Starting phenix.real_space_refine on Sun Aug 24 17:28:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eau_27986/08_2025/8eau_27986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eau_27986/08_2025/8eau_27986.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8eau_27986/08_2025/8eau_27986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eau_27986/08_2025/8eau_27986.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8eau_27986/08_2025/8eau_27986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eau_27986/08_2025/8eau_27986.map" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.207 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: 4 Type Number sf(0) Gaussians S 130 5.16 5 C 14389 2.51 5 N 3520 2.21 5 O 3870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 37 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21909 Number of models: 1 Model: "" Number of chains: 16 Chain: "a" Number of atoms: 5975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 758, 5975 Classifications: {'peptide': 758} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 21, 'TRANS': 736} Chain breaks: 2 Unresolved non-hydrogen bonds: 171 Unresolved non-hydrogen angles: 217 Unresolved non-hydrogen dihedrals: 140 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLU:plan': 6, 'TYR:plan': 5, 'ASP:plan': 10, 'ARG:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 105 Chain: "b" Number of atoms: 363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 363 Classifications: {'peptide': 47} Link IDs: {'TRANS': 46} Chain: "c" Number of atoms: 1483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1483 Classifications: {'peptide': 200} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 197} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "d" Number of atoms: 2523 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2523 Classifications: {'peptide': 324} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 314} Chain breaks: 2 Unresolved non-hydrogen bonds: 112 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 7, 'GLN:plan1': 3, 'ARG:plan': 2, 'ASP:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 2} Unresolved non-hydrogen planarities: 82 Chain: "e" Number of atoms: 572 Number of conformers: 1 Conformer: "" Number of residues, atoms: 72, 572 Classifications: {'peptide': 72} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 67} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'GLU%COO:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 522 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "g" Number of atoms: 1106 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1106 Classifications: {'peptide': 155} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 149} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "h" Number of atoms: 1138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1138 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 153} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "i" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1128 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "j" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1111 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "k" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1104 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 11 Chain: "l" Number of atoms: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1131 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "m" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1111 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "n" Number of atoms: 1084 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1084 Classifications: {'peptide': 158} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 152} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 24 Chain: "o" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1133 Classifications: {'peptide': 158} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 151} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "p" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 425 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Time building chain proxies: 4.80, per 1000 atoms: 0.22 Number of scatterers: 21909 At special positions: 0 Unit cell: (122.57, 114.33, 132.87, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 130 16.00 O 3870 8.00 N 3520 7.00 C 14389 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 973.2 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5312 Finding SS restraints... Secondary structure from input PDB file: 121 helices and 6 sheets defined 80.2% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'a' and resid 25 through 37 Processing helix chain 'a' and resid 49 through 53 Processing helix chain 'a' and resid 55 through 79 Processing helix chain 'a' and resid 87 through 93 Processing helix chain 'a' and resid 105 through 146 removed outlier: 3.567A pdb=" N GLU a 119 " --> pdb=" O SER a 115 " (cutoff:3.500A) Processing helix chain 'a' and resid 194 through 207 removed outlier: 4.333A pdb=" N THR a 198 " --> pdb=" O ASP a 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 242 through 255 removed outlier: 3.576A pdb=" N SER a 255 " --> pdb=" O LYS a 251 " (cutoff:3.500A) Processing helix chain 'a' and resid 266 through 324 removed outlier: 3.876A pdb=" N THR a 290 " --> pdb=" O THR a 286 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N GLU a 305 " --> pdb=" O ALA a 301 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ASP a 307 " --> pdb=" O ALA a 303 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N SER a 308 " --> pdb=" O LYS a 304 " (cutoff:3.500A) Processing helix chain 'a' and resid 345 through 361 Processing helix chain 'a' and resid 387 through 395 Processing helix chain 'a' and resid 407 through 424 removed outlier: 4.415A pdb=" N VAL a 413 " --> pdb=" O LEU a 409 " (cutoff:3.500A) Proline residue: a 416 - end of helix Processing helix chain 'a' and resid 425 through 441 removed outlier: 3.624A pdb=" N LEU a 439 " --> pdb=" O ALA a 435 " (cutoff:3.500A) Processing helix chain 'a' and resid 442 through 447 Processing helix chain 'a' and resid 453 through 461 Processing helix chain 'a' and resid 461 through 479 Processing helix chain 'a' and resid 519 through 523 Processing helix chain 'a' and resid 527 through 562 removed outlier: 3.637A pdb=" N PHE a 531 " --> pdb=" O ASN a 527 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N PHE a 554 " --> pdb=" O TYR a 550 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N SER a 555 " --> pdb=" O SER a 551 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU a 556 " --> pdb=" O TYR a 552 " (cutoff:3.500A) Processing helix chain 'a' and resid 564 through 571 Processing helix chain 'a' and resid 571 through 596 removed outlier: 4.768A pdb=" N TYR a 585 " --> pdb=" O GLY a 581 " (cutoff:3.500A) Processing helix chain 'a' and resid 597 through 602 Processing helix chain 'a' and resid 607 through 618 removed outlier: 3.947A pdb=" N PHE a 616 " --> pdb=" O LEU a 612 " (cutoff:3.500A) Processing helix chain 'a' and resid 629 through 660 removed outlier: 3.707A pdb=" N ILE a 645 " --> pdb=" O ALA a 641 " (cutoff:3.500A) Proline residue: a 646 - end of helix removed outlier: 4.711A pdb=" N LYS a 652 " --> pdb=" O LEU a 648 " (cutoff:3.500A) Proline residue: a 653 - end of helix Processing helix chain 'a' and resid 711 through 733 removed outlier: 3.771A pdb=" N VAL a 727 " --> pdb=" O CYS a 723 " (cutoff:3.500A) Processing helix chain 'a' and resid 734 through 755 Processing helix chain 'a' and resid 757 through 761 Processing helix chain 'a' and resid 763 through 784 Processing helix chain 'a' and resid 789 through 803 Processing helix chain 'a' and resid 805 through 810 removed outlier: 4.150A pdb=" N PHE a 809 " --> pdb=" O SER a 805 " (cutoff:3.500A) Processing helix chain 'a' and resid 826 through 831 Processing helix chain 'b' and resid 220 through 246 Processing helix chain 'b' and resid 250 through 254 removed outlier: 3.682A pdb=" N ALA b 253 " --> pdb=" O THR b 250 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 39 Processing helix chain 'c' and resid 41 through 45 Processing helix chain 'c' and resid 46 through 54 Processing helix chain 'c' and resid 55 through 90 removed outlier: 3.859A pdb=" N TRP c 59 " --> pdb=" O SER c 55 " (cutoff:3.500A) Processing helix chain 'c' and resid 91 through 92 No H-bonds generated for 'chain 'c' and resid 91 through 92' Processing helix chain 'c' and resid 93 through 94 No H-bonds generated for 'chain 'c' and resid 93 through 94' Processing helix chain 'c' and resid 95 through 123 removed outlier: 3.665A pdb=" N LYS c 99 " --> pdb=" O ARG c 95 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ILE c 102 " --> pdb=" O THR c 98 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N SER c 103 " --> pdb=" O LYS c 99 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ILE c 104 " --> pdb=" O ASN c 100 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA c 111 " --> pdb=" O CYS c 107 " (cutoff:3.500A) Processing helix chain 'c' and resid 129 through 133 Processing helix chain 'c' and resid 135 through 177 Processing helix chain 'c' and resid 180 through 208 removed outlier: 4.043A pdb=" N ILE c 184 " --> pdb=" O LEU c 180 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N VAL c 186 " --> pdb=" O VAL c 182 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE c 187 " --> pdb=" O LYS c 183 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LYS c 208 " --> pdb=" O LEU c 204 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 7 removed outlier: 3.799A pdb=" N PHE d 6 " --> pdb=" O GLU d 2 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ASN d 7 " --> pdb=" O GLY d 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 2 through 7' Processing helix chain 'd' and resid 9 through 23 removed outlier: 4.586A pdb=" N ILE d 13 " --> pdb=" O ASP d 9 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 35 Processing helix chain 'd' and resid 38 through 48 Processing helix chain 'd' and resid 64 through 86 Processing helix chain 'd' and resid 88 through 111 removed outlier: 3.583A pdb=" N ARG d 92 " --> pdb=" O SER d 88 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY d 101 " --> pdb=" O TYR d 97 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N TYR d 102 " --> pdb=" O ILE d 98 " (cutoff:3.500A) Processing helix chain 'd' and resid 128 through 132 Processing helix chain 'd' and resid 136 through 142 Processing helix chain 'd' and resid 144 through 146 No H-bonds generated for 'chain 'd' and resid 144 through 146' Processing helix chain 'd' and resid 147 through 152 Processing helix chain 'd' and resid 153 through 156 Processing helix chain 'd' and resid 177 through 200 Processing helix chain 'd' and resid 201 through 228 Processing helix chain 'd' and resid 236 through 241 Processing helix chain 'd' and resid 250 through 259 Processing helix chain 'd' and resid 261 through 270 Processing helix chain 'd' and resid 283 through 301 removed outlier: 3.680A pdb=" N THR d 301 " --> pdb=" O ARG d 297 " (cutoff:3.500A) Processing helix chain 'd' and resid 306 through 332 removed outlier: 4.009A pdb=" N TRP d 310 " --> pdb=" O ILE d 306 " (cutoff:3.500A) Processing helix chain 'd' and resid 334 through 338 Processing helix chain 'e' and resid 4 through 25 removed outlier: 3.586A pdb=" N VAL e 8 " --> pdb=" O PHE e 4 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 55 removed outlier: 4.581A pdb=" N ILE e 38 " --> pdb=" O ARG e 34 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN e 55 " --> pdb=" O THR e 51 " (cutoff:3.500A) Processing helix chain 'e' and resid 68 through 72 Processing helix chain 'f' and resid 6 through 33 Processing helix chain 'f' and resid 35 through 40 Processing helix chain 'f' and resid 47 through 72 removed outlier: 3.597A pdb=" N VAL f 51 " --> pdb=" O ASP f 47 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR f 54 " --> pdb=" O ALA f 50 " (cutoff:3.500A) Processing helix chain 'g' and resid 8 through 44 removed outlier: 4.193A pdb=" N PHE g 12 " --> pdb=" O TYR g 8 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLY g 13 " --> pdb=" O ALA g 9 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ILE g 21 " --> pdb=" O CYS g 17 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N VAL g 44 " --> pdb=" O CYS g 40 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 48 No H-bonds generated for 'chain 'g' and resid 46 through 48' Processing helix chain 'g' and resid 49 through 54 Processing helix chain 'g' and resid 54 through 76 Processing helix chain 'g' and resid 83 through 122 Processing helix chain 'g' and resid 124 through 152 removed outlier: 4.423A pdb=" N GLY g 128 " --> pdb=" O ARG g 124 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE g 135 " --> pdb=" O LEU g 131 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU g 139 " --> pdb=" O PHE g 135 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY g 140 " --> pdb=" O ALA g 136 " (cutoff:3.500A) Processing helix chain 'h' and resid 8 through 44 removed outlier: 4.196A pdb=" N PHE h 12 " --> pdb=" O TYR h 8 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY h 13 " --> pdb=" O ALA h 9 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE h 21 " --> pdb=" O CYS h 17 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL h 44 " --> pdb=" O CYS h 40 " (cutoff:3.500A) Processing helix chain 'h' and resid 46 through 48 No H-bonds generated for 'chain 'h' and resid 46 through 48' Processing helix chain 'h' and resid 49 through 54 removed outlier: 3.518A pdb=" N ILE h 54 " --> pdb=" O LEU h 50 " (cutoff:3.500A) Processing helix chain 'h' and resid 54 through 77 Processing helix chain 'h' and resid 83 through 120 Processing helix chain 'h' and resid 124 through 154 removed outlier: 4.372A pdb=" N GLY h 128 " --> pdb=" O ARG h 124 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N LEU h 139 " --> pdb=" O PHE h 135 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLY h 140 " --> pdb=" O ALA h 136 " (cutoff:3.500A) Processing helix chain 'i' and resid 8 through 44 removed outlier: 4.296A pdb=" N PHE i 12 " --> pdb=" O TYR i 8 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLY i 13 " --> pdb=" O ALA i 9 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE i 21 " --> pdb=" O CYS i 17 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR i 24 " --> pdb=" O ALA i 20 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N GLY i 38 " --> pdb=" O LYS i 34 " (cutoff:3.500A) Processing helix chain 'i' and resid 46 through 48 No H-bonds generated for 'chain 'i' and resid 46 through 48' Processing helix chain 'i' and resid 49 through 54 Processing helix chain 'i' and resid 54 through 78 removed outlier: 3.608A pdb=" N ILE i 63 " --> pdb=" O MET i 59 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA i 64 " --> pdb=" O ALA i 60 " (cutoff:3.500A) Processing helix chain 'i' and resid 83 through 122 removed outlier: 4.039A pdb=" N ARG i 117 " --> pdb=" O ASP i 113 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 155 removed outlier: 4.140A pdb=" N GLY i 128 " --> pdb=" O ARG i 124 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N LEU i 139 " --> pdb=" O PHE i 135 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY i 140 " --> pdb=" O ALA i 136 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N THR i 155 " --> pdb=" O ASN i 151 " (cutoff:3.500A) Processing helix chain 'j' and resid 8 through 44 removed outlier: 4.193A pdb=" N PHE j 12 " --> pdb=" O TYR j 8 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY j 13 " --> pdb=" O ALA j 9 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE j 21 " --> pdb=" O CYS j 17 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N THR j 24 " --> pdb=" O ALA j 20 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N THR j 42 " --> pdb=" O GLY j 38 " (cutoff:3.500A) Processing helix chain 'j' and resid 46 through 48 No H-bonds generated for 'chain 'j' and resid 46 through 48' Processing helix chain 'j' and resid 49 through 54 Processing helix chain 'j' and resid 54 through 78 Processing helix chain 'j' and resid 83 through 120 removed outlier: 3.729A pdb=" N SER j 120 " --> pdb=" O VAL j 116 " (cutoff:3.500A) Processing helix chain 'j' and resid 124 through 154 removed outlier: 4.316A pdb=" N GLY j 128 " --> pdb=" O ARG j 124 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU j 139 " --> pdb=" O PHE j 135 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY j 140 " --> pdb=" O ALA j 136 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 43 removed outlier: 4.337A pdb=" N PHE k 12 " --> pdb=" O TYR k 8 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLY k 13 " --> pdb=" O ALA k 9 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE k 21 " --> pdb=" O CYS k 17 " (cutoff:3.500A) Processing helix chain 'k' and resid 44 through 45 No H-bonds generated for 'chain 'k' and resid 44 through 45' Processing helix chain 'k' and resid 46 through 48 No H-bonds generated for 'chain 'k' and resid 46 through 48' Processing helix chain 'k' and resid 49 through 54 Processing helix chain 'k' and resid 54 through 76 Processing helix chain 'k' and resid 83 through 122 removed outlier: 3.871A pdb=" N ARG k 117 " --> pdb=" O ASP k 113 " (cutoff:3.500A) Processing helix chain 'k' and resid 125 through 153 removed outlier: 3.960A pdb=" N LEU k 139 " --> pdb=" O PHE k 135 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLY k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) Processing helix chain 'l' and resid 8 through 46 removed outlier: 4.232A pdb=" N PHE l 12 " --> pdb=" O TYR l 8 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY l 13 " --> pdb=" O ALA l 9 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ILE l 21 " --> pdb=" O CYS l 17 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR l 24 " --> pdb=" O ALA l 20 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL l 44 " --> pdb=" O CYS l 40 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N LEU l 45 " --> pdb=" O ALA l 41 " (cutoff:3.500A) Processing helix chain 'l' and resid 49 through 54 Processing helix chain 'l' and resid 54 through 76 Processing helix chain 'l' and resid 83 through 120 removed outlier: 3.592A pdb=" N SER l 100 " --> pdb=" O SER l 96 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N SER l 120 " --> pdb=" O VAL l 116 " (cutoff:3.500A) Processing helix chain 'l' and resid 124 through 153 removed outlier: 4.452A pdb=" N GLY l 128 " --> pdb=" O ARG l 124 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY l 140 " --> pdb=" O ALA l 136 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY l 143 " --> pdb=" O LEU l 139 " (cutoff:3.500A) Processing helix chain 'm' and resid 8 through 40 removed outlier: 4.062A pdb=" N PHE m 12 " --> pdb=" O TYR m 8 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLY m 13 " --> pdb=" O ALA m 9 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE m 21 " --> pdb=" O CYS m 17 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N THR m 24 " --> pdb=" O ALA m 20 " (cutoff:3.500A) Processing helix chain 'm' and resid 41 through 44 removed outlier: 3.776A pdb=" N VAL m 44 " --> pdb=" O ALA m 41 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 41 through 44' Processing helix chain 'm' and resid 45 through 49 removed outlier: 3.724A pdb=" N ASP m 48 " --> pdb=" O LEU m 45 " (cutoff:3.500A) Processing helix chain 'm' and resid 54 through 77 Processing helix chain 'm' and resid 83 through 122 Processing helix chain 'm' and resid 124 through 153 removed outlier: 4.572A pdb=" N GLY m 128 " --> pdb=" O ARG m 124 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LEU m 139 " --> pdb=" O PHE m 135 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLY m 140 " --> pdb=" O ALA m 136 " (cutoff:3.500A) Processing helix chain 'n' and resid 8 through 37 removed outlier: 4.340A pdb=" N PHE n 12 " --> pdb=" O TYR n 8 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLY n 13 " --> pdb=" O ALA n 9 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR n 24 " --> pdb=" O ALA n 20 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 46 removed outlier: 4.131A pdb=" N LEU n 45 " --> pdb=" O ALA n 41 " (cutoff:3.500A) Processing helix chain 'n' and resid 53 through 78 removed outlier: 4.373A pdb=" N VAL n 57 " --> pdb=" O ASN n 53 " (cutoff:3.500A) Processing helix chain 'n' and resid 83 through 118 Processing helix chain 'n' and resid 123 through 153 removed outlier: 5.426A pdb=" N ILE n 130 " --> pdb=" O PHE n 126 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N LEU n 131 " --> pdb=" O VAL n 127 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE n 132 " --> pdb=" O GLY n 128 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LEU n 139 " --> pdb=" O PHE n 135 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY n 140 " --> pdb=" O ALA n 136 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 48 removed outlier: 3.943A pdb=" N PHE o 18 " --> pdb=" O TYR o 14 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N LEU o 29 " --> pdb=" O ALA o 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLY o 44 " --> pdb=" O LYS o 40 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N GLY o 47 " --> pdb=" O ILE o 43 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 Processing helix chain 'o' and resid 60 through 83 removed outlier: 3.543A pdb=" N ASN o 83 " --> pdb=" O LEU o 79 " (cutoff:3.500A) Processing helix chain 'o' and resid 91 through 128 removed outlier: 4.370A pdb=" N VAL o 122 " --> pdb=" O MET o 118 " (cutoff:3.500A) Processing helix chain 'o' and resid 130 through 132 No H-bonds generated for 'chain 'o' and resid 130 through 132' Processing helix chain 'o' and resid 133 through 163 removed outlier: 4.035A pdb=" N LEU o 147 " --> pdb=" O PHE o 143 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N GLY o 148 " --> pdb=" O SER o 144 " (cutoff:3.500A) Processing helix chain 'p' and resid 9 through 35 removed outlier: 3.741A pdb=" N MET p 14 " --> pdb=" O ILE p 10 " (cutoff:3.500A) Proline residue: p 24 - end of helix Processing helix chain 'p' and resid 37 through 63 Processing sheet with id=AA1, first strand: chain 'a' and resid 40 through 41 Processing sheet with id=AA2, first strand: chain 'a' and resid 40 through 41 removed outlier: 4.183A pdb=" N LEU a 16 " --> pdb=" O LEU a 371 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'a' and resid 213 through 217 removed outlier: 4.103A pdb=" N THR a 188 " --> pdb=" O TYR a 261 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'a' and resid 222 through 224 Processing sheet with id=AA5, first strand: chain 'a' and resid 494 through 495 Processing sheet with id=AA6, first strand: chain 'a' and resid 506 through 507 1813 hydrogen bonds defined for protein. 5319 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.70 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 6690 1.34 - 1.46: 3449 1.46 - 1.58: 12011 1.58 - 1.70: 0 1.70 - 1.81: 201 Bond restraints: 22351 Sorted by residual: bond pdb=" CB VAL c 110 " pdb=" CG1 VAL c 110 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.64e+00 bond pdb=" CB CYS a 589 " pdb=" SG CYS a 589 " ideal model delta sigma weight residual 1.808 1.766 0.042 3.30e-02 9.18e+02 1.64e+00 bond pdb=" CB GLN m 90 " pdb=" CG GLN m 90 " ideal model delta sigma weight residual 1.520 1.483 0.037 3.00e-02 1.11e+03 1.49e+00 bond pdb=" CB ILE g 62 " pdb=" CG2 ILE g 62 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.43e+00 bond pdb=" CG LEU g 141 " pdb=" CD1 LEU g 141 " ideal model delta sigma weight residual 1.521 1.483 0.038 3.30e-02 9.18e+02 1.33e+00 ... (remaining 22346 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.10: 29944 2.10 - 4.19: 367 4.19 - 6.29: 77 6.29 - 8.38: 8 8.38 - 10.48: 1 Bond angle restraints: 30397 Sorted by residual: angle pdb=" C ASN d 333 " pdb=" CA ASN d 333 " pdb=" CB ASN d 333 " ideal model delta sigma weight residual 116.63 111.08 5.55 1.16e+00 7.43e-01 2.29e+01 angle pdb=" C ILE c 79 " pdb=" N PHE c 80 " pdb=" CA PHE c 80 " ideal model delta sigma weight residual 120.68 113.82 6.86 1.70e+00 3.46e-01 1.63e+01 angle pdb=" C ILE k 54 " pdb=" N VAL k 55 " pdb=" CA VAL k 55 " ideal model delta sigma weight residual 120.33 123.37 -3.04 8.00e-01 1.56e+00 1.45e+01 angle pdb=" CA GLY k 79 " pdb=" C GLY k 79 " pdb=" N GLN k 80 " ideal model delta sigma weight residual 114.58 117.60 -3.02 8.60e-01 1.35e+00 1.23e+01 angle pdb=" CB MET c 58 " pdb=" CG MET c 58 " pdb=" SD MET c 58 " ideal model delta sigma weight residual 112.70 123.18 -10.48 3.00e+00 1.11e-01 1.22e+01 ... (remaining 30392 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 12000 17.98 - 35.95: 783 35.95 - 53.93: 119 53.93 - 71.91: 20 71.91 - 89.89: 16 Dihedral angle restraints: 12938 sinusoidal: 4583 harmonic: 8355 Sorted by residual: dihedral pdb=" CA LEU a 256 " pdb=" C LEU a 256 " pdb=" N ASP a 257 " pdb=" CA ASP a 257 " ideal model delta harmonic sigma weight residual 180.00 159.09 20.91 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLU a 254 " pdb=" C GLU a 254 " pdb=" N SER a 255 " pdb=" CA SER a 255 " ideal model delta harmonic sigma weight residual 180.00 159.31 20.69 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA PHE a 423 " pdb=" C PHE a 423 " pdb=" N GLY a 424 " pdb=" CA GLY a 424 " ideal model delta harmonic sigma weight residual 180.00 161.07 18.93 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 12935 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 2274 0.033 - 0.066: 952 0.066 - 0.100: 341 0.100 - 0.133: 82 0.133 - 0.166: 12 Chirality restraints: 3661 Sorted by residual: chirality pdb=" CG LEU a 211 " pdb=" CB LEU a 211 " pdb=" CD1 LEU a 211 " pdb=" CD2 LEU a 211 " both_signs ideal model delta sigma weight residual False -2.59 -2.42 -0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA PHE c 80 " pdb=" N PHE c 80 " pdb=" C PHE c 80 " pdb=" CB PHE c 80 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.65e-01 chirality pdb=" CB THR a 621 " pdb=" CA THR a 621 " pdb=" OG1 THR a 621 " pdb=" CG2 THR a 621 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.34e-01 ... (remaining 3658 not shown) Planarity restraints: 3770 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR d 249 " 0.052 5.00e-02 4.00e+02 8.00e-02 1.02e+01 pdb=" N PRO d 250 " -0.138 5.00e-02 4.00e+02 pdb=" CA PRO d 250 " 0.045 5.00e-02 4.00e+02 pdb=" CD PRO d 250 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE c 80 " 0.027 2.00e-02 2.50e+03 2.40e-02 1.01e+01 pdb=" CG PHE c 80 " -0.055 2.00e-02 2.50e+03 pdb=" CD1 PHE c 80 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE c 80 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE c 80 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE c 80 " 0.008 2.00e-02 2.50e+03 pdb=" CZ PHE c 80 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG k 46 " 0.051 5.00e-02 4.00e+02 7.65e-02 9.37e+00 pdb=" N PRO k 47 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO k 47 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO k 47 " 0.042 5.00e-02 4.00e+02 ... (remaining 3767 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 185 2.66 - 3.22: 22907 3.22 - 3.78: 36962 3.78 - 4.34: 50941 4.34 - 4.90: 82707 Nonbonded interactions: 193702 Sorted by model distance: nonbonded pdb=" OG SER m 77 " pdb=" OE1 GLN m 90 " model vdw 2.097 3.040 nonbonded pdb=" OE2 GLU d 14 " pdb=" NH1 ARG d 18 " model vdw 2.205 3.120 nonbonded pdb=" OE1 GLN d 86 " pdb=" NH1 ARG g 117 " model vdw 2.209 3.120 nonbonded pdb=" NZ LYS a 251 " pdb=" O VAL d 141 " model vdw 2.213 3.120 nonbonded pdb=" OH TYR i 66 " pdb=" OE2 GLU i 137 " model vdw 2.219 3.040 ... (remaining 193697 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 'g' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 or (resid 52 thro \ ugh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thro \ ugh 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 118 or (resid 119 through 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 or (resid 124 and (name N or name CA or \ name C or name O or name CB )) or resid 125 through 155)) selection = (chain 'h' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 or (resid 52 thro \ ugh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thro \ ugh 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 118 or (resid 119 through 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 or (resid 124 and (name N or name CA or \ name C or name O or name CB )) or resid 125 through 155)) selection = (chain 'i' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 or (resid 52 thro \ ugh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thro \ ugh 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 118 or (resid 119 through 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 or (resid 124 and (name N or name CA or \ name C or name O or name CB )) or resid 125 through 155)) selection = (chain 'j' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 through 115 or (r \ esid 116 and (name N or name CA or name C or name O or name CB )) or resid 117 t \ hrough 118 or (resid 119 through 122 and (name N or name CA or name C or name O \ or name CB )) or resid 123 through 155)) selection = (chain 'k' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 through 49 or (resid 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 through 52 or (re \ sid 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thro \ ugh 123 or (resid 124 and (name N or name CA or name C or name O or name CB )) o \ r resid 125 through 155)) selection = (chain 'l' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 or (resid 52 thro \ ugh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thro \ ugh 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 118 or (resid 119 through 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 or (resid 124 and (name N or name CA or \ name C or name O or name CB )) or resid 125 through 155)) selection = (chain 'm' and (resid 2 through 36 or (resid 37 and (name N or name CA or name C \ or name O or name CB )) or resid 38 or (resid 39 through 46 and (name N or name \ CA or name C or name O or name CB )) or resid 47 or (resid 48 through 50 and (n \ ame N or name CA or name C or name O or name CB )) or resid 51 or (resid 52 thro \ ugh 53 and (name N or name CA or name C or name O or name CB )) or resid 54 thro \ ugh 115 or (resid 116 and (name N or name CA or name C or name O or name CB )) o \ r resid 117 through 118 or (resid 119 through 122 and (name N or name CA or name \ C or name O or name CB )) or resid 123 through 155)) selection = (chain 'n' and (resid 2 through 51 or (resid 52 through 53 and (name N or name C \ A or name C or name O or name CB )) or resid 54 through 115 or (resid 116 and (n \ ame N or name CA or name C or name O or name CB )) or resid 117 through 155)) } 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: 2.280 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.130 Find NCS groups from input model: 0.270 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: 0.010 Load rotamer database and sin/cos tables:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 : 0.004 0.048 22351 Z= 0.164 Angle : 0.635 10.477 30397 Z= 0.345 Chirality : 0.042 0.166 3661 Planarity : 0.005 0.080 3770 Dihedral : 12.717 89.887 7626 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.15), residues: 2906 helix: 1.12 (0.11), residues: 2165 sheet: -0.18 (0.69), residues: 35 loop : -0.29 (0.23), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG o 132 TYR 0.027 0.002 TYR o 127 PHE 0.055 0.002 PHE c 80 TRP 0.033 0.002 TRP c 77 HIS 0.005 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00351 (22351) covalent geometry : angle 0.63528 (30397) hydrogen bonds : bond 0.10418 ( 1811) hydrogen bonds : angle 5.39665 ( 5319) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 344 time to evaluate : 0.836 Fit side-chains revert: symmetry clash REVERT: a 14 MET cc_start: 0.9176 (mmp) cc_final: 0.8729 (mmt) REVERT: a 501 LYS cc_start: 0.8001 (mttp) cc_final: 0.7786 (tptp) REVERT: d 111 ILE cc_start: 0.8673 (mt) cc_final: 0.8346 (pt) REVERT: e 66 ASP cc_start: 0.8235 (p0) cc_final: 0.7982 (p0) REVERT: f 9 LYS cc_start: 0.7661 (tmtt) cc_final: 0.7450 (tptt) REVERT: g 8 TYR cc_start: 0.8961 (p90) cc_final: 0.8356 (p90) REVERT: h 100 SER cc_start: 0.9003 (t) cc_final: 0.8799 (m) REVERT: i 30 TYR cc_start: 0.9088 (t80) cc_final: 0.8873 (t80) REVERT: l 19 SER cc_start: 0.8843 (m) cc_final: 0.8640 (m) REVERT: l 59 MET cc_start: 0.8308 (mtp) cc_final: 0.7985 (mtt) REVERT: o 59 SER cc_start: 0.8850 (t) cc_final: 0.8534 (p) REVERT: o 118 MET cc_start: 0.8041 (mmm) cc_final: 0.7784 (mmm) outliers start: 0 outliers final: 0 residues processed: 344 average time/residue: 0.1504 time to fit residues: 79.3408 Evaluate side-chains 259 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 0.7980 chunk 111 optimal weight: 0.0980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 220 GLN a 384 ASN a 499 HIS c 61 ASN ** c 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN d 182 ASN d 303 GLN ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 37 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.158772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111753 restraints weight = 23557.024| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.95 r_work: 0.3215 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.1044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 22351 Z= 0.174 Angle : 0.574 8.991 30397 Z= 0.303 Chirality : 0.041 0.168 3661 Planarity : 0.004 0.064 3770 Dihedral : 4.570 51.106 3127 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.12 % Allowed : 5.62 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.44 (0.15), residues: 2906 helix: 1.40 (0.11), residues: 2177 sheet: -0.38 (0.65), residues: 38 loop : -0.22 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG i 46 TYR 0.038 0.001 TYR o 127 PHE 0.046 0.002 PHE c 80 TRP 0.015 0.001 TRP a 594 HIS 0.004 0.001 HIS a 79 Details of bonding type rmsd covalent geometry : bond 0.00392 (22351) covalent geometry : angle 0.57382 (30397) hydrogen bonds : bond 0.05276 ( 1811) hydrogen bonds : angle 4.78154 ( 5319) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 289 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 132 GLU cc_start: 0.7959 (tt0) cc_final: 0.7610 (tp30) REVERT: a 501 LYS cc_start: 0.8233 (mttp) cc_final: 0.7701 (tptp) REVERT: e 24 MET cc_start: 0.7991 (ttt) cc_final: 0.7469 (mtm) REVERT: e 66 ASP cc_start: 0.8207 (p0) cc_final: 0.7881 (p0) REVERT: f 41 SER cc_start: 0.8919 (t) cc_final: 0.8695 (p) REVERT: f 44 ASP cc_start: 0.8042 (m-30) cc_final: 0.7354 (m-30) REVERT: g 8 TYR cc_start: 0.9174 (p90) cc_final: 0.8605 (p90) REVERT: h 153 ARG cc_start: 0.8148 (mtp-110) cc_final: 0.7472 (ttm-80) REVERT: i 30 TYR cc_start: 0.9386 (t80) cc_final: 0.9134 (t80) REVERT: i 124 ARG cc_start: 0.7759 (mtp180) cc_final: 0.7518 (mtp180) REVERT: i 133 LEU cc_start: 0.8951 (mt) cc_final: 0.8724 (mt) REVERT: l 19 SER cc_start: 0.9039 (m) cc_final: 0.8817 (m) REVERT: l 59 MET cc_start: 0.8687 (mtp) cc_final: 0.8325 (mtt) REVERT: m 122 GLN cc_start: 0.7609 (tm-30) cc_final: 0.7134 (tm-30) REVERT: n 129 MET cc_start: 0.6339 (mtt) cc_final: 0.6015 (mmm) outliers start: 25 outliers final: 15 residues processed: 299 average time/residue: 0.1489 time to fit residues: 67.6355 Evaluate side-chains 269 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 254 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 116 TYR Chi-restraints excluded: chain a residue 534 SER Chi-restraints excluded: chain b residue 218 ILE Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 46 ARG Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 51 PHE Chi-restraints excluded: chain m residue 155 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 215 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 53 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 223 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 234 optimal weight: 0.1980 chunk 23 optimal weight: 40.0000 chunk 202 optimal weight: 2.9990 chunk 191 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 220 GLN a 232 HIS a 499 HIS c 61 ASN c 100 ASN d 45 GLN j 151 ASN k 82 GLN k 90 GLN m 90 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.158146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.109615 restraints weight = 23421.214| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.86 r_work: 0.3170 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22351 Z= 0.148 Angle : 0.524 9.716 30397 Z= 0.276 Chirality : 0.039 0.150 3661 Planarity : 0.004 0.059 3770 Dihedral : 4.434 69.717 3127 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.47 % Allowed : 8.44 % Favored : 90.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.15), residues: 2906 helix: 1.55 (0.11), residues: 2184 sheet: 0.05 (0.74), residues: 35 loop : -0.25 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG i 46 TYR 0.036 0.001 TYR o 127 PHE 0.035 0.001 PHE c 80 TRP 0.012 0.001 TRP a 594 HIS 0.003 0.001 HIS a 79 Details of bonding type rmsd covalent geometry : bond 0.00319 (22351) covalent geometry : angle 0.52403 (30397) hydrogen bonds : bond 0.04856 ( 1811) hydrogen bonds : angle 4.54793 ( 5319) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 289 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 132 GLU cc_start: 0.7910 (tt0) cc_final: 0.7453 (tp30) REVERT: a 139 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6671 (tm-30) REVERT: a 356 MET cc_start: 0.7766 (tmm) cc_final: 0.7495 (ttp) REVERT: a 501 LYS cc_start: 0.8257 (mttp) cc_final: 0.7722 (tptp) REVERT: e 66 ASP cc_start: 0.8294 (p0) cc_final: 0.7763 (p0) REVERT: g 8 TYR cc_start: 0.9174 (p90) cc_final: 0.8676 (p90) REVERT: h 153 ARG cc_start: 0.8083 (mtp-110) cc_final: 0.7600 (ttm-80) REVERT: i 46 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7474 (ptp-110) REVERT: l 49 LEU cc_start: 0.6469 (OUTLIER) cc_final: 0.6243 (pp) REVERT: l 59 MET cc_start: 0.8580 (mtp) cc_final: 0.8333 (mtt) REVERT: n 129 MET cc_start: 0.6445 (mtt) cc_final: 0.6201 (mmm) REVERT: o 128 MET cc_start: 0.7744 (mmm) cc_final: 0.7519 (mmp) outliers start: 33 outliers final: 19 residues processed: 307 average time/residue: 0.1532 time to fit residues: 72.8303 Evaluate side-chains 276 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 256 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 116 TYR Chi-restraints excluded: chain a residue 246 ILE Chi-restraints excluded: chain a residue 302 ILE Chi-restraints excluded: chain a residue 384 ASN Chi-restraints excluded: chain a residue 534 SER Chi-restraints excluded: chain b residue 218 ILE Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 293 MET Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 46 ARG Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 151 ASN Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 51 PHE Chi-restraints excluded: chain m residue 155 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 18 optimal weight: 8.9990 chunk 218 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 9 optimal weight: 0.1980 chunk 156 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 174 optimal weight: 2.9990 chunk 197 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN c 61 ASN c 132 ASN g 122 GLN j 151 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.154570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.107703 restraints weight = 23430.110| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.74 r_work: 0.3126 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 22351 Z= 0.213 Angle : 0.555 9.677 30397 Z= 0.292 Chirality : 0.041 0.169 3661 Planarity : 0.004 0.060 3770 Dihedral : 4.409 61.303 3127 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.70 % Allowed : 10.22 % Favored : 88.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.40 (0.15), residues: 2906 helix: 1.40 (0.11), residues: 2203 sheet: 0.22 (0.74), residues: 35 loop : -0.45 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG i 117 TYR 0.031 0.001 TYR o 127 PHE 0.035 0.002 PHE c 80 TRP 0.011 0.001 TRP a 598 HIS 0.006 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00501 (22351) covalent geometry : angle 0.55520 (30397) hydrogen bonds : bond 0.05075 ( 1811) hydrogen bonds : angle 4.62790 ( 5319) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 280 time to evaluate : 0.582 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 132 GLU cc_start: 0.7943 (tt0) cc_final: 0.7465 (tp30) REVERT: a 139 GLU cc_start: 0.7299 (mm-30) cc_final: 0.6941 (tm-30) REVERT: a 319 ILE cc_start: 0.8637 (mm) cc_final: 0.8354 (tp) REVERT: a 501 LYS cc_start: 0.8263 (mttp) cc_final: 0.7724 (tptp) REVERT: c 185 LEU cc_start: 0.7860 (tt) cc_final: 0.7590 (mt) REVERT: d 97 TYR cc_start: 0.8012 (m-80) cc_final: 0.7779 (m-80) REVERT: g 8 TYR cc_start: 0.9177 (p90) cc_final: 0.8739 (p90) REVERT: g 42 THR cc_start: 0.9003 (m) cc_final: 0.8656 (m) REVERT: h 99 LEU cc_start: 0.9384 (OUTLIER) cc_final: 0.9069 (mp) REVERT: h 153 ARG cc_start: 0.8125 (mtp-110) cc_final: 0.7768 (ttm-80) REVERT: i 46 ARG cc_start: 0.7849 (ttm110) cc_final: 0.7567 (ptp-110) REVERT: l 49 LEU cc_start: 0.6450 (OUTLIER) cc_final: 0.6200 (pp) REVERT: n 59 MET cc_start: 0.8257 (mmm) cc_final: 0.7980 (mmt) REVERT: n 129 MET cc_start: 0.6550 (mtt) cc_final: 0.6213 (mmm) REVERT: o 59 SER cc_start: 0.8807 (OUTLIER) cc_final: 0.8444 (p) REVERT: o 128 MET cc_start: 0.7775 (mmm) cc_final: 0.7564 (mmp) outliers start: 38 outliers final: 23 residues processed: 304 average time/residue: 0.1362 time to fit residues: 64.3457 Evaluate side-chains 289 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 263 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 116 TYR Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 384 ASN Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 516 ILE Chi-restraints excluded: chain a residue 534 SER Chi-restraints excluded: chain a residue 732 SER Chi-restraints excluded: chain b residue 218 ILE Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 293 MET Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 46 ARG Chi-restraints excluded: chain h residue 99 LEU Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain j residue 151 ASN Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 155 THR Chi-restraints excluded: chain o residue 59 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 85 optimal weight: 0.9980 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 14 optimal weight: 8.9990 chunk 135 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 126 optimal weight: 10.0000 chunk 103 optimal weight: 3.9990 chunk 260 optimal weight: 10.0000 chunk 161 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN a 278 ASN a 729 HIS c 132 ASN c 156 ASN j 151 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.152345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.104761 restraints weight = 23957.247| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.83 r_work: 0.3085 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2953 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 22351 Z= 0.302 Angle : 0.627 11.766 30397 Z= 0.328 Chirality : 0.044 0.186 3661 Planarity : 0.004 0.062 3770 Dihedral : 4.551 50.049 3127 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.68 % Allowed : 10.76 % Favored : 86.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.15), residues: 2906 helix: 1.14 (0.11), residues: 2187 sheet: 0.19 (0.73), residues: 35 loop : -0.60 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG i 117 TYR 0.030 0.002 TYR o 127 PHE 0.039 0.002 PHE c 80 TRP 0.014 0.002 TRP a 598 HIS 0.007 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00724 (22351) covalent geometry : angle 0.62661 (30397) hydrogen bonds : bond 0.05485 ( 1811) hydrogen bonds : angle 4.84213 ( 5319) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 339 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 279 time to evaluate : 0.718 Fit side-chains REVERT: a 122 ILE cc_start: 0.8207 (mm) cc_final: 0.7979 (mm) REVERT: a 132 GLU cc_start: 0.7952 (tt0) cc_final: 0.7493 (tp30) REVERT: a 139 GLU cc_start: 0.7303 (mm-30) cc_final: 0.7013 (tm-30) REVERT: a 501 LYS cc_start: 0.8291 (mttp) cc_final: 0.7789 (tptp) REVERT: c 185 LEU cc_start: 0.7953 (tt) cc_final: 0.7649 (mt) REVERT: d 97 TYR cc_start: 0.8272 (m-80) cc_final: 0.8043 (m-80) REVERT: g 42 THR cc_start: 0.9070 (m) cc_final: 0.8708 (m) REVERT: h 153 ARG cc_start: 0.8150 (mtp-110) cc_final: 0.7790 (ttm-80) REVERT: i 46 ARG cc_start: 0.8138 (ttm110) cc_final: 0.7859 (ptp-110) REVERT: n 59 MET cc_start: 0.8434 (mmm) cc_final: 0.8149 (mmt) REVERT: n 129 MET cc_start: 0.6733 (mtt) cc_final: 0.6465 (mmm) REVERT: o 59 SER cc_start: 0.8900 (OUTLIER) cc_final: 0.8626 (p) REVERT: o 74 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8645 (tp) REVERT: o 128 MET cc_start: 0.7847 (mmm) cc_final: 0.7634 (mmp) REVERT: p 20 MET cc_start: 0.7581 (tpp) cc_final: 0.7041 (tpp) outliers start: 60 outliers final: 36 residues processed: 319 average time/residue: 0.1412 time to fit residues: 69.6391 Evaluate side-chains 296 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 116 TYR Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 238 VAL Chi-restraints excluded: chain a residue 384 ASN Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 516 ILE Chi-restraints excluded: chain a residue 534 SER Chi-restraints excluded: chain a residue 732 SER Chi-restraints excluded: chain a residue 788 MET Chi-restraints excluded: chain b residue 218 ILE Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 24 LEU Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 46 ARG Chi-restraints excluded: chain g residue 77 SER Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 95 LEU Chi-restraints excluded: chain i residue 155 THR Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 127 VAL Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 51 PHE Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 155 THR Chi-restraints excluded: chain m residue 159 VAL Chi-restraints excluded: chain n residue 82 GLN Chi-restraints excluded: chain n residue 138 VAL Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 74 LEU Chi-restraints excluded: chain o residue 79 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 127 optimal weight: 4.9990 chunk 103 optimal weight: 0.5980 chunk 202 optimal weight: 0.6980 chunk 63 optimal weight: 7.9990 chunk 31 optimal weight: 0.6980 chunk 178 optimal weight: 0.0570 chunk 130 optimal weight: 10.0000 chunk 283 optimal weight: 5.9990 chunk 206 optimal weight: 0.6980 chunk 128 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 655 HIS c 61 ASN c 156 ASN ** i 122 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 = 0.3926 r_free = 0.3926 target = 0.158215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.110003 restraints weight = 23708.076| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.58 r_work: 0.3216 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 22351 Z= 0.137 Angle : 0.504 9.981 30397 Z= 0.266 Chirality : 0.038 0.155 3661 Planarity : 0.004 0.061 3770 Dihedral : 4.269 45.768 3127 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 2.28 % Allowed : 11.56 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.15), residues: 2906 helix: 1.46 (0.11), residues: 2207 sheet: -0.11 (0.77), residues: 38 loop : -0.46 (0.24), residues: 661 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG h 124 TYR 0.031 0.001 TYR o 127 PHE 0.025 0.001 PHE c 80 TRP 0.010 0.001 TRP a 598 HIS 0.003 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00290 (22351) covalent geometry : angle 0.50363 (30397) hydrogen bonds : bond 0.04679 ( 1811) hydrogen bonds : angle 4.50043 ( 5319) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 343 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 292 time to evaluate : 0.590 Fit side-chains revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8159 (mt-10) cc_final: 0.7918 (mt-10) REVERT: a 122 ILE cc_start: 0.8255 (mm) cc_final: 0.8028 (mm) REVERT: a 132 GLU cc_start: 0.8003 (tt0) cc_final: 0.7528 (tp30) REVERT: a 139 GLU cc_start: 0.7296 (mm-30) cc_final: 0.6965 (tm-30) REVERT: a 328 TYR cc_start: 0.7852 (t80) cc_final: 0.7386 (t80) REVERT: a 453 GLU cc_start: 0.7252 (tp30) cc_final: 0.7022 (tt0) REVERT: a 501 LYS cc_start: 0.8313 (mttp) cc_final: 0.7834 (tptp) REVERT: a 539 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8583 (tp) REVERT: d 14 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.7842 (tt0) REVERT: g 42 THR cc_start: 0.9098 (m) cc_final: 0.8720 (m) REVERT: h 153 ARG cc_start: 0.8039 (mtp-110) cc_final: 0.7804 (ttm-80) REVERT: i 46 ARG cc_start: 0.8087 (ttm110) cc_final: 0.7782 (ptp-110) REVERT: k 3 GLU cc_start: 0.7474 (tt0) cc_final: 0.7264 (tt0) REVERT: k 142 TYR cc_start: 0.9009 (m-10) cc_final: 0.8655 (m-10) REVERT: l 49 LEU cc_start: 0.6556 (OUTLIER) cc_final: 0.6236 (pp) REVERT: l 59 MET cc_start: 0.8592 (mtp) cc_final: 0.8360 (mtt) REVERT: n 129 MET cc_start: 0.6660 (mtt) cc_final: 0.6233 (mmm) REVERT: o 59 SER cc_start: 0.8898 (OUTLIER) cc_final: 0.8600 (p) REVERT: o 128 MET cc_start: 0.7789 (mmm) cc_final: 0.7556 (mmp) REVERT: p 20 MET cc_start: 0.7601 (tpp) cc_final: 0.7104 (tpp) outliers start: 51 outliers final: 31 residues processed: 327 average time/residue: 0.1414 time to fit residues: 71.9430 Evaluate side-chains 301 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 266 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 116 TYR Chi-restraints excluded: chain a residue 238 VAL Chi-restraints excluded: chain a residue 302 ILE Chi-restraints excluded: chain a residue 384 ASN Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 516 ILE Chi-restraints excluded: chain a residue 534 SER Chi-restraints excluded: chain a residue 539 LEU Chi-restraints excluded: chain a residue 720 ILE Chi-restraints excluded: chain a residue 732 SER Chi-restraints excluded: chain b residue 218 ILE Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 14 GLU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 293 MET Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain k residue 127 VAL Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 51 PHE Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 155 THR Chi-restraints excluded: chain n residue 138 VAL Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 63 VAL Chi-restraints excluded: chain p residue 51 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 78 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 150 optimal weight: 1.9990 chunk 271 optimal weight: 2.9990 chunk 115 optimal weight: 8.9990 chunk 33 optimal weight: 0.6980 chunk 214 optimal weight: 2.9990 chunk 217 optimal weight: 2.9990 chunk 117 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 61 ASN c 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.154138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.106733 restraints weight = 23809.379| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 1.80 r_work: 0.3110 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 22351 Z= 0.236 Angle : 0.579 12.970 30397 Z= 0.301 Chirality : 0.041 0.234 3661 Planarity : 0.004 0.063 3770 Dihedral : 4.323 38.551 3127 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.32 % Allowed : 12.10 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.15), residues: 2906 helix: 1.36 (0.11), residues: 2188 sheet: -0.12 (0.76), residues: 38 loop : -0.67 (0.23), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG d 266 TYR 0.026 0.001 TYR o 127 PHE 0.034 0.002 PHE c 80 TRP 0.011 0.001 TRP a 598 HIS 0.006 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00559 (22351) covalent geometry : angle 0.57914 (30397) hydrogen bonds : bond 0.05100 ( 1811) hydrogen bonds : angle 4.65977 ( 5319) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 278 time to evaluate : 0.809 Fit side-chains revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7956 (mt-10) REVERT: a 132 GLU cc_start: 0.8020 (tt0) cc_final: 0.7461 (tp30) REVERT: a 139 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6874 (tm-30) REVERT: a 328 TYR cc_start: 0.7835 (t80) cc_final: 0.7330 (t80) REVERT: a 453 GLU cc_start: 0.7371 (tp30) cc_final: 0.7051 (tt0) REVERT: a 501 LYS cc_start: 0.8329 (mttp) cc_final: 0.7836 (tptp) REVERT: c 185 LEU cc_start: 0.7909 (tt) cc_final: 0.7647 (mt) REVERT: d 14 GLU cc_start: 0.8159 (OUTLIER) cc_final: 0.7872 (tt0) REVERT: d 97 TYR cc_start: 0.8251 (m-80) cc_final: 0.7951 (m-80) REVERT: d 185 TYR cc_start: 0.7907 (OUTLIER) cc_final: 0.7421 (m-80) REVERT: g 42 THR cc_start: 0.9124 (m) cc_final: 0.8756 (m) REVERT: g 77 SER cc_start: 0.9163 (t) cc_final: 0.8892 (t) REVERT: h 153 ARG cc_start: 0.8110 (mtp-110) cc_final: 0.7834 (ttm-80) REVERT: i 46 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7788 (ptp-110) REVERT: l 49 LEU cc_start: 0.6571 (OUTLIER) cc_final: 0.6008 (pp) REVERT: n 59 MET cc_start: 0.8357 (mmm) cc_final: 0.8112 (mmt) REVERT: n 129 MET cc_start: 0.6825 (mtt) cc_final: 0.6360 (mmm) REVERT: o 59 SER cc_start: 0.8879 (OUTLIER) cc_final: 0.8639 (p) REVERT: o 74 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8607 (tp) REVERT: o 128 MET cc_start: 0.7826 (mmm) cc_final: 0.7559 (mmp) REVERT: p 20 MET cc_start: 0.7652 (tpp) cc_final: 0.7058 (tpp) outliers start: 52 outliers final: 34 residues processed: 314 average time/residue: 0.1559 time to fit residues: 76.0491 Evaluate side-chains 304 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 265 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 116 TYR Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 238 VAL Chi-restraints excluded: chain a residue 278 ASN Chi-restraints excluded: chain a residue 384 ASN Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 516 ILE Chi-restraints excluded: chain a residue 534 SER Chi-restraints excluded: chain a residue 732 SER Chi-restraints excluded: chain a residue 788 MET Chi-restraints excluded: chain b residue 218 ILE Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 27 ILE Chi-restraints excluded: chain c residue 95 ARG Chi-restraints excluded: chain c residue 104 ILE Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 14 GLU Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 185 TYR Chi-restraints excluded: chain g residue 46 ARG Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain k residue 125 LEU Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 155 THR Chi-restraints excluded: chain n residue 138 VAL Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 63 VAL Chi-restraints excluded: chain o residue 74 LEU Chi-restraints excluded: chain p residue 51 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 269 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 277 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 207 optimal weight: 0.6980 chunk 256 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 61 ASN c 132 ASN ** i 122 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 = 0.3916 r_free = 0.3916 target = 0.157202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.109083 restraints weight = 23696.044| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.57 r_work: 0.3211 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.2215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 22351 Z= 0.153 Angle : 0.527 16.652 30397 Z= 0.273 Chirality : 0.039 0.214 3661 Planarity : 0.004 0.062 3770 Dihedral : 4.186 34.129 3127 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.10 % Allowed : 12.68 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.15), residues: 2906 helix: 1.51 (0.11), residues: 2187 sheet: 0.20 (0.78), residues: 35 loop : -0.59 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG d 266 TYR 0.026 0.001 TYR o 127 PHE 0.027 0.001 PHE c 80 TRP 0.010 0.001 TRP a 598 HIS 0.004 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00339 (22351) covalent geometry : angle 0.52749 (30397) hydrogen bonds : bond 0.04699 ( 1811) hydrogen bonds : angle 4.49690 ( 5319) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 280 time to evaluate : 0.839 Fit side-chains revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7942 (mt-10) REVERT: a 132 GLU cc_start: 0.8038 (tt0) cc_final: 0.7468 (tp30) REVERT: a 139 GLU cc_start: 0.7254 (mm-30) cc_final: 0.6999 (tm-30) REVERT: a 328 TYR cc_start: 0.7798 (t80) cc_final: 0.7330 (t80) REVERT: a 453 GLU cc_start: 0.7398 (tp30) cc_final: 0.7078 (tt0) REVERT: a 501 LYS cc_start: 0.8340 (mttp) cc_final: 0.7825 (tptp) REVERT: a 794 MET cc_start: 0.8778 (ttp) cc_final: 0.8557 (ttm) REVERT: c 77 TRP cc_start: 0.8858 (OUTLIER) cc_final: 0.8168 (t-100) REVERT: d 14 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.7846 (tt0) REVERT: d 185 TYR cc_start: 0.7845 (OUTLIER) cc_final: 0.7376 (m-80) REVERT: g 15 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8111 (tp) REVERT: g 42 THR cc_start: 0.9109 (m) cc_final: 0.8754 (m) REVERT: h 153 ARG cc_start: 0.8068 (mtp-110) cc_final: 0.7856 (ttm-80) REVERT: i 46 ARG cc_start: 0.7945 (ttm110) cc_final: 0.7631 (ptp-110) REVERT: k 142 TYR cc_start: 0.9029 (m-10) cc_final: 0.8685 (m-10) REVERT: l 49 LEU cc_start: 0.6425 (OUTLIER) cc_final: 0.5980 (pp) REVERT: l 59 MET cc_start: 0.8684 (mtp) cc_final: 0.8458 (mtt) REVERT: m 122 GLN cc_start: 0.6696 (tm-30) cc_final: 0.6476 (tm-30) REVERT: n 59 MET cc_start: 0.8241 (mmm) cc_final: 0.7983 (mmt) REVERT: n 129 MET cc_start: 0.6723 (mtt) cc_final: 0.6319 (mmm) REVERT: o 59 SER cc_start: 0.8906 (OUTLIER) cc_final: 0.8648 (p) REVERT: o 128 MET cc_start: 0.7748 (mmm) cc_final: 0.7515 (mmp) REVERT: p 20 MET cc_start: 0.7681 (tpp) cc_final: 0.7146 (tpp) outliers start: 47 outliers final: 33 residues processed: 314 average time/residue: 0.1625 time to fit residues: 79.2128 Evaluate side-chains 309 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 270 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 116 TYR Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 238 VAL Chi-restraints excluded: chain a residue 278 ASN Chi-restraints excluded: chain a residue 384 ASN Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 516 ILE Chi-restraints excluded: chain a residue 534 SER Chi-restraints excluded: chain a residue 732 SER Chi-restraints excluded: chain b residue 218 ILE Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 77 TRP Chi-restraints excluded: chain c residue 104 ILE Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 14 GLU Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 185 TYR Chi-restraints excluded: chain d residue 293 MET Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 120 SER Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain k residue 127 VAL Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 155 THR Chi-restraints excluded: chain n residue 138 VAL Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 63 VAL Chi-restraints excluded: chain p residue 51 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 253 optimal weight: 3.9990 chunk 233 optimal weight: 1.9990 chunk 141 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 216 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 203 optimal weight: 0.9980 chunk 177 optimal weight: 0.9980 chunk 143 optimal weight: 6.9990 chunk 251 optimal weight: 2.9990 chunk 120 optimal weight: 9.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN ** i 122 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 = 0.3881 r_free = 0.3881 target = 0.154098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.108031 restraints weight = 23953.292| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 1.86 r_work: 0.3135 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 22351 Z= 0.232 Angle : 0.583 17.623 30397 Z= 0.301 Chirality : 0.041 0.207 3661 Planarity : 0.004 0.065 3770 Dihedral : 4.265 28.136 3127 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.37 % Allowed : 12.95 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.15), residues: 2906 helix: 1.35 (0.11), residues: 2184 sheet: 0.18 (0.78), residues: 35 loop : -0.70 (0.23), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 266 TYR 0.025 0.001 TYR o 127 PHE 0.034 0.002 PHE c 80 TRP 0.010 0.001 TRP a 598 HIS 0.006 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00549 (22351) covalent geometry : angle 0.58308 (30397) hydrogen bonds : bond 0.05050 ( 1811) hydrogen bonds : angle 4.64177 ( 5319) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 275 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8172 (mt-10) cc_final: 0.7922 (mt-10) REVERT: a 122 ILE cc_start: 0.8094 (mm) cc_final: 0.7850 (mm) REVERT: a 132 GLU cc_start: 0.8022 (tt0) cc_final: 0.7464 (tp30) REVERT: a 139 GLU cc_start: 0.7314 (mm-30) cc_final: 0.6999 (tm-30) REVERT: a 328 TYR cc_start: 0.7816 (t80) cc_final: 0.7297 (t80) REVERT: a 453 GLU cc_start: 0.7412 (tp30) cc_final: 0.7095 (tt0) REVERT: a 501 LYS cc_start: 0.8334 (mttp) cc_final: 0.7817 (tptp) REVERT: a 788 MET cc_start: 0.8429 (OUTLIER) cc_final: 0.8177 (mtm) REVERT: c 77 TRP cc_start: 0.8900 (OUTLIER) cc_final: 0.8187 (t-100) REVERT: c 185 LEU cc_start: 0.7917 (tt) cc_final: 0.7674 (mt) REVERT: d 14 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7957 (tt0) REVERT: d 185 TYR cc_start: 0.7951 (OUTLIER) cc_final: 0.7489 (m-80) REVERT: f 37 SER cc_start: 0.8913 (m) cc_final: 0.8658 (t) REVERT: g 15 ILE cc_start: 0.8794 (OUTLIER) cc_final: 0.8153 (tp) REVERT: g 42 THR cc_start: 0.9122 (m) cc_final: 0.8764 (m) REVERT: h 153 ARG cc_start: 0.8138 (mtp-110) cc_final: 0.7880 (ttm-80) REVERT: i 46 ARG cc_start: 0.7951 (ttm110) cc_final: 0.7648 (ptp-110) REVERT: l 49 LEU cc_start: 0.6394 (OUTLIER) cc_final: 0.5995 (pp) REVERT: m 122 GLN cc_start: 0.6568 (tm-30) cc_final: 0.6306 (tm-30) REVERT: n 59 MET cc_start: 0.8365 (mmm) cc_final: 0.8132 (mmt) REVERT: n 129 MET cc_start: 0.6798 (mtt) cc_final: 0.6373 (mmm) REVERT: o 59 SER cc_start: 0.8959 (OUTLIER) cc_final: 0.8711 (p) REVERT: o 128 MET cc_start: 0.7765 (mmm) cc_final: 0.7541 (mmp) REVERT: p 20 MET cc_start: 0.7699 (tpp) cc_final: 0.7143 (tpp) outliers start: 53 outliers final: 41 residues processed: 311 average time/residue: 0.1661 time to fit residues: 79.6936 Evaluate side-chains 316 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 268 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 116 TYR Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 238 VAL Chi-restraints excluded: chain a residue 278 ASN Chi-restraints excluded: chain a residue 384 ASN Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 516 ILE Chi-restraints excluded: chain a residue 534 SER Chi-restraints excluded: chain a residue 589 CYS Chi-restraints excluded: chain a residue 732 SER Chi-restraints excluded: chain a residue 788 MET Chi-restraints excluded: chain a residue 800 LEU Chi-restraints excluded: chain b residue 218 ILE Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 77 TRP Chi-restraints excluded: chain c residue 95 ARG Chi-restraints excluded: chain c residue 104 ILE Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 14 GLU Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 185 TYR Chi-restraints excluded: chain d residue 293 MET Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 46 ARG Chi-restraints excluded: chain g residue 120 SER Chi-restraints excluded: chain g residue 130 ILE Chi-restraints excluded: chain i residue 26 LEU Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain j residue 151 ASN Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 155 THR Chi-restraints excluded: chain m residue 159 VAL Chi-restraints excluded: chain n residue 138 VAL Chi-restraints excluded: chain n residue 159 VAL Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 63 VAL Chi-restraints excluded: chain o residue 118 MET Chi-restraints excluded: chain p residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 220 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 271 optimal weight: 2.9990 chunk 277 optimal weight: 0.9980 chunk 6 optimal weight: 4.9990 chunk 231 optimal weight: 0.0170 chunk 22 optimal weight: 0.4980 chunk 96 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 126 optimal weight: 5.9990 chunk 159 optimal weight: 0.5980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN ** a 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 61 ASN ** i 122 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 = 0.3944 r_free = 0.3944 target = 0.159994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110810 restraints weight = 23637.240| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.62 r_work: 0.3235 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 22351 Z= 0.140 Angle : 0.520 17.153 30397 Z= 0.268 Chirality : 0.038 0.197 3661 Planarity : 0.004 0.064 3770 Dihedral : 4.096 24.364 3127 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer: Outliers : 2.01 % Allowed : 13.30 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.55 (0.15), residues: 2906 helix: 1.56 (0.11), residues: 2189 sheet: -0.23 (0.77), residues: 38 loop : -0.54 (0.24), residues: 679 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG d 266 TYR 0.023 0.001 TYR o 127 PHE 0.025 0.001 PHE c 80 TRP 0.010 0.001 TRP a 598 HIS 0.004 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00303 (22351) covalent geometry : angle 0.51983 (30397) hydrogen bonds : bond 0.04566 ( 1811) hydrogen bonds : angle 4.43305 ( 5319) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5812 Ramachandran restraints generated. 2906 Oldfield, 0 Emsley, 2906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 285 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7909 (mt-10) REVERT: a 122 ILE cc_start: 0.8060 (mm) cc_final: 0.7808 (mm) REVERT: a 132 GLU cc_start: 0.8017 (tt0) cc_final: 0.7461 (tp30) REVERT: a 139 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7035 (tm-30) REVERT: a 328 TYR cc_start: 0.7743 (t80) cc_final: 0.7274 (t80) REVERT: a 453 GLU cc_start: 0.7391 (tp30) cc_final: 0.7066 (tt0) REVERT: a 501 LYS cc_start: 0.8330 (mttp) cc_final: 0.7836 (tptp) REVERT: a 788 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.8051 (mtm) REVERT: c 77 TRP cc_start: 0.8839 (OUTLIER) cc_final: 0.8089 (t-100) REVERT: d 14 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: d 185 TYR cc_start: 0.7865 (OUTLIER) cc_final: 0.7401 (m-80) REVERT: f 37 SER cc_start: 0.8897 (m) cc_final: 0.8667 (t) REVERT: g 8 TYR cc_start: 0.9078 (p90) cc_final: 0.8724 (p90) REVERT: g 15 ILE cc_start: 0.8740 (OUTLIER) cc_final: 0.8086 (tp) REVERT: h 153 ARG cc_start: 0.8043 (mtp-110) cc_final: 0.7795 (ttm-80) REVERT: h 155 THR cc_start: 0.8642 (m) cc_final: 0.7913 (p) REVERT: i 46 ARG cc_start: 0.7847 (ttm110) cc_final: 0.7501 (ptp-110) REVERT: k 142 TYR cc_start: 0.9015 (m-10) cc_final: 0.8590 (m-10) REVERT: l 49 LEU cc_start: 0.6390 (OUTLIER) cc_final: 0.5956 (pp) REVERT: n 129 MET cc_start: 0.6758 (mtt) cc_final: 0.6402 (mmm) REVERT: o 59 SER cc_start: 0.8981 (OUTLIER) cc_final: 0.8648 (p) REVERT: o 72 TYR cc_start: 0.8535 (m-10) cc_final: 0.8112 (m-10) REVERT: o 128 MET cc_start: 0.7667 (mmm) cc_final: 0.7450 (mmp) REVERT: p 20 MET cc_start: 0.7711 (tpp) cc_final: 0.7204 (tpp) outliers start: 45 outliers final: 34 residues processed: 317 average time/residue: 0.1734 time to fit residues: 84.8264 Evaluate side-chains 313 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 272 time to evaluate : 0.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 116 TYR Chi-restraints excluded: chain a residue 237 ILE Chi-restraints excluded: chain a residue 238 VAL Chi-restraints excluded: chain a residue 384 ASN Chi-restraints excluded: chain a residue 449 MET Chi-restraints excluded: chain a residue 516 ILE Chi-restraints excluded: chain a residue 534 SER Chi-restraints excluded: chain a residue 589 CYS Chi-restraints excluded: chain a residue 732 SER Chi-restraints excluded: chain a residue 788 MET Chi-restraints excluded: chain a residue 800 LEU Chi-restraints excluded: chain b residue 218 ILE Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 77 TRP Chi-restraints excluded: chain c residue 110 VAL Chi-restraints excluded: chain c residue 189 ILE Chi-restraints excluded: chain c residue 193 ILE Chi-restraints excluded: chain d residue 14 GLU Chi-restraints excluded: chain d residue 39 LEU Chi-restraints excluded: chain d residue 67 LEU Chi-restraints excluded: chain d residue 185 TYR Chi-restraints excluded: chain d residue 293 MET Chi-restraints excluded: chain g residue 2 THR Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 130 ILE Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 89 ILE Chi-restraints excluded: chain m residue 2 THR Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 57 VAL Chi-restraints excluded: chain m residue 155 THR Chi-restraints excluded: chain m residue 159 VAL Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 138 VAL Chi-restraints excluded: chain n residue 159 VAL Chi-restraints excluded: chain o residue 38 THR Chi-restraints excluded: chain o residue 59 SER Chi-restraints excluded: chain o residue 63 VAL Chi-restraints excluded: chain p residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 148 optimal weight: 0.8980 chunk 171 optimal weight: 4.9990 chunk 220 optimal weight: 1.9990 chunk 223 optimal weight: 0.7980 chunk 116 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 6 optimal weight: 7.9990 chunk 29 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN c 132 ASN g 53 ASN ** i 122 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 = 0.3901 r_free = 0.3901 target = 0.155809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.109992 restraints weight = 23827.435| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 1.85 r_work: 0.3165 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 22351 Z= 0.191 Angle : 0.556 17.155 30397 Z= 0.286 Chirality : 0.040 0.208 3661 Planarity : 0.004 0.065 3770 Dihedral : 4.139 20.756 3127 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.05 % Allowed : 13.39 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.46 (0.15), residues: 2906 helix: 1.53 (0.11), residues: 2176 sheet: -0.28 (0.75), residues: 38 loop : -0.67 (0.23), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG d 266 TYR 0.025 0.001 TYR m 142 PHE 0.030 0.001 PHE c 80 TRP 0.009 0.001 TRP a 598 HIS 0.005 0.001 HIS a 801 Details of bonding type rmsd covalent geometry : bond 0.00447 (22351) covalent geometry : angle 0.55628 (30397) hydrogen bonds : bond 0.04782 ( 1811) hydrogen bonds : angle 4.50875 ( 5319) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5300.10 seconds wall clock time: 91 minutes 35.83 seconds (5495.83 seconds total)