0.7413 (m-30) cc_final: 0.7042 (p0) REVERT: C 276 PHE cc_start: 0.7577 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: D 172 ASP cc_start: 0.6939 (t0) cc_final: 0.6462 (t0) REVERT: E 22 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7850 (m-30) REVERT: E 128 ASP cc_start: 0.8581 (p0) cc_final: 0.8313 (p0) REVERT: E 205 ASP cc_start: 0.8135 (t0) cc_final: 0.7281 (p0) REVERT: J 101 MET cc_start: 0.3532 (tpt) cc_final: 0.2844 (tpt) REVERT: K 62 LEU cc_start: 0.8778 (OUTLIER) cc_final: 0.8446 (mp) REVERT: K 187 VAL cc_start: 0.8376 (p) cc_final: 0.7990 (m) REVERT: K 224 TYR cc_start: 0.7602 (p90) cc_final: 0.7346 (p90) REVERT: K 250 TYR cc_start: 0.8969 (t80) cc_final: 0.8757 (t80) REVERT: K 263 ASP cc_start: 0.6596 (p0) cc_final: 0.6305 (p0) REVERT: K 265 ARG cc_start: 0.7911 (mtm180) cc_final: 0.7661 (tpt90) REVERT: F 132 GLU cc_start: 0.1788 (tm-30) cc_final: 0.1431 (mt-10) REVERT: F 262 LEU cc_start: 0.7041 (mt) cc_final: 0.6300 (tp) REVERT: F 283 GLU cc_start: 0.6004 (tm-30) cc_final: 0.5337 (mm-30) REVERT: F 284 VAL cc_start: 0.3929 (OUTLIER) cc_final: 0.3250 (p) REVERT: F 286 GLU cc_start: 0.6190 (tm-30) cc_final: 0.5458 (pm20) REVERT: F 289 LEU cc_start: 0.7829 (tp) cc_final: 0.7356 (mt) REVERT: F 301 MET cc_start: -0.1036 (ttm) cc_final: -0.1887 (ttm) REVERT: F 391 MET cc_start: -0.0037 (tmm) cc_final: -0.0480 (tmm) outliers start: 56 outliers final: 29 residues processed: 315 average time/residue: 0.1771 time to fit residues: 81.4189 Evaluate side-chains 289 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 254 time to evaluate : 0.722 ------------------------------------------------------------------------------- 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 166 SER Chi-restraints excluded: chain A residue 178 VAL 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 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 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 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 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 65 ILE Chi-restraints excluded: chain K residue 149 THR Chi-restraints excluded: chain K residue 176 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: 0.9980 chunk 141 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 196 optimal weight: 0.0670 chunk 207 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 179 optimal weight: 10.0000 chunk 178 optimal weight: 9.9990 chunk 144 optimal weight: 0.7980 chunk 136 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.9720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 183 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.199963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.155208 restraints weight = 25614.557| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 3.58 r_work: 0.3125 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 20814 Z= 0.133 Angle : 0.572 9.793 28331 Z= 0.289 Chirality : 0.043 0.238 3121 Planarity : 0.004 0.052 3462 Dihedral : 13.833 165.549 3468 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.98 % Allowed : 11.90 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.16), residues: 2325 helix: -0.79 (0.17), residues: 885 sheet: -1.62 (0.27), residues: 324 loop : -2.15 (0.17), residues: 1116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 173 TYR 0.012 0.001 TYR F 111 PHE 0.017 0.001 PHE C 276 TRP 0.012 0.001 TRP C 156 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00304 (20797) covalent geometry : angle 0.56839 (28313) hydrogen bonds : bond 0.03623 ( 663) hydrogen bonds : angle 4.73891 ( 1938) metal coordination : bond 0.00689 ( 16) metal coordination : angle 2.99040 ( 15) link_TRANS : bond 0.00012 ( 1) link_TRANS : angle 0.14142 ( 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: 58 poor density : 275 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7963 (tm-30) REVERT: A 39 ARG cc_start: 0.8023 (mtm-85) cc_final: 0.7733 (mtm180) REVERT: A 124 ASN cc_start: 0.7910 (OUTLIER) cc_final: 0.7504 (t0) REVERT: A 155 ARG cc_start: 0.7319 (ttp-110) cc_final: 0.6975 (ttm110) REVERT: A 159 LYS cc_start: 0.8431 (tmmt) cc_final: 0.8050 (mmtm) REVERT: A 181 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8438 (tptp) REVERT: A 326 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7925 (pt0) REVERT: A 493 LYS cc_start: 0.7915 (ptpp) cc_final: 0.7663 (mtmm) REVERT: A 532 MET cc_start: 0.8958 (mpp) cc_final: 0.8487 (mmm) REVERT: A 533 ASP cc_start: 0.8205 (p0) cc_final: 0.8000 (p0) REVERT: A 558 GLU cc_start: 0.7807 (tm-30) cc_final: 0.7503 (tm-30) REVERT: A 600 PHE cc_start: 0.7995 (t80) cc_final: 0.7632 (t80) REVERT: A 692 ASN cc_start: 0.8182 (OUTLIER) cc_final: 0.7573 (t0) REVERT: B 152 MET cc_start: 0.6451 (mtm) cc_final: 0.5317 (mmt) REVERT: C 256 ASP cc_start: 0.7444 (m-30) cc_final: 0.7090 (p0) REVERT: C 276 PHE cc_start: 0.7391 (OUTLIER) cc_final: 0.6792 (m-80) REVERT: D 64 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7874 (mm-30) REVERT: D 172 ASP cc_start: 0.6908 (t0) cc_final: 0.6426 (t0) REVERT: D 184 GLU cc_start: 0.8398 (OUTLIER) cc_final: 0.7807 (tt0) REVERT: E 22 ASP cc_start: 0.8076 (OUTLIER) cc_final: 0.7816 (m-30) REVERT: E 128 ASP cc_start: 0.8500 (p0) cc_final: 0.8225 (p0) REVERT: E 205 ASP cc_start: 0.7995 (t0) cc_final: 0.7180 (p0) REVERT: J 101 MET cc_start: 0.3507 (tpt) cc_final: 0.2897 (tpt) REVERT: K 62 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8407 (mp) REVERT: K 66 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8253 (tt) REVERT: K 187 VAL cc_start: 0.8404 (p) cc_final: 0.8087 (m) REVERT: K 224 TYR cc_start: 0.7490 (p90) cc_final: 0.7241 (p90) REVERT: K 250 TYR cc_start: 0.8949 (t80) cc_final: 0.8748 (t80) REVERT: K 263 ASP cc_start: 0.6499 (p0) cc_final: 0.6218 (p0) REVERT: K 265 ARG cc_start: 0.7747 (mtm180) cc_final: 0.7538 (tpt90) REVERT: K 267 LYS cc_start: 0.7549 (mmmt) cc_final: 0.6798 (tptt) REVERT: F 132 GLU cc_start: 0.1842 (tm-30) cc_final: 0.1457 (mt-10) REVERT: F 283 GLU cc_start: 0.5861 (tm-30) cc_final: 0.5255 (mm-30) REVERT: F 284 VAL cc_start: 0.3908 (OUTLIER) cc_final: 0.3129 (p) REVERT: F 286 GLU cc_start: 0.6005 (tm-30) cc_final: 0.5311 (pm20) REVERT: F 289 LEU cc_start: 0.7727 (tp) cc_final: 0.7435 (mt) REVERT: F 301 MET cc_start: -0.1186 (ttm) cc_final: -0.1996 (ttm) REVERT: F 397 GLU cc_start: 0.5148 (pp20) cc_final: 0.3294 (tt0) outliers start: 58 outliers final: 25 residues processed: 312 average time/residue: 0.1606 time to fit residues: 74.1622 Evaluate side-chains 279 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 245 time to evaluate : 0.877 ------------------------------------------------------------------------------- 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 166 SER Chi-restraints excluded: chain A residue 365 VAL 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 692 ASN Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 761 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 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 203 THR Chi-restraints excluded: chain E residue 22 ASP Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 62 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 176 SER Chi-restraints excluded: chain F residue 253 ILE 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: 2.9990 chunk 167 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 87 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 150 optimal weight: 7.9990 chunk 6 optimal weight: 9.9990 chunk 159 optimal weight: 0.4980 chunk 4 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.199025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.152218 restraints weight = 25433.045| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 3.69 r_work: 0.3110 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 20814 Z= 0.153 Angle : 0.578 10.052 28331 Z= 0.291 Chirality : 0.043 0.210 3121 Planarity : 0.004 0.049 3462 Dihedral : 13.738 165.701 3466 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 2.36 % Allowed : 13.08 % Favored : 84.56 % 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: -2.07 (0.17), residues: 2325 helix: -0.52 (0.17), residues: 893 sheet: -1.52 (0.27), residues: 335 loop : -2.02 (0.17), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 173 TYR 0.013 0.001 TYR F 111 PHE 0.020 0.001 PHE C 276 TRP 0.015 0.001 TRP C 156 HIS 0.005 0.001 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00356 (20797) covalent geometry : angle 0.57382 (28313) hydrogen bonds : bond 0.03609 ( 663) hydrogen bonds : angle 4.66632 ( 1938) metal coordination : bond 0.00554 ( 16) metal coordination : angle 2.91237 ( 15) link_TRANS : bond 0.00015 ( 1) link_TRANS : angle 0.14250 ( 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 313 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 267 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7637 (tm-30) REVERT: A 9 LEU cc_start: 0.8920 (mt) cc_final: 0.8582 (mt) REVERT: A 39 ARG cc_start: 0.8086 (mtm-85) cc_final: 0.7820 (mtm180) REVERT: A 124 ASN cc_start: 0.7957 (OUTLIER) cc_final: 0.7607 (t0) REVERT: A 155 ARG cc_start: 0.7289 (ttp-110) cc_final: 0.6977 (ttm110) REVERT: A 159 LYS cc_start: 0.8320 (tmmt) cc_final: 0.8059 (mmtm) REVERT: A 192 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7011 (mp0) REVERT: A 326 GLU cc_start: 0.8332 (mm-30) cc_final: 0.8021 (pt0) REVERT: A 336 GLU cc_start: 0.7378 (tm-30) cc_final: 0.7160 (tm-30) REVERT: A 493 LYS cc_start: 0.7847 (ptpp) cc_final: 0.7644 (mtmm) REVERT: A 532 MET cc_start: 0.8974 (mpp) cc_final: 0.8599 (mpp) REVERT: A 533 ASP cc_start: 0.8227 (p0) cc_final: 0.7990 (p0) REVERT: A 558 GLU cc_start: 0.7826 (tm-30) cc_final: 0.7519 (tm-30) REVERT: A 600 PHE cc_start: 0.8062 (t80) cc_final: 0.7680 (t80) REVERT: A 692 ASN cc_start: 0.8184 (OUTLIER) cc_final: 0.7571 (t0) REVERT: B 152 MET cc_start: 0.6422 (mtm) cc_final: 0.5234 (mmt) REVERT: C 256 ASP cc_start: 0.7393 (m-30) cc_final: 0.7069 (p0) REVERT: C 276 PHE cc_start: 0.7475 (OUTLIER) cc_final: 0.6857 (m-80) REVERT: D 172 ASP cc_start: 0.6938 (t0) cc_final: 0.6352 (t0) REVERT: D 184 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: E 22 ASP cc_start: 0.8143 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: E 128 ASP cc_start: 0.8560 (p0) cc_final: 0.8274 (p0) REVERT: E 205 ASP cc_start: 0.7928 (t0) cc_final: 0.7179 (p0) REVERT: J 101 MET cc_start: 0.3495 (tpt) cc_final: 0.2927 (tpt) REVERT: K 62 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8391 (mp) REVERT: K 66 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8257 (tt) REVERT: K 187 VAL cc_start: 0.8453 (p) cc_final: 0.8136 (m) REVERT: K 224 TYR cc_start: 0.7506 (p90) cc_final: 0.7259 (p90) REVERT: K 237 LYS cc_start: 0.7140 (tttt) cc_final: 0.6823 (tptp) REVERT: K 265 ARG cc_start: 0.7755 (mtm180) cc_final: 0.7529 (tpt90) REVERT: F 132 GLU cc_start: 0.1700 (tm-30) cc_final: 0.1343 (mt-10) REVERT: F 258 GLU cc_start: 0.5494 (tp30) cc_final: 0.5015 (tp30) REVERT: F 283 GLU cc_start: 0.5889 (tm-30) cc_final: 0.5246 (mm-30) REVERT: F 284 VAL cc_start: 0.3879 (OUTLIER) cc_final: 0.3085 (p) REVERT: F 286 GLU cc_start: 0.6054 (tm-30) cc_final: 0.5405 (pm20) REVERT: F 289 LEU cc_start: 0.7754 (tp) cc_final: 0.7466 (mt) REVERT: F 301 MET cc_start: -0.1218 (ttm) cc_final: -0.2021 (ttm) REVERT: F 397 GLU cc_start: 0.5197 (pp20) cc_final: 0.3625 (tt0) outliers start: 46 outliers final: 32 residues processed: 297 average time/residue: 0.1703 time to fit residues: 74.6120 Evaluate side-chains 290 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 249 time to evaluate : 0.750 ------------------------------------------------------------------------------- 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 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 580 ILE Chi-restraints excluded: chain A residue 692 ASN Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 761 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 21 LEU Chi-restraints excluded: chain D residue 66 LEU 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 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 18 VAL Chi-restraints excluded: chain K residue 47 LEU Chi-restraints excluded: chain K residue 62 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 176 SER Chi-restraints excluded: chain F residue 253 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: 0.8980 chunk 59 optimal weight: 0.9990 chunk 157 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 108 optimal weight: 0.6980 chunk 152 optimal weight: 0.8980 chunk 55 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN C 183 ASN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.200686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155213 restraints weight = 25285.774| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.57 r_work: 0.3141 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20814 Z= 0.113 Angle : 0.540 12.612 28331 Z= 0.271 Chirality : 0.042 0.192 3121 Planarity : 0.004 0.049 3462 Dihedral : 13.620 169.632 3466 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 2.26 % Allowed : 13.70 % Favored : 84.04 % 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: -1.75 (0.17), residues: 2325 helix: -0.18 (0.18), residues: 884 sheet: -1.33 (0.27), residues: 341 loop : -1.92 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 173 TYR 0.015 0.001 TYR K 250 PHE 0.049 0.001 PHE A 561 TRP 0.011 0.001 TRP C 156 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00256 (20797) covalent geometry : angle 0.53614 (28313) hydrogen bonds : bond 0.03321 ( 663) hydrogen bonds : angle 4.48529 ( 1938) metal coordination : bond 0.00842 ( 16) metal coordination : angle 2.71618 ( 15) link_TRANS : bond 0.00019 ( 1) link_TRANS : angle 0.14079 ( 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 314 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 270 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7626 (tm-30) REVERT: A 9 LEU cc_start: 0.8793 (mt) cc_final: 0.8494 (mt) REVERT: A 92 ASN cc_start: 0.8457 (m-40) cc_final: 0.7867 (m110) REVERT: A 124 ASN cc_start: 0.7938 (OUTLIER) cc_final: 0.7577 (t0) REVERT: A 155 ARG cc_start: 0.7215 (ttp-110) cc_final: 0.6969 (ttm110) REVERT: A 159 LYS cc_start: 0.8395 (tmmt) cc_final: 0.7891 (mmmm) REVERT: A 326 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7988 (pt0) REVERT: A 336 GLU cc_start: 0.7354 (tm-30) cc_final: 0.7077 (tm-30) REVERT: A 402 GLU cc_start: 0.8272 (mp0) cc_final: 0.8026 (mp0) REVERT: A 493 LYS cc_start: 0.7740 (ptpp) cc_final: 0.7347 (mtmm) REVERT: A 532 MET cc_start: 0.8921 (mpp) cc_final: 0.8468 (mpp) REVERT: A 558 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7506 (tm-30) REVERT: A 600 PHE cc_start: 0.7988 (t80) cc_final: 0.7590 (t80) REVERT: A 692 ASN cc_start: 0.8089 (OUTLIER) cc_final: 0.7477 (t0) REVERT: B 152 MET cc_start: 0.6070 (mtm) cc_final: 0.5096 (mmt) REVERT: C 256 ASP cc_start: 0.7403 (m-30) cc_final: 0.7096 (p0) REVERT: C 276 PHE cc_start: 0.7308 (OUTLIER) cc_final: 0.6808 (m-80) REVERT: D 64 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7967 (mm-30) REVERT: D 172 ASP cc_start: 0.6898 (t0) cc_final: 0.6297 (t0) REVERT: D 184 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: E 128 ASP cc_start: 0.8538 (p0) cc_final: 0.8213 (p0) REVERT: E 205 ASP cc_start: 0.7936 (t0) cc_final: 0.7167 (p0) REVERT: J 101 MET cc_start: 0.3481 (tpt) cc_final: 0.2686 (tpt) REVERT: J 123 MET cc_start: 0.3028 (ttt) cc_final: 0.2818 (ttt) REVERT: K 66 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8242 (tt) REVERT: K 76 GLU cc_start: 0.6851 (pp20) cc_final: 0.6446 (tp30) REVERT: K 187 VAL cc_start: 0.8424 (p) cc_final: 0.8119 (m) REVERT: K 224 TYR cc_start: 0.7443 (p90) cc_final: 0.7138 (p90) REVERT: K 267 LYS cc_start: 0.7576 (mmmt) cc_final: 0.6867 (tptp) REVERT: F 3 GLU cc_start: 0.5567 (tm-30) cc_final: 0.4255 (mp0) REVERT: F 258 GLU cc_start: 0.5376 (tp30) cc_final: 0.3594 (mm-30) REVERT: F 283 GLU cc_start: 0.5788 (tm-30) cc_final: 0.5217 (mm-30) REVERT: F 284 VAL cc_start: 0.3859 (OUTLIER) cc_final: 0.3109 (p) REVERT: F 286 GLU cc_start: 0.6074 (tm-30) cc_final: 0.5428 (pm20) REVERT: F 289 LEU cc_start: 0.7744 (tp) cc_final: 0.7473 (mt) REVERT: F 301 MET cc_start: -0.1187 (ttm) cc_final: -0.1987 (ttm) REVERT: F 397 GLU cc_start: 0.5266 (pp20) cc_final: 0.3835 (tt0) outliers start: 44 outliers final: 29 residues processed: 298 average time/residue: 0.1618 time to fit residues: 70.5880 Evaluate side-chains 292 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 256 time to evaluate : 0.576 ------------------------------------------------------------------------------- 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 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 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 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 1 MET Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 182 THR Chi-restraints excluded: chain E residue 244 MET Chi-restraints excluded: chain K residue 18 VAL 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 149 THR Chi-restraints excluded: chain K residue 164 GLU Chi-restraints excluded: chain K residue 176 SER Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 253 ILE 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: 2.9990 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 1.9990 chunk 200 optimal weight: 20.0000 chunk 102 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 175 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.194551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.150026 restraints weight = 25424.140| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.55 r_work: 0.3042 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 20814 Z= 0.284 Angle : 0.689 13.738 28331 Z= 0.347 Chirality : 0.048 0.269 3121 Planarity : 0.005 0.063 3462 Dihedral : 13.759 156.752 3466 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.57 % Favored : 92.43 % Rotamer: Outliers : 3.08 % Allowed : 13.19 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.88 (0.17), residues: 2325 helix: -0.37 (0.17), residues: 885 sheet: -1.35 (0.27), residues: 333 loop : -1.94 (0.18), residues: 1107 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 181 TYR 0.016 0.002 TYR A 634 PHE 0.050 0.002 PHE A 561 TRP 0.024 0.002 TRP C 156 HIS 0.010 0.002 HIS C 205 Details of bonding type rmsd covalent geometry : bond 0.00681 (20797) covalent geometry : angle 0.68518 (28313) hydrogen bonds : bond 0.04099 ( 663) hydrogen bonds : angle 4.91535 ( 1938) metal coordination : bond 0.00687 ( 16) metal coordination : angle 3.07742 ( 15) link_TRANS : bond 0.00021 ( 1) link_TRANS : angle 0.14035 ( 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 310 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 250 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8324 (OUTLIER) cc_final: 0.7898 (tm-30) REVERT: A 92 ASN cc_start: 0.8481 (m-40) cc_final: 0.7929 (m110) REVERT: A 124 ASN cc_start: 0.8124 (OUTLIER) cc_final: 0.7710 (t0) REVERT: A 159 LYS cc_start: 0.8488 (tmmt) cc_final: 0.7992 (mmmm) REVERT: A 336 GLU cc_start: 0.7470 (tm-30) cc_final: 0.7177 (tm-30) REVERT: A 493 LYS cc_start: 0.7746 (ptpp) cc_final: 0.7289 (mtmm) REVERT: A 558 GLU cc_start: 0.8030 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 629 GLU cc_start: 0.5490 (mp0) cc_final: 0.4273 (mp0) REVERT: A 692 ASN cc_start: 0.8094 (OUTLIER) cc_final: 0.7487 (t0) REVERT: B 149 LEU cc_start: 0.6755 (mt) cc_final: 0.6508 (mt) REVERT: B 152 MET cc_start: 0.6247 (mtm) cc_final: 0.5278 (mmt) REVERT: C 276 PHE cc_start: 0.7775 (OUTLIER) cc_final: 0.6819 (m-80) REVERT: D 84 TYR cc_start: 0.8864 (m-80) cc_final: 0.8627 (m-80) REVERT: D 172 ASP cc_start: 0.7039 (t0) cc_final: 0.6457 (t0) REVERT: D 184 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: E 22 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: E 128 ASP cc_start: 0.8666 (p0) cc_final: 0.8336 (p0) REVERT: E 205 ASP cc_start: 0.8144 (t0) cc_final: 0.7419 (p0) REVERT: J 101 MET cc_start: 0.3558 (tpt) cc_final: 0.2911 (tpt) REVERT: K 62 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8371 (mp) REVERT: K 97 CYS cc_start: 0.6201 (p) cc_final: 0.5833 (p) REVERT: K 187 VAL cc_start: 0.8537 (p) cc_final: 0.8227 (m) REVERT: K 267 LYS cc_start: 0.7608 (mmmt) cc_final: 0.6809 (tptp) REVERT: F 284 VAL cc_start: 0.3868 (OUTLIER) cc_final: 0.3429 (p) REVERT: F 286 GLU cc_start: 0.6112 (tm-30) cc_final: 0.5371 (pm20) REVERT: F 289 LEU cc_start: 0.7792 (tp) cc_final: 0.7507 (mt) REVERT: F 301 MET cc_start: -0.1118 (ttm) cc_final: -0.1883 (ttm) outliers start: 60 outliers final: 40 residues processed: 291 average time/residue: 0.1631 time to fit residues: 70.9108 Evaluate side-chains 286 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 238 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 25 LEU 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 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 761 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 96 ASN 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 148 LEU Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 203 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 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 65 ILE 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 F residue 6 LEU Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 249 THR 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: 0.9980 chunk 203 optimal weight: 3.9990 chunk 121 optimal weight: 0.2980 chunk 37 optimal weight: 0.2980 chunk 210 optimal weight: 1.9990 chunk 164 optimal weight: 0.7980 chunk 6 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 206 optimal weight: 8.9990 chunk 163 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 164 ASN C 205 HIS D 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.199897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.153278 restraints weight = 25467.694| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.60 r_work: 0.3146 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.3606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 20814 Z= 0.112 Angle : 0.556 13.935 28331 Z= 0.278 Chirality : 0.042 0.201 3121 Planarity : 0.004 0.055 3462 Dihedral : 13.678 166.583 3466 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 2.21 % Allowed : 14.67 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.17), residues: 2325 helix: -0.00 (0.18), residues: 887 sheet: -1.31 (0.26), residues: 341 loop : -1.85 (0.18), residues: 1097 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 181 TYR 0.027 0.001 TYR K 224 PHE 0.044 0.001 PHE A 561 TRP 0.029 0.001 TRP A 596 HIS 0.004 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00254 (20797) covalent geometry : angle 0.55195 (28313) hydrogen bonds : bond 0.03338 ( 663) hydrogen bonds : angle 4.49684 ( 1938) metal coordination : bond 0.00859 ( 16) metal coordination : angle 2.82961 ( 15) link_TRANS : bond 0.00021 ( 1) link_TRANS : angle 0.13988 ( 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 306 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 263 time to evaluate : 0.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7886 (tm-30) REVERT: A 39 ARG cc_start: 0.8033 (mtm180) cc_final: 0.7793 (mtm-85) REVERT: A 124 ASN cc_start: 0.7964 (OUTLIER) cc_final: 0.7585 (t0) REVERT: A 326 GLU cc_start: 0.8295 (mm-30) cc_final: 0.8006 (pt0) REVERT: A 336 GLU cc_start: 0.7285 (tm-30) cc_final: 0.6982 (tm-30) REVERT: A 402 GLU cc_start: 0.8105 (mp0) cc_final: 0.7805 (mp0) REVERT: A 493 LYS cc_start: 0.7768 (ptpp) cc_final: 0.7551 (mtmm) REVERT: A 532 MET cc_start: 0.8945 (mpp) cc_final: 0.8582 (mpp) REVERT: A 600 PHE cc_start: 0.8053 (t80) cc_final: 0.7727 (t80) REVERT: A 692 ASN cc_start: 0.8088 (OUTLIER) cc_final: 0.7467 (t0) REVERT: B 152 MET cc_start: 0.6177 (mtm) cc_final: 0.5201 (mmt) REVERT: B 153 LEU cc_start: 0.5704 (mm) cc_final: 0.4924 (tp) REVERT: B 164 ASN cc_start: 0.3625 (OUTLIER) cc_final: 0.2804 (p0) REVERT: C 256 ASP cc_start: 0.7453 (m-30) cc_final: 0.7163 (p0) REVERT: C 276 PHE cc_start: 0.7429 (OUTLIER) cc_final: 0.6814 (m-80) REVERT: D 64 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7947 (mm-30) REVERT: D 172 ASP cc_start: 0.6953 (t0) cc_final: 0.6429 (t0) REVERT: D 184 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7781 (tt0) REVERT: E 128 ASP cc_start: 0.8518 (p0) cc_final: 0.8203 (p0) REVERT: E 205 ASP cc_start: 0.8071 (t0) cc_final: 0.7291 (p0) REVERT: E 239 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8523 (mmm-85) REVERT: E 262 ARG cc_start: 0.8581 (ptm-80) cc_final: 0.8326 (ttp-110) REVERT: K 76 GLU cc_start: 0.6870 (pp20) cc_final: 0.6482 (tp30) REVERT: K 183 ASN cc_start: 0.6905 (t0) cc_final: 0.6537 (t0) REVERT: K 187 VAL cc_start: 0.8457 (p) cc_final: 0.8175 (m) REVERT: K 267 LYS cc_start: 0.7428 (mmmt) cc_final: 0.6676 (tptp) REVERT: F 252 GLU cc_start: 0.7936 (mt-10) cc_final: 0.7337 (mp0) REVERT: F 258 GLU cc_start: 0.5723 (tp30) cc_final: 0.5439 (tp30) REVERT: F 283 GLU cc_start: 0.5679 (tm-30) cc_final: 0.5171 (mm-30) REVERT: F 284 VAL cc_start: 0.3567 (OUTLIER) cc_final: 0.2943 (p) REVERT: F 286 GLU cc_start: 0.6095 (tm-30) cc_final: 0.5469 (pm20) REVERT: F 289 LEU cc_start: 0.7829 (tp) cc_final: 0.7581 (mt) REVERT: F 301 MET cc_start: -0.1129 (ttm) cc_final: -0.1998 (ttm) REVERT: F 397 GLU cc_start: 0.5395 (pp20) cc_final: 0.4219 (tt0) outliers start: 43 outliers final: 30 residues processed: 290 average time/residue: 0.1617 time to fit residues: 69.7154 Evaluate side-chains 283 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 246 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ASN 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 630 ARG 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 164 ASN 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 1 MET Chi-restraints excluded: chain D residue 21 LEU Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain E residue 23 THR Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 182 THR 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 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 F residue 6 LEU 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: 5.9990 chunk 170 optimal weight: 30.0000 chunk 74 optimal weight: 0.8980 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 174 optimal weight: 40.0000 chunk 112 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 205 optimal weight: 7.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 179 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.195258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.149585 restraints weight = 25122.446| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.53 r_work: 0.3060 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 20814 Z= 0.247 Angle : 0.669 14.106 28331 Z= 0.336 Chirality : 0.046 0.242 3121 Planarity : 0.005 0.059 3462 Dihedral : 13.705 160.056 3466 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.35 % Favored : 92.65 % Rotamer: Outliers : 2.51 % Allowed : 14.78 % Favored : 82.71 % 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: -1.70 (0.17), residues: 2325 helix: -0.16 (0.18), residues: 893 sheet: -1.28 (0.27), residues: 330 loop : -1.89 (0.18), residues: 1102 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 212 TYR 0.030 0.002 TYR K 224 PHE 0.051 0.002 PHE A 561 TRP 0.022 0.002 TRP C 156 HIS 0.007 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00588 (20797) covalent geometry : angle 0.66574 (28313) hydrogen bonds : bond 0.03894 ( 663) hydrogen bonds : angle 4.77630 ( 1938) metal coordination : bond 0.00568 ( 16) metal coordination : angle 2.98080 ( 15) link_TRANS : bond 0.00023 ( 1) link_TRANS : angle 0.13899 ( 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 294 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7891 (tm-30) REVERT: A 59 PHE cc_start: 0.8412 (m-80) cc_final: 0.8096 (m-80) REVERT: A 71 MET cc_start: 0.7085 (mmt) cc_final: 0.6757 (mmm) REVERT: A 92 ASN cc_start: 0.8444 (m-40) cc_final: 0.7894 (m110) REVERT: A 124 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7681 (t0) REVERT: A 159 LYS cc_start: 0.8415 (tmmt) cc_final: 0.7956 (mmmm) REVERT: A 336 GLU cc_start: 0.7421 (tm-30) cc_final: 0.7093 (tm-30) REVERT: A 402 GLU cc_start: 0.8055 (mp0) cc_final: 0.7712 (mp0) REVERT: A 493 LYS cc_start: 0.7681 (ptpp) cc_final: 0.7426 (mtmm) REVERT: A 600 PHE cc_start: 0.8178 (t80) cc_final: 0.7764 (t80) REVERT: A 692 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7465 (t0) REVERT: B 152 MET cc_start: 0.6100 (mtm) cc_final: 0.5111 (mmt) REVERT: B 153 LEU cc_start: 0.5757 (mm) cc_final: 0.4967 (tp) REVERT: C 276 PHE cc_start: 0.7779 (OUTLIER) cc_final: 0.6893 (m-80) REVERT: D 172 ASP cc_start: 0.6992 (t0) cc_final: 0.6449 (t0) REVERT: D 184 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7891 (tt0) REVERT: E 22 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7845 (m-30) REVERT: E 128 ASP cc_start: 0.8622 (p0) cc_final: 0.8288 (p0) REVERT: E 205 ASP cc_start: 0.8062 (t0) cc_final: 0.7431 (p0) REVERT: E 262 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.8279 (ttp-110) REVERT: K 76 GLU cc_start: 0.7018 (pp20) cc_final: 0.6522 (tp30) REVERT: K 97 CYS cc_start: 0.6494 (p) cc_final: 0.6132 (p) REVERT: K 187 VAL cc_start: 0.8489 (p) cc_final: 0.8190 (m) REVERT: F 252 GLU cc_start: 0.7924 (mt-10) cc_final: 0.7222 (mp0) REVERT: F 284 VAL cc_start: 0.3801 (OUTLIER) cc_final: 0.3375 (p) REVERT: F 286 GLU cc_start: 0.6032 (tm-30) cc_final: 0.5305 (pm20) REVERT: F 289 LEU cc_start: 0.7899 (tp) cc_final: 0.7642 (mt) REVERT: F 301 MET cc_start: -0.1163 (ttm) cc_final: -0.1891 (ttm) outliers start: 49 outliers final: 37 residues processed: 278 average time/residue: 0.1582 time to fit residues: 65.7037 Evaluate side-chains 283 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 239 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ASN 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 476 ILE 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 692 ASN Chi-restraints excluded: chain A residue 705 LEU Chi-restraints excluded: chain A residue 753 VAL Chi-restraints excluded: chain A residue 761 VAL Chi-restraints excluded: chain A residue 764 VAL Chi-restraints excluded: chain B residue 127 LEU 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 148 LEU Chi-restraints excluded: chain D residue 179 ASN Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 203 THR 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 182 THR 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 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 F residue 6 LEU Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain F residue 249 THR 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: 2.9990 chunk 188 optimal weight: 0.9990 chunk 140 optimal weight: 5.9990 chunk 195 optimal weight: 0.9980 chunk 96 optimal weight: 0.9980 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 160 optimal weight: 0.5980 chunk 22 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 GLN C 136 ASN D 179 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.198979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.152895 restraints weight = 25362.828| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 3.63 r_work: 0.3125 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 20814 Z= 0.121 Angle : 0.569 13.908 28331 Z= 0.283 Chirality : 0.042 0.195 3121 Planarity : 0.004 0.048 3462 Dihedral : 13.648 167.418 3466 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.76 % Favored : 94.24 % Rotamer: Outliers : 2.05 % Allowed : 15.29 % Favored : 82.66 % 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: -1.46 (0.17), residues: 2325 helix: 0.11 (0.18), residues: 888 sheet: -1.23 (0.27), residues: 331 loop : -1.77 (0.18), residues: 1106 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 181 TYR 0.029 0.001 TYR K 224 PHE 0.044 0.001 PHE A 561 TRP 0.018 0.001 TRP A 596 HIS 0.004 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00277 (20797) covalent geometry : angle 0.56511 (28313) hydrogen bonds : bond 0.03330 ( 663) hydrogen bonds : angle 4.45444 ( 1938) metal coordination : bond 0.00794 ( 16) metal coordination : angle 2.77490 ( 15) link_TRANS : bond 0.00025 ( 1) link_TRANS : angle 0.13672 ( 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 304 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 264 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8270 (OUTLIER) cc_final: 0.7897 (tm-30) REVERT: A 59 PHE cc_start: 0.8329 (m-80) cc_final: 0.8099 (m-80) REVERT: A 71 MET cc_start: 0.7215 (mmt) cc_final: 0.6952 (mmm) REVERT: A 124 ASN cc_start: 0.7984 (OUTLIER) cc_final: 0.7594 (t0) REVERT: A 159 LYS cc_start: 0.8345 (tmmt) cc_final: 0.7905 (mmmm) REVERT: A 336 GLU cc_start: 0.7315 (tm-30) cc_final: 0.6957 (tm-30) REVERT: A 402 GLU cc_start: 0.8047 (mp0) cc_final: 0.7718 (mp0) REVERT: A 493 LYS cc_start: 0.7666 (ptpp) cc_final: 0.7387 (mtmm) REVERT: A 532 MET cc_start: 0.8939 (mpp) cc_final: 0.8558 (mpp) REVERT: A 600 PHE cc_start: 0.8090 (t80) cc_final: 0.7770 (t80) REVERT: A 692 ASN cc_start: 0.7986 (OUTLIER) cc_final: 0.7430 (t0) REVERT: B 149 LEU cc_start: 0.6736 (mt) cc_final: 0.6152 (mt) REVERT: B 152 MET cc_start: 0.6116 (mtm) cc_final: 0.5144 (mmt) REVERT: B 153 LEU cc_start: 0.5462 (mm) cc_final: 0.4594 (tp) REVERT: C 276 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6912 (m-80) REVERT: D 64 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7966 (mm-30) REVERT: D 90 ARG cc_start: 0.8314 (ttm-80) cc_final: 0.7490 (ttp-170) REVERT: D 172 ASP cc_start: 0.6954 (t0) cc_final: 0.6448 (t0) REVERT: D 184 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7819 (tt0) REVERT: E 22 ASP cc_start: 0.8146 (OUTLIER) cc_final: 0.7899 (m-30) REVERT: E 128 ASP cc_start: 0.8574 (p0) cc_final: 0.8239 (p0) REVERT: E 239 ARG cc_start: 0.8826 (mmm-85) cc_final: 0.8540 (mmm-85) REVERT: E 262 ARG cc_start: 0.8526 (ptm-80) cc_final: 0.8296 (ttp-110) REVERT: K 76 GLU cc_start: 0.6924 (pp20) cc_final: 0.6494 (tp30) REVERT: K 187 VAL cc_start: 0.8444 (p) cc_final: 0.8142 (m) REVERT: K 267 LYS cc_start: 0.7457 (mmmt) cc_final: 0.6695 (tptp) REVERT: F 209 LEU cc_start: 0.7008 (tt) cc_final: 0.6689 (tt) REVERT: F 252 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7258 (mp0) REVERT: F 258 GLU cc_start: 0.5646 (tp30) cc_final: 0.5435 (tp30) REVERT: F 283 GLU cc_start: 0.5696 (tm-30) cc_final: 0.5150 (mm-30) REVERT: F 284 VAL cc_start: 0.3539 (OUTLIER) cc_final: 0.2881 (p) REVERT: F 286 GLU cc_start: 0.6071 (tm-30) cc_final: 0.5437 (pm20) REVERT: F 289 LEU cc_start: 0.7795 (tp) cc_final: 0.7585 (mt) REVERT: F 301 MET cc_start: -0.0336 (ttm) cc_final: -0.1221 (ttm) REVERT: F 397 GLU cc_start: 0.5105 (pp20) cc_final: 0.4182 (tt0) outliers start: 40 outliers final: 29 residues processed: 288 average time/residue: 0.1665 time to fit residues: 70.7654 Evaluate side-chains 289 residues out of total 2020 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 253 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 GLU Chi-restraints excluded: chain A residue 25 LEU Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 217 CYS 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 476 ILE Chi-restraints excluded: chain A residue 527 GLU Chi-restraints excluded: chain A residue 580 ILE 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 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 179 ASN 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 69 LYS Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 143 ILE Chi-restraints excluded: chain E residue 182 THR 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 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 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: 9.9990 chunk 8 optimal weight: 6.9990 chunk 211 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 192 optimal weight: 0.9990 chunk 156 optimal weight: 3.9990 chunk 202 optimal weight: 0.6980 chunk 128 optimal weight: 0.7980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 30 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 ASN D 179 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.197608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151174 restraints weight = 25344.136| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 3.72 r_work: 0.3101 rms_B_bonded: 4.67 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 20814 Z= 0.156 Angle : 0.600 13.398 28331 Z= 0.297 Chirality : 0.043 0.208 3121 Planarity : 0.004 0.057 3462 Dihedral : 13.619 166.388 3466 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.05 % Allowed : 15.85 % Favored : 82.09 % 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: -1.45 (0.17), residues: 2325 helix: 0.08 (0.18), residues: 895 sheet: -1.22 (0.27), residues: 329 loop : -1.75 (0.18), residues: 1101 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 173 TYR 0.029 0.001 TYR K 224 PHE 0.046 0.001 PHE A 561 TRP 0.018 0.001 TRP A 596 HIS 0.005 0.001 HIS C 111 Details of bonding type rmsd covalent geometry : bond 0.00367 (20797) covalent geometry : angle 0.59665 (28313) hydrogen bonds : bond 0.03479 ( 663) hydrogen bonds : angle 4.52717 ( 1938) metal coordination : bond 0.00518 ( 16) metal coordination : angle 2.70586 ( 15) link_TRANS : bond 0.00026 ( 1) link_TRANS : angle 0.13534 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5065.91 seconds wall clock time: 87 minutes 20.96 seconds (5240.96 seconds total)