Starting phenix.real_space_refine on Sun Oct 12 00:07:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6ifk_9653/10_2025/6ifk_9653.cif Found real_map, /net/cci-nas-00/data/ceres_data/6ifk_9653/10_2025/6ifk_9653.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6ifk_9653/10_2025/6ifk_9653.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6ifk_9653/10_2025/6ifk_9653.map" model { file = "/net/cci-nas-00/data/ceres_data/6ifk_9653/10_2025/6ifk_9653.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6ifk_9653/10_2025/6ifk_9653.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 73 5.49 5 Mg 2 5.21 5 S 37 5.16 5 C 12148 2.51 5 N 3307 2.21 5 O 3880 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 33 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19448 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 5812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 734, 5812 Classifications: {'peptide': 734} Incomplete info: {'truncation_to_alanine': 44} Link IDs: {'PTRANS': 8, 'TRANS': 725} Chain breaks: 3 Unresolved non-hydrogen bonds: 136 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 4, 'TYR:plan': 1, 'GLU:plan': 5, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 71 Chain: "D" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 995 Classifications: {'peptide': 121} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 119} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1695 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 6, 'TRANS': 210} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1697 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1697 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 209} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "E" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 207, 1626 Classifications: {'peptide': 207} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 201} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 2347 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 283} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 2786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2786 Classifications: {'peptide': 345} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 327} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "N" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 715 Classifications: {'RNA': 34} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 9, 'rna3p_pur': 8, 'rna3p_pyr': 10} Link IDs: {'rna2p': 16, 'rna3p': 17} Chain: "J" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 715 Classifications: {'RNA': 33} Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 1, 'rna3p_pur': 20, 'rna3p_pyr': 9} Link IDs: {'rna2p': 3, 'rna3p': 29} Chain: "A" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 65 Unusual residues: {' MG': 2, ' ZN': 1, 'ANP': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2925 SG CYS A 401 58.703 31.302 67.415 1.00 59.23 S ATOM 2948 SG CYS A 404 56.038 32.182 65.030 1.00 58.39 S ATOM 3070 SG CYS A 419 59.384 30.986 63.808 1.00 60.57 S ATOM 3092 SG CYS A 422 59.244 34.801 64.709 1.00 59.65 S Time building chain proxies: 4.74, per 1000 atoms: 0.24 Number of scatterers: 19448 At special positions: 0 Unit cell: (93.6, 137.28, 173.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 37 16.00 P 73 15.00 Mg 2 11.99 O 3880 8.00 N 3307 7.00 C 12148 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 705.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 805 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 404 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 419 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 401 " pdb="ZN ZN A 805 " - pdb=" SG CYS A 422 " Number of angles added : 6 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4258 Finding SS restraints... Secondary structure from input PDB file: 87 helices and 25 sheets defined 39.7% alpha, 12.7% beta 20 base pairs and 30 stacking pairs defined. Time for finding SS restraints: 2.45 Creating SS restraints... Processing helix chain 'A' and resid 5 through 12 Processing helix chain 'A' and resid 17 through 26 removed outlier: 3.540A pdb=" N ILE A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ARG A 23 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing helix chain 'A' and resid 30 through 39 removed outlier: 4.094A pdb=" N GLY A 35 " --> pdb=" O HIS A 31 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ALA A 36 " --> pdb=" O ALA A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 42 No H-bonds generated for 'chain 'A' and resid 40 through 42' Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.573A pdb=" N GLN A 51 " --> pdb=" O VAL A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 69 through 81 removed outlier: 3.629A pdb=" N SER A 81 " --> pdb=" O ASP A 77 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.767A pdb=" N VAL A 113 " --> pdb=" O ILE A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 142 removed outlier: 3.658A pdb=" N TYR A 141 " --> pdb=" O SER A 138 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N GLU A 142 " --> pdb=" O ALA A 139 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 138 through 142' Processing helix chain 'A' and resid 148 through 160 removed outlier: 3.890A pdb=" N ILE A 152 " --> pdb=" O ASP A 148 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A 154 " --> pdb=" O ALA A 150 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG A 155 " --> pdb=" O ALA A 151 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N GLU A 159 " --> pdb=" O ARG A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 181 removed outlier: 3.845A pdb=" N ASN A 175 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N THR A 180 " --> pdb=" O LEU A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 219 removed outlier: 3.777A pdb=" N ARG A 203 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 210 " --> pdb=" O ALA A 206 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS A 219 " --> pdb=" O TYR A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 removed outlier: 3.568A pdb=" N PHE A 229 " --> pdb=" O LYS A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 231 through 236 removed outlier: 3.561A pdb=" N PHE A 235 " --> pdb=" O LYS A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 256 Processing helix chain 'A' and resid 266 through 274 removed outlier: 4.255A pdb=" N ARG A 272 " --> pdb=" O GLN A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 289 removed outlier: 3.548A pdb=" N ALA A 284 " --> pdb=" O SER A 280 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N LEU A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 298 Processing helix chain 'A' and resid 313 through 335 removed outlier: 3.562A pdb=" N THR A 319 " --> pdb=" O LYS A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 362 removed outlier: 4.056A pdb=" N SER A 362 " --> pdb=" O SER A 359 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 359 through 362' Processing helix chain 'A' and resid 363 through 378 removed outlier: 3.984A pdb=" N LYS A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ALA A 370 " --> pdb=" O VAL A 366 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N SER A 371 " --> pdb=" O TYR A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 Processing helix chain 'A' and resid 412 through 416 removed outlier: 3.595A pdb=" N GLN A 416 " --> pdb=" O TYR A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 431 removed outlier: 4.723A pdb=" N TYR A 426 " --> pdb=" O CYS A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 461 removed outlier: 3.575A pdb=" N LYS A 460 " --> pdb=" O ALA A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 removed outlier: 4.408A pdb=" N ALA A 500 " --> pdb=" O TYR A 496 " (cutoff:3.500A) Processing helix chain 'A' and resid 524 through 529 Processing helix chain 'A' and resid 541 through 564 removed outlier: 3.882A pdb=" N SER A 545 " --> pdb=" O THR A 541 " (cutoff:3.500A) removed outlier: 5.354A pdb=" N ILE A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) removed outlier: 5.855A pdb=" N ASN A 561 " --> pdb=" O LYS A 557 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLN A 562 " --> pdb=" O VAL A 558 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 603 removed outlier: 3.779A pdb=" N PHE A 591 " --> pdb=" O ASP A 587 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS A 601 " --> pdb=" O GLU A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 638 removed outlier: 3.980A pdb=" N GLN A 628 " --> pdb=" O LEU A 624 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU A 632 " --> pdb=" O GLN A 628 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 638 " --> pdb=" O GLU A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 665 through 676 removed outlier: 3.631A pdb=" N HIS A 676 " --> pdb=" O TYR A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 681 through 694 removed outlier: 3.613A pdb=" N ILE A 685 " --> pdb=" O GLY A 681 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 712 removed outlier: 3.798A pdb=" N ALA A 701 " --> pdb=" O ARG A 697 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR A 708 " --> pdb=" O ALA A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 734 removed outlier: 4.057A pdb=" N LEU A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N SER A 731 " --> pdb=" O ASN A 727 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP A 732 " --> pdb=" O LEU A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 755 removed outlier: 3.760A pdb=" N ALA A 744 " --> pdb=" O ASP A 740 " (cutoff:3.500A) Processing helix chain 'D' and resid 8 through 18 Processing helix chain 'D' and resid 36 through 54 removed outlier: 3.698A pdb=" N LEU D 43 " --> pdb=" O LYS D 39 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU D 46 " --> pdb=" O ASN D 42 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N THR D 47 " --> pdb=" O LEU D 43 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N THR D 49 " --> pdb=" O SER D 45 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N LEU D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ASP D 52 " --> pdb=" O SER D 48 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 78 removed outlier: 3.858A pdb=" N ILE D 66 " --> pdb=" O LEU D 62 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG D 70 " --> pdb=" O ILE D 66 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N VAL D 71 " --> pdb=" O ALA D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 Processing helix chain 'D' and resid 85 through 90 Processing helix chain 'D' and resid 91 through 98 removed outlier: 3.764A pdb=" N LYS D 97 " --> pdb=" O LEU D 93 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N GLU D 98 " --> pdb=" O GLU D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 122 removed outlier: 3.558A pdb=" N LEU D 105 " --> pdb=" O ASP D 101 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG D 107 " --> pdb=" O GLU D 103 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG D 110 " --> pdb=" O GLN D 106 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU D 113 " --> pdb=" O CYS D 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 18 removed outlier: 3.581A pdb=" N ILE C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 36 through 39 Processing helix chain 'C' and resid 40 through 52 removed outlier: 3.654A pdb=" N LEU C 46 " --> pdb=" O ASN C 42 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 47 " --> pdb=" O LEU C 43 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N THR C 49 " --> pdb=" O SER C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 61 Processing helix chain 'C' and resid 62 through 80 removed outlier: 3.595A pdb=" N ALA C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TYR C 68 " --> pdb=" O ASP C 64 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ARG C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N GLU C 80 " --> pdb=" O GLN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 101 through 122 Processing helix chain 'G' and resid 48 through 60 removed outlier: 3.617A pdb=" N LYS G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N THR G 58 " --> pdb=" O GLY G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 65 removed outlier: 3.537A pdb=" N ASN G 65 " --> pdb=" O ALA G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 112 Processing helix chain 'G' and resid 166 through 178 removed outlier: 3.811A pdb=" N ARG G 171 " --> pdb=" O PHE G 167 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASP G 172 " --> pdb=" O LYS G 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 61 removed outlier: 3.578A pdb=" N LEU F 52 " --> pdb=" O PRO F 48 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N MET F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 75 Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.881A pdb=" N ARG F 81 " --> pdb=" O ASP F 77 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N LEU F 82 " --> pdb=" O ILE F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 112 Processing helix chain 'F' and resid 162 through 180 removed outlier: 3.721A pdb=" N LYS F 168 " --> pdb=" O GLU F 164 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL F 169 " --> pdb=" O GLU F 165 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ASP F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 189 Processing helix chain 'F' and resid 209 through 217 removed outlier: 4.153A pdb=" N GLU F 214 " --> pdb=" O LYS F 210 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N LEU F 215 " --> pdb=" O THR F 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 64 removed outlier: 3.609A pdb=" N LEU E 52 " --> pdb=" O PRO E 48 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS E 62 " --> pdb=" O THR E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 84 removed outlier: 3.843A pdb=" N ARG E 81 " --> pdb=" O ASP E 77 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU E 82 " --> pdb=" O ILE E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 removed outlier: 4.268A pdb=" N LYS E 92 " --> pdb=" O LYS E 89 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 113 removed outlier: 4.155A pdb=" N ASP E 110 " --> pdb=" O ALA E 106 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N SER E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 159 through 167 removed outlier: 3.895A pdb=" N VAL E 163 " --> pdb=" O GLU E 160 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N GLU E 164 " --> pdb=" O ASN E 161 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU E 165 " --> pdb=" O GLN E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 180 removed outlier: 3.688A pdb=" N LEU E 176 " --> pdb=" O ASP E 172 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LEU E 177 " --> pdb=" O GLY E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 189 removed outlier: 3.608A pdb=" N ARG E 188 " --> pdb=" O SER E 185 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N GLY E 189 " --> pdb=" O GLY E 186 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 185 through 189' Processing helix chain 'E' and resid 212 through 217 removed outlier: 3.600A pdb=" N THR E 217 " --> pdb=" O ASN E 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 41 Processing helix chain 'B' and resid 45 through 54 Processing helix chain 'B' and resid 89 through 100 removed outlier: 3.777A pdb=" N ARG B 95 " --> pdb=" O LYS B 91 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA B 97 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LYS B 98 " --> pdb=" O ARG B 94 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 99 " --> pdb=" O ARG B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 110 through 115 removed outlier: 3.658A pdb=" N LEU B 115 " --> pdb=" O VAL B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 177 removed outlier: 4.248A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 174 " --> pdb=" O MET B 170 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR B 175 " --> pdb=" O SER B 171 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 51 Processing helix chain 'H' and resid 52 through 54 No H-bonds generated for 'chain 'H' and resid 52 through 54' Processing helix chain 'H' and resid 55 through 64 removed outlier: 3.599A pdb=" N ILE H 64 " --> pdb=" O GLU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 73 Processing helix chain 'H' and resid 75 through 82 removed outlier: 3.807A pdb=" N LEU H 79 " --> pdb=" O LEU H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 143 removed outlier: 3.620A pdb=" N THR H 138 " --> pdb=" O GLY H 134 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE H 139 " --> pdb=" O ALA H 135 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 148 removed outlier: 3.771A pdb=" N ASN H 148 " --> pdb=" O PRO H 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 197 Processing helix chain 'H' and resid 236 through 245 removed outlier: 3.601A pdb=" N LEU H 242 " --> pdb=" O GLU H 238 " (cutoff:3.500A) Processing helix chain 'H' and resid 245 through 259 removed outlier: 3.659A pdb=" N GLN H 251 " --> pdb=" O GLY H 247 " (cutoff:3.500A) Processing helix chain 'H' and resid 266 through 270 Processing helix chain 'H' and resid 285 through 289 removed outlier: 3.624A pdb=" N THR H 288 " --> pdb=" O GLY H 285 " (cutoff:3.500A) Processing helix chain 'H' and resid 291 through 295 removed outlier: 3.639A pdb=" N ALA H 295 " --> pdb=" O PHE H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 303 removed outlier: 3.559A pdb=" N ARG H 302 " --> pdb=" O LEU H 299 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 311 removed outlier: 3.624A pdb=" N GLY A 344 " --> pdb=" O SER A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 Processing sheet with id=AA3, first strand: chain 'A' and resid 445 through 448 removed outlier: 6.566A pdb=" N ALA A 451 " --> pdb=" O ILE A 447 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N HIS A 436 " --> pdb=" O VAL A 456 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N ARG A 468 " --> pdb=" O ILE A 439 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 490 through 491 removed outlier: 4.245A pdb=" N TYR A 490 " --> pdb=" O ILE A 571 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE A 580 " --> pdb=" O ILE A 572 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ALA A 574 " --> pdb=" O ASP A 578 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASP A 578 " --> pdb=" O ALA A 574 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL A 579 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.976A pdb=" N PHE G 102 " --> pdb=" O ASP G 148 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 46 through 47 removed outlier: 3.976A pdb=" N PHE G 102 " --> pdb=" O ASP G 148 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS G 5 " --> pdb=" O VAL G 203 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLN G 11 " --> pdb=" O ASN G 197 " (cutoff:3.500A) removed outlier: 5.821A pdb=" N ASN G 197 " --> pdb=" O GLN G 11 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N ARG G 13 " --> pdb=" O PHE G 195 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N PHE G 195 " --> pdb=" O ARG G 13 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 118 through 122 Processing sheet with id=AA8, first strand: chain 'F' and resid 148 through 149 Processing sheet with id=AA9, first strand: chain 'F' and resid 148 through 149 removed outlier: 6.650A pdb=" N LYS F 5 " --> pdb=" O VAL F 203 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLN F 11 " --> pdb=" O ASN F 197 " (cutoff:3.500A) removed outlier: 5.583A pdb=" N ASN F 197 " --> pdb=" O GLN F 11 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG F 13 " --> pdb=" O PHE F 195 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N PHE F 195 " --> pdb=" O ARG F 13 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 118 through 126 Processing sheet with id=AB2, first strand: chain 'E' and resid 96 through 97 Processing sheet with id=AB3, first strand: chain 'E' and resid 96 through 97 removed outlier: 7.239A pdb=" N LYS E 5 " --> pdb=" O THR E 202 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N THR E 202 " --> pdb=" O LYS E 5 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N LYS E 7 " --> pdb=" O ALA E 200 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N ALA E 200 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N SER E 9 " --> pdb=" O LEU E 198 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU E 198 " --> pdb=" O SER E 9 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 38 through 39 removed outlier: 3.663A pdb=" N LEU E 44 " --> pdb=" O ASP E 39 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 118 through 123 Processing sheet with id=AB6, first strand: chain 'B' and resid 158 through 159 removed outlier: 3.822A pdb=" N VAL B 158 " --> pdb=" O TYR B 6 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 71 through 73 Processing sheet with id=AB8, first strand: chain 'B' and resid 127 through 128 removed outlier: 3.515A pdb=" N VAL B 127 " --> pdb=" O ARG B 149 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AC1, first strand: chain 'B' and resid 212 through 213 Processing sheet with id=AC2, first strand: chain 'B' and resid 273 through 274 Processing sheet with id=AC3, first strand: chain 'H' and resid 184 through 186 removed outlier: 3.887A pdb=" N ILE H 232 " --> pdb=" O PHE H 8 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 184 through 186 removed outlier: 3.887A pdb=" N ILE H 232 " --> pdb=" O PHE H 8 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 25 through 26 Processing sheet with id=AC6, first strand: chain 'H' and resid 37 through 40 Processing sheet with id=AC7, first strand: chain 'H' and resid 212 through 214 615 hydrogen bonds defined for protein. 1680 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 48 hydrogen bonds 96 hydrogen bond angles 0 basepair planarities 20 basepair parallelities 30 stacking parallelities Total time for adding SS restraints: 3.59 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 3672 1.32 - 1.45: 5301 1.45 - 1.57: 10770 1.57 - 1.69: 145 1.69 - 1.81: 67 Bond restraints: 19955 Sorted by residual: bond pdb=" O3A ANP A 802 " pdb=" PB ANP A 802 " ideal model delta sigma weight residual 1.700 1.550 0.150 2.00e-02 2.50e+03 5.64e+01 bond pdb=" O3A ANP A 801 " pdb=" PB ANP A 801 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.57e+01 bond pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 1.795 1.682 0.113 2.00e-02 2.50e+03 3.21e+01 bond pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " ideal model delta sigma weight residual 1.795 1.691 0.104 2.00e-02 2.50e+03 2.72e+01 bond pdb=" O5' ANP A 801 " pdb=" PA ANP A 801 " ideal model delta sigma weight residual 1.655 1.557 0.098 2.00e-02 2.50e+03 2.40e+01 ... (remaining 19950 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.59: 26977 4.59 - 9.18: 235 9.18 - 13.77: 25 13.77 - 18.36: 3 18.36 - 22.95: 2 Bond angle restraints: 27242 Sorted by residual: angle pdb=" N VAL H 336 " pdb=" CA VAL H 336 " pdb=" C VAL H 336 " ideal model delta sigma weight residual 110.62 120.90 -10.28 1.02e+00 9.61e-01 1.02e+02 angle pdb=" CA LEU H 199 " pdb=" CB LEU H 199 " pdb=" CG LEU H 199 " ideal model delta sigma weight residual 116.30 139.25 -22.95 3.50e+00 8.16e-02 4.30e+01 angle pdb=" PB ANP A 801 " pdb=" N3B ANP A 801 " pdb=" PG ANP A 801 " ideal model delta sigma weight residual 126.95 107.88 19.07 3.00e+00 1.11e-01 4.04e+01 angle pdb=" PB ANP A 802 " pdb=" N3B ANP A 802 " pdb=" PG ANP A 802 " ideal model delta sigma weight residual 126.95 109.21 17.74 3.00e+00 1.11e-01 3.50e+01 angle pdb=" O4' G N 9 " pdb=" C1' G N 9 " pdb=" N9 G N 9 " ideal model delta sigma weight residual 108.20 115.79 -7.59 1.50e+00 4.44e-01 2.56e+01 ... (remaining 27237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.96: 11767 33.96 - 67.93: 261 67.93 - 101.89: 46 101.89 - 135.86: 2 135.86 - 169.82: 3 Dihedral angle restraints: 12079 sinusoidal: 5478 harmonic: 6601 Sorted by residual: dihedral pdb=" CA PRO H 105 " pdb=" C PRO H 105 " pdb=" N ASN H 106 " pdb=" CA ASN H 106 " ideal model delta harmonic sigma weight residual 180.00 -135.66 -44.34 0 5.00e+00 4.00e-02 7.87e+01 dihedral pdb=" O4' C N 8 " pdb=" C1' C N 8 " pdb=" N1 C N 8 " pdb=" C2 C N 8 " ideal model delta sinusoidal sigma weight residual -128.00 41.82 -169.82 1 1.70e+01 3.46e-03 6.59e+01 dihedral pdb=" CA GLY H 90 " pdb=" C GLY H 90 " pdb=" N GLY H 91 " pdb=" CA GLY H 91 " ideal model delta harmonic sigma weight residual 180.00 -139.97 -40.03 0 5.00e+00 4.00e-02 6.41e+01 ... (remaining 12076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.084: 2582 0.084 - 0.167: 431 0.167 - 0.251: 40 0.251 - 0.334: 8 0.334 - 0.418: 5 Chirality restraints: 3066 Sorted by residual: chirality pdb=" CA VAL H 336 " pdb=" N VAL H 336 " pdb=" C VAL H 336 " pdb=" CB VAL H 336 " both_signs ideal model delta sigma weight residual False 2.44 2.02 0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" C1' G N 9 " pdb=" O4' G N 9 " pdb=" C2' G N 9 " pdb=" N9 G N 9 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.39 2.00e-01 2.50e+01 3.83e+00 chirality pdb=" C1' G N 21 " pdb=" O4' G N 21 " pdb=" C2' G N 21 " pdb=" N9 G N 21 " both_signs ideal model delta sigma weight residual False 2.44 2.07 0.36 2.00e-01 2.50e+01 3.30e+00 ... (remaining 3063 not shown) Planarity restraints: 3252 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G N 9 " 0.059 2.00e-02 2.50e+03 2.49e-02 1.86e+01 pdb=" N9 G N 9 " -0.057 2.00e-02 2.50e+03 pdb=" C8 G N 9 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G N 9 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G N 9 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G N 9 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G N 9 " 0.012 2.00e-02 2.50e+03 pdb=" N1 G N 9 " 0.009 2.00e-02 2.50e+03 pdb=" C2 G N 9 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G N 9 " -0.005 2.00e-02 2.50e+03 pdb=" N3 G N 9 " -0.013 2.00e-02 2.50e+03 pdb=" C4 G N 9 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 732 " -0.033 2.00e-02 2.50e+03 2.45e-02 1.51e+01 pdb=" CG TRP A 732 " 0.065 2.00e-02 2.50e+03 pdb=" CD1 TRP A 732 " -0.025 2.00e-02 2.50e+03 pdb=" CD2 TRP A 732 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 732 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP A 732 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 732 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 732 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 732 " -0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 732 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G N 21 " 0.048 2.00e-02 2.50e+03 2.22e-02 1.48e+01 pdb=" N9 G N 21 " -0.056 2.00e-02 2.50e+03 pdb=" C8 G N 21 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G N 21 " -0.003 2.00e-02 2.50e+03 pdb=" C5 G N 21 " 0.000 2.00e-02 2.50e+03 pdb=" C6 G N 21 " 0.000 2.00e-02 2.50e+03 pdb=" O6 G N 21 " 0.015 2.00e-02 2.50e+03 pdb=" N1 G N 21 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G N 21 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G N 21 " -0.008 2.00e-02 2.50e+03 pdb=" N3 G N 21 " -0.007 2.00e-02 2.50e+03 pdb=" C4 G N 21 " -0.005 2.00e-02 2.50e+03 ... (remaining 3249 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 248 2.62 - 3.19: 16546 3.19 - 3.76: 31361 3.76 - 4.33: 45137 4.33 - 4.90: 72667 Nonbonded interactions: 165959 Sorted by model distance: nonbonded pdb=" O1A ANP A 801 " pdb="MG MG A 803 " model vdw 2.046 2.170 nonbonded pdb=" OD2 ASP A 519 " pdb="MG MG A 803 " model vdw 2.140 2.170 nonbonded pdb=" O2B ANP A 801 " pdb="MG MG A 803 " model vdw 2.141 2.170 nonbonded pdb=" OD1 ASP A 519 " pdb="MG MG A 803 " model vdw 2.168 2.170 nonbonded pdb=" O PHE B 71 " pdb=" OH TYR B 157 " model vdw 2.170 3.040 ... (remaining 165954 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = (chain 'E' and (resid 2 through 159 or (resid 160 and (name N or name CA or name \ C or name O or name CB )) or resid 161 through 217)) selection = (chain 'F' and (resid 2 through 66 or resid 76 through 156 or (resid 157 through \ 158 and (name N or name CA or name C or name O or name CB )) or resid 159 or (r \ esid 160 and (name N or name CA or name C or name O or name CB )) or resid 161 t \ hrough 217)) selection = (chain 'G' and (resid 2 through 66 or resid 76 through 217)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 22.370 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7999 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 : 0.009 0.150 19961 Z= 0.418 Angle : 1.210 22.953 27248 Z= 0.626 Chirality : 0.064 0.418 3066 Planarity : 0.007 0.073 3252 Dihedral : 14.752 169.820 7821 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.31 % Allowed : 10.73 % Favored : 88.96 % Rotamer: Outliers : 1.01 % Allowed : 5.61 % Favored : 93.38 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 1.82 % Twisted General : 0.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.87 (0.13), residues: 2228 helix: -3.50 (0.11), residues: 805 sheet: -2.79 (0.25), residues: 332 loop : -3.13 (0.15), residues: 1091 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.002 ARG G 95 TYR 0.035 0.004 TYR H 218 PHE 0.060 0.004 PHE B 10 TRP 0.065 0.005 TRP A 732 HIS 0.016 0.003 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00926 (19955) covalent geometry : angle 1.19864 (27242) hydrogen bonds : bond 0.19239 ( 643) hydrogen bonds : angle 7.62905 ( 1776) metal coordination : bond 0.10934 ( 4) metal coordination : angle 11.26859 ( 6) Misc. bond : bond 0.00199 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 535 time to evaluate : 0.723 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 74 TYR cc_start: 0.7472 (t80) cc_final: 0.7119 (t80) REVERT: A 719 ARG cc_start: 0.7610 (ttt180) cc_final: 0.7127 (ttm-80) REVERT: C 14 GLU cc_start: 0.7859 (tp30) cc_final: 0.7599 (tp30) REVERT: G 138 ILE cc_start: 0.9133 (pt) cc_final: 0.8597 (mt) REVERT: F 11 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7643 (mp10) REVERT: E 12 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8230 (tt) REVERT: B 132 THR cc_start: 0.8745 (t) cc_final: 0.8436 (m) REVERT: B 198 LEU cc_start: 0.8342 (mt) cc_final: 0.8023 (mp) REVERT: H 4 ASP cc_start: 0.5886 (t0) cc_final: 0.5537 (t0) REVERT: H 249 ARG cc_start: 0.8352 (mtt-85) cc_final: 0.7949 (mtt-85) REVERT: H 307 LYS cc_start: 0.7418 (pmmt) cc_final: 0.7050 (pmmt) outliers start: 19 outliers final: 6 residues processed: 545 average time/residue: 0.1774 time to fit residues: 137.1615 Evaluate side-chains 303 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 296 time to evaluate : 0.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain H residue 218 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 5.9990 chunk 194 optimal weight: 8.9990 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 45 ASN A 78 ASN ** A 201 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 268 GLN A 305 HIS A 312 ASN A 414 HIS A 491 GLN A 562 GLN A 604 ASN ** A 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 677 GLN D 106 GLN G 159 ASN F 33 ASN F 85 ASN F 213 ASN E 33 ASN E 134 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 125 HIS B 152 ASN ** B 174 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 273 GLN B 284 HIS H 3 ASN ** H 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 104 ASN H 115 ASN H 151 ASN H 194 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.115025 restraints weight = 30900.562| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.84 r_work: 0.3291 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 19961 Z= 0.145 Angle : 0.704 14.709 27248 Z= 0.368 Chirality : 0.044 0.331 3066 Planarity : 0.004 0.044 3252 Dihedral : 15.922 171.352 3534 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.38 % Favored : 90.62 % Rotamer: Outliers : 1.69 % Allowed : 12.08 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.80 (0.15), residues: 2228 helix: -2.24 (0.15), residues: 816 sheet: -2.56 (0.25), residues: 342 loop : -2.69 (0.17), residues: 1070 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 107 TYR 0.017 0.002 TYR E 181 PHE 0.019 0.002 PHE A 655 TRP 0.028 0.002 TRP A 732 HIS 0.008 0.001 HIS A 695 Details of bonding type rmsd covalent geometry : bond 0.00306 (19955) covalent geometry : angle 0.70329 (27242) hydrogen bonds : bond 0.04142 ( 643) hydrogen bonds : angle 5.35652 ( 1776) metal coordination : bond 0.00571 ( 4) metal coordination : angle 1.93863 ( 6) Misc. bond : bond 0.00119 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 383 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 351 time to evaluate : 0.766 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8044 (t80) cc_final: 0.7765 (t80) REVERT: A 521 ASP cc_start: 0.9076 (m-30) cc_final: 0.8574 (m-30) REVERT: D 85 ASP cc_start: 0.8613 (t0) cc_final: 0.8110 (t0) REVERT: C 20 LEU cc_start: 0.7562 (tt) cc_final: 0.7239 (mp) REVERT: G 144 ASN cc_start: 0.8153 (t0) cc_final: 0.7949 (t0) REVERT: F 18 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8938 (tp) REVERT: F 123 GLU cc_start: 0.8468 (tt0) cc_final: 0.8223 (mt-10) REVERT: B 101 LYS cc_start: 0.8000 (ttmm) cc_final: 0.7640 (mmtm) REVERT: B 132 THR cc_start: 0.8984 (t) cc_final: 0.8641 (m) REVERT: B 152 ASN cc_start: 0.6753 (t160) cc_final: 0.6473 (p0) REVERT: B 229 MET cc_start: 0.8209 (mtp) cc_final: 0.7678 (mtp) REVERT: H 50 MET cc_start: 0.7308 (tmm) cc_final: 0.7090 (tmm) REVERT: H 54 ARG cc_start: 0.8005 (tpp80) cc_final: 0.7537 (mmp80) outliers start: 32 outliers final: 17 residues processed: 372 average time/residue: 0.1574 time to fit residues: 86.7471 Evaluate side-chains 292 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 274 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 98 GLU Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 86 optimal weight: 9.9990 chunk 127 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 48 optimal weight: 0.0370 chunk 201 optimal weight: 5.9990 chunk 146 optimal weight: 5.9990 chunk 57 optimal weight: 0.9980 chunk 175 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 107 optimal weight: 0.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 HIS A 158 ASN A 166 ASN A 463 GLN E 162 GLN B 11 GLN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN B 174 GLN H 19 HIS ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 148 ASN H 349 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.135971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.115665 restraints weight = 31097.500| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 1.84 r_work: 0.3295 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19961 Z= 0.129 Angle : 0.650 14.375 27248 Z= 0.337 Chirality : 0.043 0.327 3066 Planarity : 0.004 0.037 3252 Dihedral : 15.424 171.668 3532 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.02 % Favored : 90.93 % Rotamer: Outliers : 2.75 % Allowed : 12.87 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (0.16), residues: 2228 helix: -1.61 (0.16), residues: 833 sheet: -2.31 (0.26), residues: 335 loop : -2.51 (0.17), residues: 1060 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 107 TYR 0.018 0.001 TYR E 181 PHE 0.025 0.001 PHE D 51 TRP 0.021 0.002 TRP A 732 HIS 0.008 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00271 (19955) covalent geometry : angle 0.64993 (27242) hydrogen bonds : bond 0.03829 ( 643) hydrogen bonds : angle 4.92103 ( 1776) metal coordination : bond 0.00262 ( 4) metal coordination : angle 1.59050 ( 6) Misc. bond : bond 0.00134 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 316 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8081 (t80) cc_final: 0.7777 (t80) REVERT: A 521 ASP cc_start: 0.9058 (m-30) cc_final: 0.8731 (m-30) REVERT: D 98 GLU cc_start: 0.8056 (tm-30) cc_final: 0.7706 (tm-30) REVERT: C 20 LEU cc_start: 0.7574 (tt) cc_final: 0.7299 (mp) REVERT: G 32 ILE cc_start: 0.8854 (mt) cc_final: 0.8565 (mp) REVERT: G 144 ASN cc_start: 0.8046 (t0) cc_final: 0.7696 (t0) REVERT: F 215 LEU cc_start: 0.7500 (tt) cc_final: 0.6906 (mm) REVERT: E 117 TYR cc_start: 0.8789 (m-80) cc_final: 0.8542 (m-80) REVERT: B 5 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8616 (pp) REVERT: B 39 GLU cc_start: 0.7582 (tp30) cc_final: 0.7335 (tp30) REVERT: B 101 LYS cc_start: 0.8001 (ttmm) cc_final: 0.7618 (mmtm) REVERT: B 132 THR cc_start: 0.9001 (t) cc_final: 0.8615 (m) REVERT: B 157 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7918 (p90) REVERT: B 229 MET cc_start: 0.8292 (mtp) cc_final: 0.7889 (mtp) REVERT: H 50 MET cc_start: 0.7401 (OUTLIER) cc_final: 0.7165 (tmm) REVERT: H 54 ARG cc_start: 0.7935 (tpp80) cc_final: 0.7500 (mmp80) outliers start: 52 outliers final: 29 residues processed: 351 average time/residue: 0.1493 time to fit residues: 78.5109 Evaluate side-chains 302 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 218 TYR Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 2 optimal weight: 9.9990 chunk 170 optimal weight: 7.9990 chunk 99 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 221 optimal weight: 10.0000 chunk 201 optimal weight: 4.9990 chunk 7 optimal weight: 20.0000 chunk 150 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 115 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 ASN A 463 GLN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 GLN B 134 ASN B 152 ASN B 273 GLN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 72 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.129882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.109180 restraints weight = 31316.464| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.95 r_work: 0.3197 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 19961 Z= 0.244 Angle : 0.717 14.985 27248 Z= 0.373 Chirality : 0.046 0.361 3066 Planarity : 0.004 0.043 3252 Dihedral : 15.324 170.606 3532 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.23 % Favored : 89.72 % Rotamer: Outliers : 3.50 % Allowed : 14.30 % Favored : 82.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.98 (0.16), residues: 2228 helix: -1.29 (0.17), residues: 835 sheet: -2.29 (0.26), residues: 348 loop : -2.40 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 188 TYR 0.026 0.002 TYR D 9 PHE 0.027 0.002 PHE A 655 TRP 0.019 0.002 TRP A 732 HIS 0.007 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00549 (19955) covalent geometry : angle 0.71691 (27242) hydrogen bonds : bond 0.04046 ( 643) hydrogen bonds : angle 4.95695 ( 1776) metal coordination : bond 0.00770 ( 4) metal coordination : angle 1.79425 ( 6) Misc. bond : bond 0.00129 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 268 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8116 (t80) cc_final: 0.7810 (t80) REVERT: A 166 ASN cc_start: 0.7726 (OUTLIER) cc_final: 0.7379 (p0) REVERT: A 463 GLN cc_start: 0.7426 (OUTLIER) cc_final: 0.7181 (pt0) REVERT: A 521 ASP cc_start: 0.9146 (m-30) cc_final: 0.8702 (m-30) REVERT: D 21 GLU cc_start: 0.7086 (pm20) cc_final: 0.6767 (pm20) REVERT: C 20 LEU cc_start: 0.7538 (tt) cc_final: 0.7202 (mp) REVERT: G 32 ILE cc_start: 0.8907 (mt) cc_final: 0.8652 (mp) REVERT: G 144 ASN cc_start: 0.8318 (t0) cc_final: 0.7927 (t0) REVERT: F 215 LEU cc_start: 0.7437 (tt) cc_final: 0.7036 (mm) REVERT: E 117 TYR cc_start: 0.8770 (m-80) cc_final: 0.8482 (m-80) REVERT: B 5 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8444 (pp) REVERT: B 39 GLU cc_start: 0.7778 (tp30) cc_final: 0.7212 (tp30) REVERT: B 132 THR cc_start: 0.9138 (t) cc_final: 0.8682 (m) REVERT: B 157 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8100 (p90) REVERT: H 4 ASP cc_start: 0.6100 (t0) cc_final: 0.5482 (t0) REVERT: H 50 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.7132 (tmm) REVERT: H 54 ARG cc_start: 0.8160 (tpp80) cc_final: 0.7603 (mpt180) REVERT: H 229 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7819 (pt0) REVERT: H 262 LEU cc_start: 0.8371 (OUTLIER) cc_final: 0.8139 (mt) outliers start: 66 outliers final: 46 residues processed: 316 average time/residue: 0.1695 time to fit residues: 79.9658 Evaluate side-chains 301 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 249 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 463 GLN Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 624 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 717 THR Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 39 optimal weight: 9.9990 chunk 24 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 111 optimal weight: 20.0000 chunk 77 optimal weight: 0.9990 chunk 37 optimal weight: 8.9990 chunk 128 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 216 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** B 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.131872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.111906 restraints weight = 30884.937| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.79 r_work: 0.3254 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3130 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 19961 Z= 0.149 Angle : 0.642 14.213 27248 Z= 0.333 Chirality : 0.043 0.329 3066 Planarity : 0.004 0.035 3252 Dihedral : 15.202 171.219 3530 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.74 % Favored : 90.22 % Rotamer: Outliers : 3.87 % Allowed : 14.78 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.72 (0.17), residues: 2228 helix: -1.02 (0.17), residues: 840 sheet: -2.00 (0.27), residues: 331 loop : -2.37 (0.18), residues: 1057 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 149 TYR 0.021 0.002 TYR E 181 PHE 0.019 0.001 PHE B 58 TRP 0.016 0.002 TRP A 732 HIS 0.008 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00328 (19955) covalent geometry : angle 0.64149 (27242) hydrogen bonds : bond 0.03579 ( 643) hydrogen bonds : angle 4.79841 ( 1776) metal coordination : bond 0.00345 ( 4) metal coordination : angle 1.75721 ( 6) Misc. bond : bond 0.00102 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 276 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.8022 (t80) cc_final: 0.7711 (t80) REVERT: A 521 ASP cc_start: 0.9083 (m-30) cc_final: 0.8717 (m-30) REVERT: D 112 MET cc_start: 0.8656 (mmm) cc_final: 0.8435 (mmm) REVERT: C 20 LEU cc_start: 0.7495 (tt) cc_final: 0.7227 (mp) REVERT: G 18 LEU cc_start: 0.9030 (OUTLIER) cc_final: 0.8639 (pt) REVERT: G 144 ASN cc_start: 0.8204 (t0) cc_final: 0.7764 (t0) REVERT: F 215 LEU cc_start: 0.7234 (tt) cc_final: 0.6993 (mm) REVERT: E 117 TYR cc_start: 0.8722 (m-80) cc_final: 0.8380 (m-80) REVERT: B 5 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8463 (pp) REVERT: B 39 GLU cc_start: 0.7625 (tp30) cc_final: 0.7087 (tp30) REVERT: B 114 TYR cc_start: 0.8500 (t80) cc_final: 0.8251 (t80) REVERT: B 132 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8705 (m) REVERT: B 157 TYR cc_start: 0.8632 (OUTLIER) cc_final: 0.8312 (p90) REVERT: H 4 ASP cc_start: 0.6071 (t0) cc_final: 0.5434 (t0) REVERT: H 50 MET cc_start: 0.7312 (OUTLIER) cc_final: 0.7090 (tmm) REVERT: H 54 ARG cc_start: 0.8027 (tpp80) cc_final: 0.7651 (mpp80) REVERT: H 229 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7830 (pt0) REVERT: H 262 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8097 (mt) REVERT: H 307 LYS cc_start: 0.8040 (pmmt) cc_final: 0.7766 (pmmt) outliers start: 73 outliers final: 37 residues processed: 333 average time/residue: 0.1610 time to fit residues: 80.8185 Evaluate side-chains 301 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 258 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 728 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain H residue 50 MET Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 86 optimal weight: 7.9990 chunk 216 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 153 optimal weight: 5.9990 chunk 177 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 185 optimal weight: 0.0980 chunk 40 optimal weight: 3.9990 chunk 62 optimal weight: 10.0000 chunk 215 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 208 HIS ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.132908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.112916 restraints weight = 30814.731| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.81 r_work: 0.3269 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3145 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 19961 Z= 0.136 Angle : 0.625 13.816 27248 Z= 0.324 Chirality : 0.042 0.318 3066 Planarity : 0.003 0.034 3252 Dihedral : 15.074 171.132 3530 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 3.50 % Allowed : 15.36 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.17), residues: 2228 helix: -0.74 (0.18), residues: 834 sheet: -1.89 (0.27), residues: 336 loop : -2.31 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 149 TYR 0.025 0.001 TYR H 33 PHE 0.024 0.001 PHE B 58 TRP 0.015 0.001 TRP A 732 HIS 0.008 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00297 (19955) covalent geometry : angle 0.62445 (27242) hydrogen bonds : bond 0.03406 ( 643) hydrogen bonds : angle 4.65814 ( 1776) metal coordination : bond 0.00343 ( 4) metal coordination : angle 1.81667 ( 6) Misc. bond : bond 0.00120 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 282 time to evaluate : 0.780 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 TYR cc_start: 0.7982 (t80) cc_final: 0.7676 (t80) REVERT: A 521 ASP cc_start: 0.9075 (m-30) cc_final: 0.8721 (m-30) REVERT: A 548 PHE cc_start: 0.8468 (t80) cc_final: 0.8203 (t80) REVERT: D 58 GLU cc_start: 0.8082 (tp30) cc_final: 0.7687 (pm20) REVERT: D 98 GLU cc_start: 0.8061 (tm-30) cc_final: 0.7731 (tm-30) REVERT: C 20 LEU cc_start: 0.7457 (tt) cc_final: 0.7254 (mp) REVERT: G 18 LEU cc_start: 0.9050 (OUTLIER) cc_final: 0.8676 (pt) REVERT: G 144 ASN cc_start: 0.8159 (t0) cc_final: 0.7698 (t0) REVERT: F 80 SER cc_start: 0.9219 (m) cc_final: 0.8909 (m) REVERT: E 81 ARG cc_start: 0.8394 (ptt180) cc_final: 0.7991 (ptt-90) REVERT: E 117 TYR cc_start: 0.8709 (m-80) cc_final: 0.8317 (m-80) REVERT: E 190 TYR cc_start: 0.8687 (m-80) cc_final: 0.8336 (m-80) REVERT: B 5 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8425 (pp) REVERT: B 114 TYR cc_start: 0.8534 (t80) cc_final: 0.8320 (t80) REVERT: B 132 THR cc_start: 0.9146 (OUTLIER) cc_final: 0.8712 (m) REVERT: H 54 ARG cc_start: 0.8001 (tpp80) cc_final: 0.7489 (mpp80) REVERT: H 229 GLU cc_start: 0.8035 (mm-30) cc_final: 0.7832 (pt0) REVERT: H 262 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8088 (mt) REVERT: H 307 LYS cc_start: 0.8024 (pmmt) cc_final: 0.7794 (pmmt) outliers start: 66 outliers final: 41 residues processed: 329 average time/residue: 0.1677 time to fit residues: 82.0763 Evaluate side-chains 306 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 261 time to evaluate : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain E residue 215 LEU Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 217 LEU Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 209 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 140 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 113 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 overall best weight: 3.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 ASN A 322 GLN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.130471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.110254 restraints weight = 31153.138| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.86 r_work: 0.3215 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 19961 Z= 0.190 Angle : 0.656 14.075 27248 Z= 0.340 Chirality : 0.044 0.335 3066 Planarity : 0.004 0.041 3252 Dihedral : 15.008 171.203 3524 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.74 % Favored : 90.22 % Rotamer: Outliers : 3.28 % Allowed : 15.68 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.43 (0.17), residues: 2228 helix: -0.69 (0.18), residues: 819 sheet: -1.95 (0.26), residues: 351 loop : -2.22 (0.18), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 219 TYR 0.026 0.002 TYR B 157 PHE 0.030 0.002 PHE B 58 TRP 0.015 0.002 TRP A 732 HIS 0.009 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00427 (19955) covalent geometry : angle 0.65500 (27242) hydrogen bonds : bond 0.03622 ( 643) hydrogen bonds : angle 4.71999 ( 1776) metal coordination : bond 0.00579 ( 4) metal coordination : angle 1.99121 ( 6) Misc. bond : bond 0.00118 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 265 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8255 (tt) cc_final: 0.8053 (tt) REVERT: A 42 ILE cc_start: 0.7427 (OUTLIER) cc_final: 0.7191 (mp) REVERT: A 74 TYR cc_start: 0.8003 (t80) cc_final: 0.7701 (t80) REVERT: A 521 ASP cc_start: 0.9133 (m-30) cc_final: 0.8826 (m-30) REVERT: D 58 GLU cc_start: 0.8095 (tp30) cc_final: 0.7715 (pm20) REVERT: C 20 LEU cc_start: 0.7500 (tt) cc_final: 0.7116 (mp) REVERT: G 18 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8679 (pt) REVERT: G 32 ILE cc_start: 0.8962 (mt) cc_final: 0.8745 (mp) REVERT: G 144 ASN cc_start: 0.8227 (t0) cc_final: 0.7759 (t0) REVERT: E 81 ARG cc_start: 0.8458 (ptt180) cc_final: 0.8071 (ptt-90) REVERT: E 117 TYR cc_start: 0.8735 (m-80) cc_final: 0.8327 (m-80) REVERT: B 5 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8324 (pp) REVERT: B 39 GLU cc_start: 0.7668 (tp30) cc_final: 0.7355 (tp30) REVERT: B 132 THR cc_start: 0.9171 (OUTLIER) cc_final: 0.8718 (m) REVERT: B 157 TYR cc_start: 0.8763 (OUTLIER) cc_final: 0.8201 (p90) REVERT: H 4 ASP cc_start: 0.6171 (t0) cc_final: 0.5539 (t0) REVERT: H 54 ARG cc_start: 0.8087 (tpp80) cc_final: 0.7640 (mpt180) REVERT: H 65 GLN cc_start: 0.7794 (OUTLIER) cc_final: 0.7445 (pt0) REVERT: H 229 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7818 (pt0) REVERT: H 262 LEU cc_start: 0.8321 (OUTLIER) cc_final: 0.8096 (mt) outliers start: 62 outliers final: 43 residues processed: 310 average time/residue: 0.1656 time to fit residues: 76.5561 Evaluate side-chains 307 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 257 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 322 GLN Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain G residue 212 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 262 LEU Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 39 optimal weight: 7.9990 chunk 189 optimal weight: 0.9980 chunk 47 optimal weight: 8.9990 chunk 152 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 177 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 chunk 153 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.112008 restraints weight = 31055.852| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.85 r_work: 0.3247 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19961 Z= 0.161 Angle : 0.645 13.695 27248 Z= 0.334 Chirality : 0.043 0.328 3066 Planarity : 0.004 0.039 3252 Dihedral : 14.985 171.003 3524 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.56 % Favored : 90.39 % Rotamer: Outliers : 2.97 % Allowed : 16.53 % Favored : 80.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.17), residues: 2228 helix: -0.62 (0.18), residues: 821 sheet: -1.68 (0.28), residues: 331 loop : -2.20 (0.18), residues: 1076 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 149 TYR 0.027 0.002 TYR B 157 PHE 0.037 0.002 PHE B 58 TRP 0.015 0.002 TRP A 732 HIS 0.009 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00358 (19955) covalent geometry : angle 0.64396 (27242) hydrogen bonds : bond 0.03494 ( 643) hydrogen bonds : angle 4.67829 ( 1776) metal coordination : bond 0.00443 ( 4) metal coordination : angle 1.90891 ( 6) Misc. bond : bond 0.00115 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 264 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ILE cc_start: 0.7535 (OUTLIER) cc_final: 0.7263 (mp) REVERT: A 74 TYR cc_start: 0.7996 (t80) cc_final: 0.7699 (t80) REVERT: A 521 ASP cc_start: 0.9074 (m-30) cc_final: 0.8768 (m-30) REVERT: A 548 PHE cc_start: 0.8480 (t80) cc_final: 0.8218 (t80) REVERT: D 58 GLU cc_start: 0.8089 (tp30) cc_final: 0.7799 (pm20) REVERT: D 80 GLU cc_start: 0.7478 (tp30) cc_final: 0.7145 (tm-30) REVERT: C 20 LEU cc_start: 0.7520 (tt) cc_final: 0.7296 (mp) REVERT: G 18 LEU cc_start: 0.9104 (OUTLIER) cc_final: 0.8716 (pt) REVERT: G 32 ILE cc_start: 0.8928 (mt) cc_final: 0.8717 (mp) REVERT: G 144 ASN cc_start: 0.8172 (t0) cc_final: 0.7719 (t0) REVERT: E 117 TYR cc_start: 0.8735 (m-80) cc_final: 0.8323 (m-80) REVERT: E 214 GLU cc_start: 0.7265 (mp0) cc_final: 0.6796 (pt0) REVERT: B 5 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8386 (pp) REVERT: B 39 GLU cc_start: 0.7530 (tp30) cc_final: 0.7288 (tp30) REVERT: B 132 THR cc_start: 0.9131 (OUTLIER) cc_final: 0.8692 (m) REVERT: B 157 TYR cc_start: 0.8712 (OUTLIER) cc_final: 0.8227 (p90) REVERT: H 4 ASP cc_start: 0.6188 (t0) cc_final: 0.5561 (t0) REVERT: H 54 ARG cc_start: 0.8083 (tpp80) cc_final: 0.7642 (mpt180) REVERT: H 65 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7395 (pt0) REVERT: H 179 ASP cc_start: 0.7001 (OUTLIER) cc_final: 0.6209 (t0) REVERT: H 229 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7853 (pt0) outliers start: 56 outliers final: 42 residues processed: 303 average time/residue: 0.1642 time to fit residues: 75.0239 Evaluate side-chains 305 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 256 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain A residue 746 LEU Chi-restraints excluded: chain D residue 19 LYS Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 36 THR Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 11 GLN Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain E residue 12 ILE Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 101 SER Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 80 optimal weight: 10.0000 chunk 92 optimal weight: 0.9980 chunk 131 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 136 optimal weight: 6.9990 chunk 211 optimal weight: 9.9990 chunk 133 optimal weight: 0.0980 chunk 219 optimal weight: 7.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.114140 restraints weight = 30801.822| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 1.83 r_work: 0.3278 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19961 Z= 0.131 Angle : 0.628 13.366 27248 Z= 0.326 Chirality : 0.042 0.320 3066 Planarity : 0.004 0.047 3252 Dihedral : 14.916 171.063 3524 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.74 % Favored : 90.22 % Rotamer: Outliers : 2.81 % Allowed : 17.06 % Favored : 80.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.19 (0.17), residues: 2228 helix: -0.50 (0.18), residues: 825 sheet: -1.61 (0.28), residues: 326 loop : -2.17 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 149 TYR 0.028 0.001 TYR B 157 PHE 0.034 0.001 PHE B 58 TRP 0.018 0.002 TRP A 732 HIS 0.009 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00283 (19955) covalent geometry : angle 0.62717 (27242) hydrogen bonds : bond 0.03322 ( 643) hydrogen bonds : angle 4.57612 ( 1776) metal coordination : bond 0.00346 ( 4) metal coordination : angle 1.83314 ( 6) Misc. bond : bond 0.00107 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 274 time to evaluate : 0.777 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.7106 (tpp) cc_final: 0.6760 (tpp) REVERT: A 74 TYR cc_start: 0.7986 (t80) cc_final: 0.7685 (t80) REVERT: A 521 ASP cc_start: 0.9035 (m-30) cc_final: 0.8750 (m-30) REVERT: A 548 PHE cc_start: 0.8480 (t80) cc_final: 0.8246 (t80) REVERT: D 21 GLU cc_start: 0.6901 (pm20) cc_final: 0.6628 (pm20) REVERT: D 58 GLU cc_start: 0.8129 (tp30) cc_final: 0.7824 (pm20) REVERT: D 80 GLU cc_start: 0.7506 (tp30) cc_final: 0.7182 (tm-30) REVERT: D 85 ASP cc_start: 0.8525 (t0) cc_final: 0.8242 (t0) REVERT: C 20 LEU cc_start: 0.7435 (tt) cc_final: 0.7227 (mp) REVERT: G 18 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8656 (pt) REVERT: G 144 ASN cc_start: 0.8145 (t0) cc_final: 0.7681 (t0) REVERT: E 117 TYR cc_start: 0.8699 (m-80) cc_final: 0.8232 (m-80) REVERT: E 214 GLU cc_start: 0.7122 (mp0) cc_final: 0.6868 (pt0) REVERT: B 5 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8406 (pp) REVERT: B 132 THR cc_start: 0.9133 (OUTLIER) cc_final: 0.8714 (m) REVERT: B 157 TYR cc_start: 0.8630 (OUTLIER) cc_final: 0.8256 (p90) REVERT: H 54 ARG cc_start: 0.8013 (tpp80) cc_final: 0.7618 (mpp80) REVERT: H 65 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7430 (pt0) REVERT: H 179 ASP cc_start: 0.6933 (OUTLIER) cc_final: 0.6111 (t0) outliers start: 53 outliers final: 37 residues processed: 313 average time/residue: 0.1624 time to fit residues: 76.8017 Evaluate side-chains 298 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 255 time to evaluate : 0.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 18 LEU Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 324 LYS Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 173 optimal weight: 0.9990 chunk 139 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 98 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 181 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 224 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 166 ASN A 598 ASN ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 197 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.130019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.109765 restraints weight = 31229.477| |-----------------------------------------------------------------------------| r_work (start): 0.3350 rms_B_bonded: 1.85 r_work: 0.3205 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19961 Z= 0.226 Angle : 0.695 14.092 27248 Z= 0.360 Chirality : 0.045 0.348 3066 Planarity : 0.004 0.047 3252 Dihedral : 14.951 170.775 3524 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.05 % Favored : 89.90 % Rotamer: Outliers : 2.60 % Allowed : 17.48 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.26 (0.17), residues: 2228 helix: -0.60 (0.18), residues: 819 sheet: -1.63 (0.28), residues: 332 loop : -2.17 (0.18), residues: 1077 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 149 TYR 0.026 0.002 TYR B 157 PHE 0.044 0.002 PHE G 167 TRP 0.018 0.002 TRP A 732 HIS 0.009 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00512 (19955) covalent geometry : angle 0.69418 (27242) hydrogen bonds : bond 0.03704 ( 643) hydrogen bonds : angle 4.70055 ( 1776) metal coordination : bond 0.00731 ( 4) metal coordination : angle 2.19520 ( 6) Misc. bond : bond 0.00112 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4456 Ramachandran restraints generated. 2228 Oldfield, 0 Emsley, 2228 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 252 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LEU cc_start: 0.8230 (tt) cc_final: 0.8009 (tt) REVERT: A 74 TYR cc_start: 0.8024 (t80) cc_final: 0.7724 (t80) REVERT: A 521 ASP cc_start: 0.9085 (m-30) cc_final: 0.8766 (m-30) REVERT: D 21 GLU cc_start: 0.6974 (pm20) cc_final: 0.6729 (pm20) REVERT: D 58 GLU cc_start: 0.8200 (tp30) cc_final: 0.7882 (pm20) REVERT: D 80 GLU cc_start: 0.7577 (tp30) cc_final: 0.7070 (tm-30) REVERT: D 85 ASP cc_start: 0.8548 (t0) cc_final: 0.8257 (t0) REVERT: C 20 LEU cc_start: 0.7552 (tt) cc_final: 0.7176 (mp) REVERT: G 18 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8701 (pt) REVERT: G 144 ASN cc_start: 0.8235 (t0) cc_final: 0.7763 (t0) REVERT: E 81 ARG cc_start: 0.8485 (ptt180) cc_final: 0.8107 (ptt-90) REVERT: E 117 TYR cc_start: 0.8751 (m-80) cc_final: 0.8317 (m-80) REVERT: B 5 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8311 (pp) REVERT: B 157 TYR cc_start: 0.8875 (OUTLIER) cc_final: 0.8123 (p90) REVERT: H 54 ARG cc_start: 0.8157 (tpp80) cc_final: 0.7656 (mpt180) REVERT: H 65 GLN cc_start: 0.7792 (OUTLIER) cc_final: 0.7478 (pt0) REVERT: H 179 ASP cc_start: 0.7144 (OUTLIER) cc_final: 0.6324 (t0) outliers start: 49 outliers final: 38 residues processed: 287 average time/residue: 0.1643 time to fit residues: 71.0368 Evaluate side-chains 288 residues out of total 1952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 245 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Chi-restraints excluded: chain A residue 110 ILE Chi-restraints excluded: chain A residue 166 ASN Chi-restraints excluded: chain A residue 172 SER Chi-restraints excluded: chain A residue 193 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 366 VAL Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 469 VAL Chi-restraints excluded: chain A residue 615 LEU Chi-restraints excluded: chain A residue 689 ILE Chi-restraints excluded: chain A residue 703 LEU Chi-restraints excluded: chain D residue 31 ASP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 104 THR Chi-restraints excluded: chain C residue 3 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 74 VAL Chi-restraints excluded: chain G residue 15 GLU Chi-restraints excluded: chain G residue 18 LEU Chi-restraints excluded: chain G residue 41 ILE Chi-restraints excluded: chain G residue 111 SER Chi-restraints excluded: chain G residue 163 VAL Chi-restraints excluded: chain G residue 177 LEU Chi-restraints excluded: chain F residue 67 LYS Chi-restraints excluded: chain F residue 180 ASP Chi-restraints excluded: chain F residue 196 GLU Chi-restraints excluded: chain F residue 212 LEU Chi-restraints excluded: chain E residue 180 ASP Chi-restraints excluded: chain B residue 5 LEU Chi-restraints excluded: chain B residue 132 THR Chi-restraints excluded: chain B residue 157 TYR Chi-restraints excluded: chain B residue 237 THR Chi-restraints excluded: chain H residue 51 VAL Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 169 TRP Chi-restraints excluded: chain H residue 179 ASP Chi-restraints excluded: chain H residue 221 SER Chi-restraints excluded: chain H residue 274 LEU Chi-restraints excluded: chain H residue 315 VAL Chi-restraints excluded: chain H residue 323 LEU Chi-restraints excluded: chain H residue 352 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 228 random chunks: chunk 100 optimal weight: 0.7980 chunk 140 optimal weight: 8.9990 chunk 178 optimal weight: 5.9990 chunk 157 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 227 optimal weight: 10.0000 chunk 122 optimal weight: 5.9990 chunk 165 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 159 ASN ** B 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 152 ASN ** H 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.128864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.108719 restraints weight = 31251.125| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.84 r_work: 0.3199 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 19961 Z= 0.231 Angle : 0.701 14.148 27248 Z= 0.364 Chirality : 0.045 0.351 3066 Planarity : 0.004 0.047 3252 Dihedral : 14.973 169.976 3524 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 10.05 % Favored : 89.90 % Rotamer: Outliers : 2.81 % Allowed : 17.48 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.30 (0.17), residues: 2228 helix: -0.60 (0.18), residues: 813 sheet: -1.72 (0.27), residues: 343 loop : -2.18 (0.18), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 171 TYR 0.025 0.002 TYR B 157 PHE 0.042 0.002 PHE G 167 TRP 0.020 0.002 TRP A 732 HIS 0.009 0.001 HIS B 81 Details of bonding type rmsd covalent geometry : bond 0.00522 (19955) covalent geometry : angle 0.70070 (27242) hydrogen bonds : bond 0.03740 ( 643) hydrogen bonds : angle 4.77094 ( 1776) metal coordination : bond 0.00681 ( 4) metal coordination : angle 2.18131 ( 6) Misc. bond : bond 0.00112 ( 2) =============================================================================== Job complete usr+sys time: 5294.96 seconds wall clock time: 91 minutes 35.95 seconds (5495.95 seconds total)