Starting phenix.real_space_refine on Wed May 21 15:55:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8eau_27986/05_2025/8eau_27986.cif Found real_map, /net/cci-nas-00/data/ceres_data/8eau_27986/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8eau_27986/05_2025/8eau_27986.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8eau_27986/05_2025/8eau_27986.map" model { file = "/net/cci-nas-00/data/ceres_data/8eau_27986/05_2025/8eau_27986.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8eau_27986/05_2025/8eau_27986.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'TYR:plan': 5, 'GLU:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 10} 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: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 7, 'ARG:plan': 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: {'GLN:plan1': 2, 'ASP:plan': 1} 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: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 1} 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: 12.60, per 1000 atoms: 0.58 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: 5.11 Conformation dependent library (CDL) restraints added in 3.0 seconds 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: 1.76 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: 7.72 Time building geometry restraints manager: 6.07 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: 2.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.130 Find NCS groups from input model: 0.940 Set up NCS constraints: 0.090 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 54.830 ------------------------------------------------------------------------------- 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 : 9.07 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.033 0.002 TRP c 77 HIS 0.005 0.001 HIS a 801 PHE 0.055 0.002 PHE c 80 TYR 0.027 0.002 TYR o 127 ARG 0.009 0.001 ARG o 132 Details of bonding type rmsd hydrogen bonds : bond 0.10418 ( 1811) hydrogen bonds : angle 5.39665 ( 5319) covalent geometry : bond 0.00351 (22351) covalent geometry : angle 0.63528 (30397) *********************** 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 : 2.396 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: 0.3671 time to fit residues: 194.4988 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 : 2.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 239 optimal weight: 0.7980 chunk 215 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 222 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 135 optimal weight: 3.9990 chunk 165 optimal weight: 0.6980 chunk 257 optimal weight: 1.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** c 132 ASN d 45 GLN d 182 ASN d 303 GLN j 151 ASN ** k 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 90 GLN m 90 GLN p 37 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.153711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105963 restraints weight = 23783.438| |-----------------------------------------------------------------------------| r_work (start): 0.3258 rms_B_bonded: 1.87 r_work: 0.3098 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 22351 Z= 0.264 Angle : 0.652 8.837 30397 Z= 0.341 Chirality : 0.044 0.181 3661 Planarity : 0.004 0.066 3770 Dihedral : 4.749 52.848 3127 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.38 % Allowed : 6.83 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.15), residues: 2906 helix: 1.17 (0.11), residues: 2169 sheet: -0.26 (0.63), residues: 37 loop : -0.47 (0.24), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP a 594 HIS 0.005 0.001 HIS a 801 PHE 0.049 0.002 PHE c 80 TYR 0.042 0.002 TYR o 127 ARG 0.005 0.001 ARG i 46 Details of bonding type rmsd hydrogen bonds : bond 0.05676 ( 1811) hydrogen bonds : angle 4.93949 ( 5319) covalent geometry : bond 0.00630 (22351) covalent geometry : angle 0.65155 (30397) *********************** 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 328 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 297 time to evaluate : 2.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 132 GLU cc_start: 0.7961 (tt0) cc_final: 0.7575 (tp30) REVERT: a 487 MET cc_start: 0.8772 (mtm) cc_final: 0.8523 (mtm) REVERT: a 501 LYS cc_start: 0.8223 (mttp) cc_final: 0.7733 (tptp) REVERT: e 24 MET cc_start: 0.7905 (ttt) cc_final: 0.7422 (mtp) REVERT: e 66 ASP cc_start: 0.8287 (p0) cc_final: 0.7776 (p0) REVERT: f 44 ASP cc_start: 0.8240 (m-30) cc_final: 0.8040 (m-30) REVERT: g 8 TYR cc_start: 0.9253 (p90) cc_final: 0.8854 (p90) REVERT: i 124 ARG cc_start: 0.7921 (mtp180) cc_final: 0.7689 (mtp180) REVERT: l 19 SER cc_start: 0.9103 (m) cc_final: 0.8835 (m) REVERT: m 122 GLN cc_start: 0.7800 (tm-30) cc_final: 0.7296 (tm-30) REVERT: o 59 SER cc_start: 0.8892 (t) cc_final: 0.8454 (p) REVERT: p 48 MET cc_start: 0.7126 (tpp) cc_final: 0.6922 (tpp) outliers start: 31 outliers final: 21 residues processed: 310 average time/residue: 0.3415 time to fit residues: 162.2444 Evaluate side-chains 284 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 263 time to evaluate : 2.110 ------------------------------------------------------------------------------- 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 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 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 155 THR Chi-restraints excluded: chain j residue 151 ASN 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 74 VAL Chi-restraints excluded: chain m residue 155 THR Chi-restraints excluded: chain m residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 67 optimal weight: 0.9990 chunk 247 optimal weight: 0.6980 chunk 259 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 256 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 91 optimal weight: 0.5980 chunk 0 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 160 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 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 499 HIS c 100 ASN c 132 ASN g 122 GLN i 53 ASN j 151 ASN k 82 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.156435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.107615 restraints weight = 23153.363| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.85 r_work: 0.3142 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 22351 Z= 0.152 Angle : 0.527 10.313 30397 Z= 0.280 Chirality : 0.039 0.155 3661 Planarity : 0.004 0.060 3770 Dihedral : 4.516 66.913 3127 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 1.70 % Allowed : 9.33 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.15), residues: 2906 helix: 1.42 (0.11), residues: 2185 sheet: 0.06 (0.72), residues: 35 loop : -0.31 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP e 48 HIS 0.003 0.001 HIS a 801 PHE 0.033 0.001 PHE c 80 TYR 0.034 0.001 TYR o 127 ARG 0.007 0.001 ARG o 132 Details of bonding type rmsd hydrogen bonds : bond 0.04979 ( 1811) hydrogen bonds : angle 4.63616 ( 5319) covalent geometry : bond 0.00325 (22351) covalent geometry : angle 0.52721 (30397) *********************** 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 328 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 290 time to evaluate : 2.272 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 132 GLU cc_start: 0.7918 (tt0) cc_final: 0.7455 (tp30) REVERT: a 139 GLU cc_start: 0.7132 (mm-30) cc_final: 0.6785 (tm-30) REVERT: a 487 MET cc_start: 0.8690 (mtm) cc_final: 0.8472 (mtm) REVERT: a 501 LYS cc_start: 0.8243 (mttp) cc_final: 0.7713 (tptp) REVERT: d 97 TYR cc_start: 0.7901 (m-80) cc_final: 0.7671 (m-80) REVERT: e 66 ASP cc_start: 0.8280 (p0) cc_final: 0.7721 (p0) REVERT: g 8 TYR cc_start: 0.9192 (p90) cc_final: 0.8728 (p90) REVERT: g 42 THR cc_start: 0.9107 (m) cc_final: 0.8732 (m) REVERT: h 157 ASP cc_start: 0.7994 (m-30) cc_final: 0.7771 (m-30) REVERT: i 89 ILE cc_start: 0.8632 (tt) cc_final: 0.8380 (tt) REVERT: l 49 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.6006 (pp) REVERT: l 59 MET cc_start: 0.8661 (mtp) cc_final: 0.8354 (mtt) REVERT: n 129 MET cc_start: 0.6463 (mtt) cc_final: 0.6165 (mmm) REVERT: o 59 SER cc_start: 0.8827 (t) cc_final: 0.8403 (p) REVERT: o 128 MET cc_start: 0.7758 (mmm) cc_final: 0.7539 (mmp) REVERT: o 132 ARG cc_start: 0.7638 (ttp-110) cc_final: 0.7344 (ttp-110) REVERT: p 48 MET cc_start: 0.7012 (tpp) cc_final: 0.6674 (tpp) outliers start: 38 outliers final: 17 residues processed: 315 average time/residue: 0.3398 time to fit residues: 165.8341 Evaluate side-chains 278 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 260 time to evaluate : 2.381 ------------------------------------------------------------------------------- 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 278 ASN Chi-restraints excluded: chain a residue 302 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 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 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 247 optimal weight: 0.9990 chunk 234 optimal weight: 0.0970 chunk 99 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 276 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 130 optimal weight: 0.0370 chunk 9 optimal weight: 0.0570 chunk 101 optimal weight: 4.9990 chunk 68 optimal weight: 4.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- 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 655 HIS ** i 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 151 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.158707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.110066 restraints weight = 23424.151| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.61 r_work: 0.3183 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 22351 Z= 0.130 Angle : 0.503 8.965 30397 Z= 0.265 Chirality : 0.038 0.147 3661 Planarity : 0.004 0.058 3770 Dihedral : 4.304 61.198 3127 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.65 % Allowed : 10.67 % Favored : 87.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.15), residues: 2906 helix: 1.57 (0.11), residues: 2209 sheet: -0.03 (0.73), residues: 38 loop : -0.27 (0.24), residues: 659 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 48 HIS 0.002 0.001 HIS a 801 PHE 0.028 0.001 PHE c 80 TYR 0.033 0.001 TYR o 127 ARG 0.005 0.000 ARG i 46 Details of bonding type rmsd hydrogen bonds : bond 0.04640 ( 1811) hydrogen bonds : angle 4.43884 ( 5319) covalent geometry : bond 0.00263 (22351) covalent geometry : angle 0.50268 (30397) *********************** 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 323 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 2.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: a 132 GLU cc_start: 0.7933 (tt0) cc_final: 0.7449 (tp30) REVERT: a 139 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6749 (tm-30) REVERT: a 319 ILE cc_start: 0.8691 (mm) cc_final: 0.8368 (tp) REVERT: a 487 MET cc_start: 0.8656 (mtm) cc_final: 0.8382 (mtm) REVERT: a 501 LYS cc_start: 0.8287 (mttp) cc_final: 0.7748 (tptp) REVERT: d 97 TYR cc_start: 0.7963 (m-80) cc_final: 0.7707 (m-80) REVERT: e 66 ASP cc_start: 0.8329 (p0) cc_final: 0.7709 (p0) REVERT: g 8 TYR cc_start: 0.9132 (p90) cc_final: 0.8732 (p90) REVERT: g 42 THR cc_start: 0.9082 (m) cc_final: 0.8718 (m) REVERT: i 46 ARG cc_start: 0.7898 (ttm110) cc_final: 0.7629 (ptp-110) REVERT: i 89 ILE cc_start: 0.8585 (tt) cc_final: 0.8352 (tt) REVERT: i 125 LEU cc_start: 0.8084 (tp) cc_final: 0.7846 (tt) REVERT: i 141 LEU cc_start: 0.8651 (tp) cc_final: 0.8449 (tp) REVERT: k 142 TYR cc_start: 0.8988 (m-10) cc_final: 0.8550 (m-10) REVERT: l 49 LEU cc_start: 0.6474 (OUTLIER) cc_final: 0.6211 (pp) REVERT: l 59 MET cc_start: 0.8464 (mtp) cc_final: 0.8239 (mtt) REVERT: n 129 MET cc_start: 0.6531 (mtt) cc_final: 0.6242 (mmm) REVERT: o 59 SER cc_start: 0.8783 (t) cc_final: 0.8369 (p) REVERT: o 128 MET cc_start: 0.7734 (mmm) cc_final: 0.7486 (mmp) REVERT: p 48 MET cc_start: 0.7012 (tpp) cc_final: 0.6656 (tpp) outliers start: 37 outliers final: 19 residues processed: 313 average time/residue: 0.3441 time to fit residues: 164.6302 Evaluate side-chains 284 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 264 time to evaluate : 2.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 116 TYR 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 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 42 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 65 ILE 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 125 optimal weight: 7.9990 chunk 165 optimal weight: 1.9990 chunk 278 optimal weight: 4.9990 chunk 263 optimal weight: 2.9990 chunk 233 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 148 optimal weight: 8.9990 chunk 194 optimal weight: 3.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- 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 729 HIS c 132 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.152771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.104856 restraints weight = 24043.036| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.93 r_work: 0.3096 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 22351 Z= 0.303 Angle : 0.624 11.683 30397 Z= 0.327 Chirality : 0.044 0.185 3661 Planarity : 0.004 0.061 3770 Dihedral : 4.487 50.357 3127 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.54 % Allowed : 11.03 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.15), residues: 2906 helix: 1.22 (0.11), residues: 2194 sheet: -0.08 (0.72), residues: 38 loop : -0.54 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP a 598 HIS 0.007 0.001 HIS a 801 PHE 0.040 0.002 PHE c 80 TYR 0.027 0.002 TYR o 127 ARG 0.006 0.001 ARG h 153 Details of bonding type rmsd hydrogen bonds : bond 0.05454 ( 1811) hydrogen bonds : angle 4.78778 ( 5319) covalent geometry : bond 0.00732 (22351) covalent geometry : angle 0.62415 (30397) *********************** 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 335 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 278 time to evaluate : 2.479 Fit side-chains REVERT: a 132 GLU cc_start: 0.8015 (tt0) cc_final: 0.7532 (tp30) REVERT: a 139 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6877 (tm-30) REVERT: a 501 LYS cc_start: 0.8339 (mttp) cc_final: 0.7813 (tptp) REVERT: a 539 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8694 (tp) REVERT: c 185 LEU cc_start: 0.7968 (tt) cc_final: 0.7578 (mt) REVERT: d 14 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7936 (tt0) REVERT: d 97 TYR cc_start: 0.8328 (m-80) cc_final: 0.8085 (m-80) REVERT: g 42 THR cc_start: 0.9150 (m) cc_final: 0.8749 (m) REVERT: g 77 SER cc_start: 0.9183 (t) cc_final: 0.8911 (t) REVERT: i 46 ARG cc_start: 0.8307 (ttm110) cc_final: 0.8037 (ptp-110) REVERT: l 49 LEU cc_start: 0.6532 (OUTLIER) cc_final: 0.6250 (pp) REVERT: n 59 MET cc_start: 0.8421 (mmm) cc_final: 0.8117 (mmt) REVERT: n 129 MET cc_start: 0.6754 (mtt) cc_final: 0.6453 (mmm) REVERT: o 59 SER cc_start: 0.8852 (t) cc_final: 0.8547 (p) REVERT: o 128 MET cc_start: 0.7846 (mmm) cc_final: 0.7620 (mmp) REVERT: p 48 MET cc_start: 0.7029 (tpp) cc_final: 0.6811 (tpp) outliers start: 57 outliers final: 39 residues processed: 317 average time/residue: 0.3423 time to fit residues: 169.7510 Evaluate side-chains 305 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 263 time to evaluate : 2.492 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain a residue 732 SER Chi-restraints excluded: chain a residue 788 MET Chi-restraints excluded: chain b residue 217 SER Chi-restraints excluded: chain b residue 218 ILE Chi-restraints excluded: chain b residue 254 LEU Chi-restraints excluded: chain c residue 21 LEU Chi-restraints excluded: chain c residue 24 LEU 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 g residue 2 THR Chi-restraints excluded: chain g residue 46 ARG Chi-restraints excluded: chain g residue 120 SER Chi-restraints excluded: chain g residue 155 THR 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 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 65 ILE 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 63 VAL Chi-restraints excluded: chain o residue 116 ILE Chi-restraints excluded: chain p residue 51 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 158 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 146 optimal weight: 2.9990 chunk 186 optimal weight: 2.9990 chunk 255 optimal weight: 0.9990 chunk 67 optimal weight: 0.6980 chunk 279 optimal weight: 0.0770 chunk 149 optimal weight: 0.4980 chunk 161 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 276 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.158463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.110266 restraints weight = 23548.041| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.58 r_work: 0.3217 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3088 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22351 Z= 0.135 Angle : 0.498 8.664 30397 Z= 0.264 Chirality : 0.038 0.169 3661 Planarity : 0.003 0.059 3770 Dihedral : 4.236 45.827 3127 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.88 % Allowed : 12.63 % Favored : 85.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.15), residues: 2906 helix: 1.49 (0.11), residues: 2214 sheet: 0.28 (0.79), residues: 35 loop : -0.48 (0.24), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 598 HIS 0.004 0.001 HIS a 801 PHE 0.026 0.001 PHE c 80 TYR 0.027 0.001 TYR o 127 ARG 0.006 0.000 ARG h 153 Details of bonding type rmsd hydrogen bonds : bond 0.04666 ( 1811) hydrogen bonds : angle 4.45792 ( 5319) covalent geometry : bond 0.00281 (22351) covalent geometry : angle 0.49809 (30397) *********************** 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 329 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 2.446 Fit side-chains revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8192 (mt-10) cc_final: 0.7911 (mt-10) REVERT: a 132 GLU cc_start: 0.8008 (tt0) cc_final: 0.7535 (tp30) REVERT: a 139 GLU cc_start: 0.7243 (mm-30) cc_final: 0.6967 (tm-30) REVERT: a 328 TYR cc_start: 0.7829 (t80) cc_final: 0.7447 (t80) REVERT: a 453 GLU cc_start: 0.7325 (tp30) cc_final: 0.7054 (tt0) REVERT: a 501 LYS cc_start: 0.8292 (mttp) cc_final: 0.7834 (tptp) REVERT: g 42 THR cc_start: 0.9087 (m) cc_final: 0.8699 (m) REVERT: i 46 ARG cc_start: 0.8171 (ttm110) cc_final: 0.7847 (ptp-110) REVERT: k 3 GLU cc_start: 0.7428 (tt0) cc_final: 0.7212 (tt0) REVERT: k 142 TYR cc_start: 0.9008 (m-10) cc_final: 0.8575 (m-10) REVERT: l 49 LEU cc_start: 0.6587 (OUTLIER) cc_final: 0.6053 (pp) REVERT: l 59 MET cc_start: 0.8552 (mtp) cc_final: 0.8278 (mtt) REVERT: n 129 MET cc_start: 0.6689 (mtt) cc_final: 0.6272 (mmm) REVERT: o 59 SER cc_start: 0.8875 (t) cc_final: 0.8590 (p) REVERT: o 128 MET cc_start: 0.7805 (mmm) cc_final: 0.7521 (mmp) REVERT: p 20 MET cc_start: 0.7537 (tpp) cc_final: 0.7015 (tpp) outliers start: 42 outliers final: 27 residues processed: 316 average time/residue: 0.3349 time to fit residues: 164.3497 Evaluate side-chains 291 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 263 time to evaluate : 2.149 ------------------------------------------------------------------------------- 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 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 732 SER Chi-restraints excluded: chain b residue 218 ILE Chi-restraints excluded: chain c residue 21 LEU 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 67 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 65 ILE 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 n residue 159 VAL Chi-restraints excluded: chain o residue 63 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 29 optimal weight: 7.9990 chunk 194 optimal weight: 0.0170 chunk 226 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 176 optimal weight: 0.7980 chunk 109 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 274 optimal weight: 4.9990 chunk 129 optimal weight: 4.9990 chunk 171 optimal weight: 5.9990 overall best weight: 1.5624 ------------------------------------------------------------------------------- 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 = 0.3897 r_free = 0.3897 target = 0.155470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.107997 restraints weight = 23805.386| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.83 r_work: 0.3150 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22351 Z= 0.209 Angle : 0.553 12.818 30397 Z= 0.289 Chirality : 0.040 0.170 3661 Planarity : 0.004 0.060 3770 Dihedral : 4.258 39.331 3127 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.28 % Allowed : 12.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.15), residues: 2906 helix: 1.45 (0.11), residues: 2184 sheet: -0.08 (0.76), residues: 38 loop : -0.60 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 598 HIS 0.005 0.001 HIS a 801 PHE 0.032 0.002 PHE c 80 TYR 0.028 0.001 TYR o 127 ARG 0.014 0.001 ARG d 266 Details of bonding type rmsd hydrogen bonds : bond 0.04968 ( 1811) hydrogen bonds : angle 4.57645 ( 5319) covalent geometry : bond 0.00487 (22351) covalent geometry : angle 0.55278 (30397) *********************** 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 325 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 274 time to evaluate : 2.259 Fit side-chains revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7958 (mt-10) REVERT: a 132 GLU cc_start: 0.8029 (tt0) cc_final: 0.7468 (tp30) REVERT: a 139 GLU cc_start: 0.7280 (mm-30) cc_final: 0.6957 (tm-30) REVERT: a 328 TYR cc_start: 0.7840 (t80) cc_final: 0.7341 (t80) REVERT: a 453 GLU cc_start: 0.7347 (tp30) cc_final: 0.7014 (tt0) REVERT: a 501 LYS cc_start: 0.8325 (mttp) cc_final: 0.7829 (tptp) REVERT: a 539 LEU cc_start: 0.8867 (OUTLIER) cc_final: 0.8624 (tp) REVERT: c 185 LEU cc_start: 0.7908 (tt) cc_final: 0.7559 (mt) REVERT: d 14 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7876 (tt0) REVERT: d 185 TYR cc_start: 0.7886 (OUTLIER) cc_final: 0.7407 (m-80) REVERT: g 42 THR cc_start: 0.9141 (m) cc_final: 0.8733 (m) REVERT: i 46 ARG cc_start: 0.8142 (ttm110) cc_final: 0.7808 (ptp-110) REVERT: l 49 LEU cc_start: 0.6392 (OUTLIER) cc_final: 0.5982 (pp) REVERT: n 59 MET cc_start: 0.8321 (mmm) cc_final: 0.8060 (mmt) REVERT: n 129 MET cc_start: 0.6757 (mtt) cc_final: 0.6306 (mmm) REVERT: o 59 SER cc_start: 0.8883 (t) cc_final: 0.8610 (p) REVERT: o 128 MET cc_start: 0.7767 (mmm) cc_final: 0.7534 (mmp) REVERT: p 48 MET cc_start: 0.7211 (tpp) cc_final: 0.6981 (tpp) outliers start: 51 outliers final: 32 residues processed: 311 average time/residue: 0.3317 time to fit residues: 161.3348 Evaluate side-chains 294 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 258 time to evaluate : 2.522 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain a residue 589 CYS 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 27 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 151 ASN Chi-restraints excluded: chain j residue 155 THR Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain l residue 65 ILE 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 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 63 VAL Chi-restraints excluded: chain o residue 118 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 223 optimal weight: 0.3980 chunk 219 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 237 optimal weight: 5.9990 chunk 260 optimal weight: 6.9990 chunk 177 optimal weight: 4.9990 chunk 273 optimal weight: 0.6980 chunk 208 optimal weight: 8.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 220 GLN a 324 ASN c 61 ASN c 132 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.155615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.109494 restraints weight = 23771.622| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 1.89 r_work: 0.3150 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 22351 Z= 0.195 Angle : 0.550 16.920 30397 Z= 0.286 Chirality : 0.040 0.225 3661 Planarity : 0.004 0.062 3770 Dihedral : 4.235 34.188 3127 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.28 % Allowed : 12.86 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.15), residues: 2906 helix: 1.43 (0.11), residues: 2184 sheet: -0.08 (0.76), residues: 38 loop : -0.63 (0.23), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 598 HIS 0.005 0.001 HIS a 801 PHE 0.031 0.002 PHE c 80 TYR 0.027 0.001 TYR o 127 ARG 0.013 0.000 ARG d 266 Details of bonding type rmsd hydrogen bonds : bond 0.04910 ( 1811) hydrogen bonds : angle 4.56640 ( 5319) covalent geometry : bond 0.00453 (22351) covalent geometry : angle 0.54968 (30397) *********************** 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 325 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 274 time to evaluate : 2.346 Fit side-chains revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8210 (mt-10) cc_final: 0.7971 (mt-10) REVERT: a 132 GLU cc_start: 0.8025 (tt0) cc_final: 0.7452 (tp30) REVERT: a 139 GLU cc_start: 0.7250 (mm-30) cc_final: 0.6933 (tm-30) REVERT: a 328 TYR cc_start: 0.7813 (t80) cc_final: 0.7291 (t80) REVERT: a 453 GLU cc_start: 0.7383 (tp30) cc_final: 0.7049 (tt0) REVERT: a 501 LYS cc_start: 0.8328 (mttp) cc_final: 0.7816 (tptp) REVERT: a 539 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8657 (tp) REVERT: a 788 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.8083 (mtm) REVERT: c 77 TRP cc_start: 0.8896 (OUTLIER) cc_final: 0.8200 (t-100) REVERT: c 185 LEU cc_start: 0.7861 (tt) cc_final: 0.7514 (mt) REVERT: d 14 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.7868 (tt0) REVERT: d 185 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7451 (m-80) REVERT: g 15 ILE cc_start: 0.8775 (OUTLIER) cc_final: 0.8131 (tp) REVERT: g 42 THR cc_start: 0.9140 (m) cc_final: 0.8734 (m) REVERT: i 46 ARG cc_start: 0.8040 (ttm110) cc_final: 0.7727 (ptp-110) REVERT: l 49 LEU cc_start: 0.6386 (OUTLIER) cc_final: 0.5998 (pp) REVERT: l 59 MET cc_start: 0.8776 (mtp) cc_final: 0.8435 (mtt) REVERT: n 59 MET cc_start: 0.8325 (mmm) cc_final: 0.8071 (mmt) REVERT: n 129 MET cc_start: 0.6801 (mtt) cc_final: 0.6385 (mmm) REVERT: o 59 SER cc_start: 0.8862 (t) cc_final: 0.8577 (p) REVERT: o 128 MET cc_start: 0.7782 (mmm) cc_final: 0.7556 (mmp) REVERT: p 20 MET cc_start: 0.7572 (tpp) cc_final: 0.7056 (tpp) REVERT: p 48 MET cc_start: 0.7200 (tpp) cc_final: 0.6917 (tpp) outliers start: 51 outliers final: 37 residues processed: 310 average time/residue: 0.3321 time to fit residues: 159.9770 Evaluate side-chains 306 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 262 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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 539 LEU 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 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 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 141 VAL Chi-restraints excluded: chain d residue 185 TYR 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 57 VAL 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 65 ILE 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 134 ILE Chi-restraints excluded: chain m residue 155 THR 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 63 VAL Chi-restraints excluded: chain o residue 118 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 284 random chunks: chunk 18 optimal weight: 6.9990 chunk 166 optimal weight: 0.1980 chunk 96 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 223 optimal weight: 10.0000 chunk 159 optimal weight: 0.1980 chunk 101 optimal weight: 4.9990 chunk 128 optimal weight: 1.9990 chunk 198 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 ** 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 = 0.3925 r_free = 0.3925 target = 0.157968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.109980 restraints weight = 23602.068| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.57 r_work: 0.3209 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 22351 Z= 0.149 Angle : 0.520 17.060 30397 Z= 0.271 Chirality : 0.039 0.201 3661 Planarity : 0.004 0.062 3770 Dihedral : 4.125 28.677 3127 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.14 % Allowed : 12.81 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.15), residues: 2906 helix: 1.57 (0.11), residues: 2188 sheet: -0.16 (0.78), residues: 38 loop : -0.52 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 598 HIS 0.002 0.001 HIS a 801 PHE 0.026 0.001 PHE c 80 TYR 0.025 0.001 TYR o 127 ARG 0.011 0.000 ARG d 266 Details of bonding type rmsd hydrogen bonds : bond 0.04636 ( 1811) hydrogen bonds : angle 4.44550 ( 5319) covalent geometry : bond 0.00329 (22351) covalent geometry : angle 0.52008 (30397) *********************** 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 326 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 278 time to evaluate : 2.377 Fit side-chains revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8147 (mt-10) cc_final: 0.7911 (mt-10) REVERT: a 132 GLU cc_start: 0.8013 (tt0) cc_final: 0.7457 (tp30) REVERT: a 139 GLU cc_start: 0.7261 (mm-30) cc_final: 0.7036 (tm-30) REVERT: a 328 TYR cc_start: 0.7707 (t80) cc_final: 0.7250 (t80) REVERT: a 453 GLU cc_start: 0.7369 (tp30) cc_final: 0.7081 (tt0) REVERT: a 501 LYS cc_start: 0.8315 (mttp) cc_final: 0.7857 (tptp) REVERT: a 539 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8623 (tp) REVERT: c 77 TRP cc_start: 0.8831 (OUTLIER) cc_final: 0.8100 (t-100) REVERT: d 14 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7855 (tt0) REVERT: d 185 TYR cc_start: 0.7887 (OUTLIER) cc_final: 0.7422 (m-80) REVERT: f 9 LYS cc_start: 0.7671 (tmtt) cc_final: 0.7468 (tptt) REVERT: g 15 ILE cc_start: 0.8776 (OUTLIER) cc_final: 0.8111 (tp) REVERT: i 46 ARG cc_start: 0.7989 (ttm110) cc_final: 0.7708 (ptp-110) REVERT: k 142 TYR cc_start: 0.9015 (m-10) cc_final: 0.8615 (m-10) REVERT: l 49 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6059 (pp) REVERT: l 59 MET cc_start: 0.8659 (mtp) cc_final: 0.8446 (mtt) REVERT: m 122 GLN cc_start: 0.6826 (tm-30) cc_final: 0.6554 (tm-30) REVERT: n 59 MET cc_start: 0.8221 (mmm) cc_final: 0.7950 (mmt) REVERT: n 129 MET cc_start: 0.6788 (mtt) cc_final: 0.6432 (mmm) REVERT: o 59 SER cc_start: 0.8882 (t) cc_final: 0.8599 (p) REVERT: o 72 TYR cc_start: 0.8594 (m-10) cc_final: 0.8240 (m-10) REVERT: o 128 MET cc_start: 0.7695 (mmm) cc_final: 0.7474 (mmp) REVERT: p 20 MET cc_start: 0.7578 (tpp) cc_final: 0.7059 (tpp) outliers start: 48 outliers final: 39 residues processed: 312 average time/residue: 0.3415 time to fit residues: 164.8754 Evaluate side-chains 311 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 266 time to evaluate : 2.219 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain a residue 589 CYS 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 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 141 VAL Chi-restraints excluded: chain d residue 185 TYR 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 i residue 26 LEU Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 59 MET Chi-restraints excluded: chain i residue 95 LEU 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 65 ILE 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 134 ILE Chi-restraints excluded: chain m residue 155 THR 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 63 VAL Chi-restraints excluded: chain o residue 116 ILE 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 245 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 57 optimal weight: 0.1980 chunk 122 optimal weight: 5.9990 chunk 149 optimal weight: 0.2980 chunk 8 optimal weight: 20.0000 chunk 1 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.5782 ------------------------------------------------------------------------------- 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 ** g 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.158689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110948 restraints weight = 23611.184| |-----------------------------------------------------------------------------| r_work (start): 0.3373 rms_B_bonded: 1.57 r_work: 0.3238 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 22351 Z= 0.135 Angle : 0.513 17.183 30397 Z= 0.266 Chirality : 0.039 0.204 3661 Planarity : 0.004 0.064 3770 Dihedral : 4.056 25.136 3127 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.05 % Allowed : 13.08 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.16 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.15), residues: 2906 helix: 1.68 (0.11), residues: 2182 sheet: -0.43 (0.76), residues: 36 loop : -0.52 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 48 HIS 0.003 0.000 HIS a 801 PHE 0.026 0.001 PHE c 80 TYR 0.025 0.001 TYR o 127 ARG 0.011 0.000 ARG d 266 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 1811) hydrogen bonds : angle 4.37951 ( 5319) covalent geometry : bond 0.00289 (22351) covalent geometry : angle 0.51279 (30397) ********************** 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 320 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 274 time to evaluate : 2.113 Fit side-chains revert: symmetry clash REVERT: a 66 GLU cc_start: 0.8103 (mt-10) cc_final: 0.7886 (mt-10) REVERT: a 132 GLU cc_start: 0.8034 (tt0) cc_final: 0.7454 (tp30) REVERT: a 139 GLU cc_start: 0.7279 (mm-30) cc_final: 0.7053 (tm-30) REVERT: a 328 TYR cc_start: 0.7683 (t80) cc_final: 0.7259 (t80) REVERT: a 453 GLU cc_start: 0.7341 (tp30) cc_final: 0.7048 (tt0) REVERT: a 501 LYS cc_start: 0.8302 (mttp) cc_final: 0.7778 (tptp) REVERT: a 539 LEU cc_start: 0.8855 (OUTLIER) cc_final: 0.8589 (tp) REVERT: c 77 TRP cc_start: 0.8813 (OUTLIER) cc_final: 0.8083 (t-100) REVERT: d 14 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.7823 (tt0) REVERT: d 185 TYR cc_start: 0.7833 (OUTLIER) cc_final: 0.7378 (m-80) REVERT: g 8 TYR cc_start: 0.9078 (p90) cc_final: 0.8738 (p90) REVERT: g 15 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8076 (tp) REVERT: h 155 THR cc_start: 0.8654 (m) cc_final: 0.7927 (p) REVERT: i 46 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7593 (ptp-110) REVERT: k 142 TYR cc_start: 0.9012 (m-10) cc_final: 0.8556 (m-10) REVERT: l 49 LEU cc_start: 0.6402 (OUTLIER) cc_final: 0.5975 (pp) REVERT: l 59 MET cc_start: 0.8599 (mtp) cc_final: 0.8399 (mtt) REVERT: m 122 GLN cc_start: 0.6655 (tm-30) cc_final: 0.6361 (tm-30) REVERT: n 129 MET cc_start: 0.6734 (mtt) cc_final: 0.6398 (mmm) REVERT: o 59 SER cc_start: 0.8858 (t) cc_final: 0.8563 (p) REVERT: o 72 TYR cc_start: 0.8527 (m-10) cc_final: 0.8199 (m-10) REVERT: o 128 MET cc_start: 0.7648 (mmm) cc_final: 0.7433 (mmp) outliers start: 46 outliers final: 35 residues processed: 308 average time/residue: 0.3433 time to fit residues: 163.6089 Evaluate side-chains 307 residues out of total 2374 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 266 time to evaluate : 2.124 ------------------------------------------------------------------------------- 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 539 LEU Chi-restraints excluded: chain a residue 589 CYS 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 95 ARG 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 67 LEU Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 185 TYR Chi-restraints excluded: chain g residue 15 ILE Chi-restraints excluded: chain g residue 57 VAL Chi-restraints excluded: chain i residue 42 THR Chi-restraints excluded: chain i residue 59 MET Chi-restraints excluded: chain i residue 95 LEU 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 134 ILE Chi-restraints excluded: chain m residue 155 THR 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 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 173 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 249 optimal weight: 0.2980 chunk 78 optimal weight: 4.9990 chunk 187 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 139 optimal weight: 5.9990 chunk 258 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 201 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.156758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.109945 restraints weight = 23884.400| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.88 r_work: 0.3191 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3056 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 22351 Z= 0.170 Angle : 0.536 17.182 30397 Z= 0.277 Chirality : 0.039 0.197 3661 Planarity : 0.004 0.064 3770 Dihedral : 4.071 21.738 3127 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 2.05 % Allowed : 13.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.15), residues: 2906 helix: 1.62 (0.11), residues: 2182 sheet: -0.26 (0.74), residues: 35 loop : -0.57 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP c 59 HIS 0.004 0.001 HIS a 801 PHE 0.029 0.001 PHE c 80 TYR 0.024 0.001 TYR o 127 ARG 0.011 0.000 ARG d 266 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 1811) hydrogen bonds : angle 4.42315 ( 5319) covalent geometry : bond 0.00390 (22351) covalent geometry : angle 0.53635 (30397) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11542.80 seconds wall clock time: 200 minutes 16.48 seconds (12016.48 seconds total)