Starting phenix.real_space_refine on Sat Aug 8 13:55:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rmc_54056/08_2026/9rmc_54056.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rmc_54056/08_2026/9rmc_54056.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9rmc_54056/08_2026/9rmc_54056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rmc_54056/08_2026/9rmc_54056.map" model { file = "/net/cci-nas-00/data/ceres_data/9rmc_54056/08_2026/9rmc_54056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rmc_54056/08_2026/9rmc_54056.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 261 5.49 5 S 42 5.16 5 C 16520 2.51 5 N 5289 2.21 5 O 5840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27953 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2021 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 10, 'TRANS': 320} Chain breaks: 4 Unresolved non-hydrogen bonds: 778 Unresolved non-hydrogen angles: 999 Unresolved non-hydrogen dihedrals: 669 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 12, 'GLU:plan': 11, 'ARG:plan': 11, 'HIS:plan': 9, 'TYR:plan': 12, 'ASN:plan1': 12, 'ASP:plan': 5, 'PHE:plan': 8, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 429 Chain: "J" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1677 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 272} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain breaks: 4 Unresolved non-hydrogen bonds: 980 Unresolved non-hydrogen angles: 1263 Unresolved non-hydrogen dihedrals: 814 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'PHE:plan': 15, 'ASP:plan': 18, 'TYR:plan': 12, 'ARG:plan': 15, 'GLU:plan': 18, 'ASN:plan1': 14, 'TRP:plan': 5, 'GLN:plan1': 15, 'HIS:plan': 8} Unresolved non-hydrogen planarities: 562 Chain: "K" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 1600 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 253} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain breaks: 3 Unresolved non-hydrogen bonds: 922 Unresolved non-hydrogen angles: 1182 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'ASP:plan': 21, 'ASN:plan1': 8, 'PHE:plan': 12, 'ARG:plan': 14, 'TRP:plan': 4, 'GLU:plan': 23, 'HIS:plan': 7, 'TYR:plan': 13, 'GLN:plan1': 9} Unresolved non-hydrogen planarities: 519 Chain: "L" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3671 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 440} Chain breaks: 4 Chain: "M" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 1488 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 252} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 920 Unresolved non-hydrogen angles: 1174 Unresolved non-hydrogen dihedrals: 755 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'PHE:plan': 11, 'GLN:plan1': 13, 'GLU:plan': 27, 'ASP:plan': 21, 'TYR:plan': 8, 'ASN:plan1': 12, 'ARG:plan': 18, 'TRP:plan': 5, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 536 Chain: "N" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1622 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain breaks: 3 Unresolved non-hydrogen bonds: 497 Unresolved non-hydrogen angles: 627 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ASN:plan1': 3, 'TYR:plan': 4, 'GLN:plan1': 9, 'ASP:plan': 7, 'GLU:plan': 20, 'TRP:plan': 1, 'HIS:plan': 5, 'ARG:plan': 9, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 283 Chain: "O" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 1605 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 19, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 978 Unresolved non-hydrogen angles: 1250 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'HIS:plan': 11, 'TYR:plan': 12, 'TRP:plan': 4, 'PHE:plan': 12, 'ASP:plan': 13, 'ASN:plan1': 9, 'GLU:plan': 31, 'ARG:plan': 19, 'GLN:plan1': 14} Unresolved non-hydrogen planarities: 588 Chain: "P" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1315 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 14, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 690 Unresolved non-hydrogen angles: 864 Unresolved non-hydrogen dihedrals: 570 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 23, 'ARG:plan': 15, 'GLU:plan': 13, 'TYR:plan': 4, 'PHE:plan': 9, 'HIS:plan': 5, 'TRP:plan': 2, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 389 Chain: "Q" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 529 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 3, 'TRANS': 101} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 10, 'ASP:plan': 7, 'TYR:plan': 1, 'PHE:plan': 4, 'HIS:plan': 4, 'ARG:plan': 10, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 203 Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 351 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 3, 'TRANS': 66} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASP:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 8, 'PHE:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 167 Chain: "V" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 338 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'PHE:plan': 5, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "W" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 373 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 5, 'TRANS': 67} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 7, 'HIS:plan': 3, 'ASP:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 160 Chain: "X" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2662 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "Y" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2706 Classifications: {'DNA': 131} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 130} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13612 SG CYS L2094 41.368 78.961 149.543 1.00196.77 S Time building chain proxies: 6.25, per 1000 atoms: 0.22 Number of scatterers: 27953 At special positions: 0 Unit cell: (126.75, 174.07, 217.165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 42 16.00 P 261 15.00 O 5840 8.00 N 5289 7.00 C 16520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2021 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2019 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2090 " pdb="ZN ZN L2301 " - pdb=" SG CYS L2094 " Number of angles added : 3 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6914 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 28 sheets defined 66.1% alpha, 5.0% beta 130 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 3.72 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 80 removed outlier: 3.913A pdb=" N ASP A 78 " --> pdb=" O GLU A 74 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N PHE A 79 " --> pdb=" O ILE A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 133 Processing helix chain 'B' and resid 25 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 removed outlier: 3.519A pdb=" N GLU B 54 " --> pdb=" O LEU B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 94 Processing helix chain 'C' and resid 17 through 23 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 38 through 40 No H-bonds generated for 'chain 'C' and resid 38 through 40' Processing helix chain 'C' and resid 46 through 74 removed outlier: 4.213A pdb=" N VAL C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 91 removed outlier: 3.664A pdb=" N ASP C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 removed outlier: 3.705A pdb=" N GLN D 48 " --> pdb=" O LYS D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 124 removed outlier: 3.547A pdb=" N ALA D 108 " --> pdb=" O PRO D 104 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LYS D 109 " --> pdb=" O GLY D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 58 Processing helix chain 'E' and resid 64 through 80 removed outlier: 3.885A pdb=" N ASP E 78 " --> pdb=" O GLU E 74 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE E 79 " --> pdb=" O ILE E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 133 Processing helix chain 'F' and resid 25 through 30 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 Processing helix chain 'F' and resid 83 through 94 Processing helix chain 'G' and resid 17 through 23 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 38 through 40 No H-bonds generated for 'chain 'G' and resid 38 through 40' Processing helix chain 'G' and resid 46 through 74 removed outlier: 4.281A pdb=" N VAL G 50 " --> pdb=" O ALA G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 91 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 50 removed outlier: 3.515A pdb=" N GLN H 48 " --> pdb=" O LYS H 44 " (cutoff:3.500A) Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 Processing helix chain 'I' and resid 362 through 387 removed outlier: 3.563A pdb=" N ILE I 366 " --> pdb=" O ASP I 362 " (cutoff:3.500A) Processing helix chain 'I' and resid 397 through 409 Processing helix chain 'I' and resid 409 through 429 Processing helix chain 'I' and resid 436 through 440 removed outlier: 3.770A pdb=" N TYR I 439 " --> pdb=" O ALA I 436 " (cutoff:3.500A) Processing helix chain 'I' and resid 446 through 509 removed outlier: 3.744A pdb=" N ASP I 485 " --> pdb=" O GLN I 481 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA I 509 " --> pdb=" O ALA I 505 " (cutoff:3.500A) Processing helix chain 'I' and resid 757 through 767 Processing helix chain 'I' and resid 784 through 795 removed outlier: 4.109A pdb=" N TYR I 795 " --> pdb=" O ALA I 791 " (cutoff:3.500A) Processing helix chain 'I' and resid 815 through 826 Processing helix chain 'I' and resid 839 through 844 Processing helix chain 'I' and resid 845 through 849 removed outlier: 4.004A pdb=" N LEU I 848 " --> pdb=" O VAL I 845 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ARG I 849 " --> pdb=" O PRO I 846 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 845 through 849' Processing helix chain 'I' and resid 917 through 925 Processing helix chain 'I' and resid 931 through 939 removed outlier: 3.687A pdb=" N SER I 935 " --> pdb=" O THR I 931 " (cutoff:3.500A) Processing helix chain 'J' and resid 70 through 77 Processing helix chain 'J' and resid 95 through 109 Processing helix chain 'J' and resid 129 through 143 Processing helix chain 'J' and resid 154 through 162 Processing helix chain 'J' and resid 189 through 192 Processing helix chain 'J' and resid 198 through 214 Processing helix chain 'J' and resid 247 through 267 Processing helix chain 'J' and resid 299 through 307 Proline residue: J 305 - end of helix Processing helix chain 'J' and resid 308 through 310 No H-bonds generated for 'chain 'J' and resid 308 through 310' Processing helix chain 'J' and resid 324 through 336 removed outlier: 3.539A pdb=" N CYS J 336 " --> pdb=" O SER J 332 " (cutoff:3.500A) Processing helix chain 'J' and resid 340 through 346 Processing helix chain 'J' and resid 352 through 357 removed outlier: 3.895A pdb=" N THR J 355 " --> pdb=" O GLY J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 359 through 372 removed outlier: 3.526A pdb=" N LEU J 364 " --> pdb=" O PHE J 360 " (cutoff:3.500A) Processing helix chain 'J' and resid 381 through 390 removed outlier: 5.924A pdb=" N VAL J 387 " --> pdb=" O ASN J 384 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N GLU J 388 " --> pdb=" O THR J 385 " (cutoff:3.500A) Processing helix chain 'J' and resid 391 through 401 Processing helix chain 'J' and resid 403 through 409 Processing helix chain 'K' and resid 3 through 7 Processing helix chain 'K' and resid 80 through 91 removed outlier: 4.241A pdb=" N TYR K 91 " --> pdb=" O HIS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 124 removed outlier: 3.976A pdb=" N ARG K 116 " --> pdb=" O PRO K 112 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR K 120 " --> pdb=" O ARG K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 146 Processing helix chain 'K' and resid 171 through 175 Processing helix chain 'K' and resid 181 through 197 Processing helix chain 'K' and resid 202 through 216 removed outlier: 3.516A pdb=" N ARG K 206 " --> pdb=" O THR K 202 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE K 208 " --> pdb=" O ALA K 204 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL K 209 " --> pdb=" O GLU K 205 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ARG K 210 " --> pdb=" O ARG K 206 " (cutoff:3.500A) Processing helix chain 'K' and resid 223 through 232 Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 258 through 262 Processing helix chain 'K' and resid 263 through 268 removed outlier: 3.738A pdb=" N LEU K 267 " --> pdb=" O GLN K 263 " (cutoff:3.500A) Processing helix chain 'K' and resid 273 through 285 Processing helix chain 'K' and resid 288 through 295 removed outlier: 4.383A pdb=" N ASP K 292 " --> pdb=" O ASP K 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 301 through 306 removed outlier: 3.827A pdb=" N TYR K 306 " --> pdb=" O THR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 308 through 321 Processing helix chain 'K' and resid 334 through 336 No H-bonds generated for 'chain 'K' and resid 334 through 336' Processing helix chain 'K' and resid 337 through 347 Processing helix chain 'K' and resid 349 through 354 removed outlier: 3.656A pdb=" N GLN K 354 " --> pdb=" O SER K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 359 through 366 removed outlier: 3.566A pdb=" N GLU K 364 " --> pdb=" O GLN K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 367 through 372 Processing helix chain 'L' and resid 1645 through 1649 Processing helix chain 'L' and resid 1660 through 1665 removed outlier: 3.647A pdb=" N ILE L1664 " --> pdb=" O THR L1660 " (cutoff:3.500A) Processing helix chain 'L' and resid 1668 through 1678 Processing helix chain 'L' and resid 1680 through 1697 Processing helix chain 'L' and resid 1700 through 1704 Processing helix chain 'L' and resid 1711 through 1729 Processing helix chain 'L' and resid 1731 through 1735 removed outlier: 4.090A pdb=" N GLU L1735 " --> pdb=" O LYS L1732 " (cutoff:3.500A) Processing helix chain 'L' and resid 1740 through 1744 Processing helix chain 'L' and resid 1840 through 1846 Processing helix chain 'L' and resid 1971 through 1992 Processing helix chain 'L' and resid 1996 through 2003 removed outlier: 4.175A pdb=" N GLU L2000 " --> pdb=" O GLY L1996 " (cutoff:3.500A) Processing helix chain 'L' and resid 2004 through 2017 removed outlier: 4.346A pdb=" N LEU L2016 " --> pdb=" O GLY L2012 " (cutoff:3.500A) Processing helix chain 'L' and resid 2049 through 2068 Processing helix chain 'L' and resid 2077 through 2094 Proline residue: L2083 - end of helix Processing helix chain 'L' and resid 2113 through 2126 Processing helix chain 'L' and resid 2128 through 2137 Processing helix chain 'L' and resid 2140 through 2158 removed outlier: 4.484A pdb=" N ARG L2158 " --> pdb=" O PHE L2154 " (cutoff:3.500A) Processing helix chain 'L' and resid 2160 through 2178 Processing helix chain 'L' and resid 2178 through 2187 Processing helix chain 'L' and resid 2190 through 2210 Processing helix chain 'L' and resid 2227 through 2243 Processing helix chain 'L' and resid 2244 through 2249 removed outlier: 4.579A pdb=" N ASN L2247 " --> pdb=" O VAL L2244 " (cutoff:3.500A) Processing helix chain 'L' and resid 2254 through 2264 Processing helix chain 'L' and resid 2268 through 2284 Processing helix chain 'M' and resid 29 through 36 Processing helix chain 'M' and resid 41 through 47 Processing helix chain 'M' and resid 56 through 66 Processing helix chain 'M' and resid 79 through 84 Processing helix chain 'M' and resid 93 through 100 removed outlier: 3.519A pdb=" N LEU M 100 " --> pdb=" O VAL M 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 173 through 181 Processing helix chain 'M' and resid 214 through 226 Processing helix chain 'M' and resid 229 through 247 Proline residue: M 235 - end of helix Processing helix chain 'M' and resid 289 through 302 Processing helix chain 'M' and resid 304 through 326 Processing helix chain 'M' and resid 327 through 329 No H-bonds generated for 'chain 'M' and resid 327 through 329' Processing helix chain 'M' and resid 342 through 350 removed outlier: 4.227A pdb=" N GLN M 348 " --> pdb=" O GLY M 344 " (cutoff:3.500A) Processing helix chain 'M' and resid 357 through 381 Processing helix chain 'N' and resid 427 through 431 Processing helix chain 'N' and resid 440 through 446 Processing helix chain 'N' and resid 447 through 450 Processing helix chain 'N' and resid 458 through 475 Processing helix chain 'N' and resid 482 through 490 Processing helix chain 'N' and resid 493 through 507 Processing helix chain 'N' and resid 603 through 617 Processing helix chain 'N' and resid 619 through 628 removed outlier: 4.012A pdb=" N VAL N 623 " --> pdb=" O ASP N 619 " (cutoff:3.500A) Processing helix chain 'N' and resid 631 through 641 Processing helix chain 'N' and resid 672 through 682 Processing helix chain 'N' and resid 685 through 701 Processing helix chain 'N' and resid 859 through 943 removed outlier: 3.579A pdb=" N HIS N 905 " --> pdb=" O ILE N 901 " (cutoff:3.500A) Processing helix chain 'O' and resid 439 through 446 Processing helix chain 'O' and resid 447 through 450 Processing helix chain 'O' and resid 458 through 474 Processing helix chain 'O' and resid 482 through 490 Processing helix chain 'O' and resid 493 through 507 Processing helix chain 'O' and resid 602 through 616 removed outlier: 3.777A pdb=" N MET O 615 " --> pdb=" O GLU O 611 " (cutoff:3.500A) Processing helix chain 'O' and resid 619 through 628 Processing helix chain 'O' and resid 631 through 641 Processing helix chain 'O' and resid 645 through 650 Processing helix chain 'O' and resid 656 through 661 removed outlier: 3.595A pdb=" N TYR O 661 " --> pdb=" O PRO O 658 " (cutoff:3.500A) Processing helix chain 'O' and resid 671 through 684 removed outlier: 4.226A pdb=" N PHE O 679 " --> pdb=" O SER O 675 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER O 682 " --> pdb=" O ALA O 678 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL O 683 " --> pdb=" O PHE O 679 " (cutoff:3.500A) Processing helix chain 'O' and resid 685 through 705 removed outlier: 3.807A pdb=" N GLU O 705 " --> pdb=" O SER O 701 " (cutoff:3.500A) Processing helix chain 'O' and resid 709 through 717 Processing helix chain 'O' and resid 868 through 942 Processing helix chain 'P' and resid 127 through 131 Processing helix chain 'P' and resid 134 through 139 Processing helix chain 'P' and resid 143 through 174 Processing helix chain 'P' and resid 298 through 306 Processing helix chain 'P' and resid 312 through 326 Processing helix chain 'P' and resid 356 through 363 removed outlier: 3.753A pdb=" N ALA P 363 " --> pdb=" O GLN P 359 " (cutoff:3.500A) Processing helix chain 'P' and resid 400 through 413 Processing helix chain 'P' and resid 414 through 447 Processing helix chain 'P' and resid 447 through 467 Processing helix chain 'P' and resid 472 through 478 removed outlier: 3.872A pdb=" N ARG P 478 " --> pdb=" O GLU P 474 " (cutoff:3.500A) Processing helix chain 'P' and resid 479 through 485 removed outlier: 3.997A pdb=" N GLN P 484 " --> pdb=" O PHE P 481 " (cutoff:3.500A) Proline residue: P 485 - end of helix Processing helix chain 'P' and resid 486 through 501 Processing helix chain 'Q' and resid 186 through 207 Processing helix chain 'Q' and resid 220 through 275 Processing helix chain 'R' and resid 14 through 39 Processing helix chain 'R' and resid 58 through 62 Processing helix chain 'V' and resid 142 through 161 Processing helix chain 'V' and resid 163 through 176 Processing helix chain 'V' and resid 180 through 189 Processing helix chain 'V' and resid 193 through 208 Proline residue: V 202 - end of helix Processing helix chain 'W' and resid 46 through 61 removed outlier: 3.653A pdb=" N GLY W 54 " --> pdb=" O VAL W 50 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG W 57 " --> pdb=" O ARG W 53 " (cutoff:3.500A) Processing helix chain 'W' and resid 67 through 82 Processing helix chain 'W' and resid 83 through 105 Proline residue: W 89 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 6.948A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 6.884A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 102 through 103 removed outlier: 6.799A pdb=" N THR C 102 " --> pdb=" O TYR F 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.935A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.192A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 Processing sheet with id=AB2, first strand: chain 'J' and resid 35 through 37 removed outlier: 6.567A pdb=" N LEU J 14 " --> pdb=" O LEU J 121 " (cutoff:3.500A) removed outlier: 8.702A pdb=" N SER J 123 " --> pdb=" O LEU J 14 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N PHE J 16 " --> pdb=" O SER J 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AB4, first strand: chain 'J' and resid 88 through 89 Processing sheet with id=AB5, first strand: chain 'J' and resid 186 through 187 Processing sheet with id=AB6, first strand: chain 'J' and resid 186 through 187 removed outlier: 6.117A pdb=" N LEU J 168 " --> pdb=" O ILE J 349 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'J' and resid 280 through 281 Processing sheet with id=AB8, first strand: chain 'K' and resid 18 through 21 removed outlier: 6.481A pdb=" N LEU K 8 " --> pdb=" O LEU K 104 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N THR K 106 " --> pdb=" O LEU K 8 " (cutoff:3.500A) removed outlier: 7.174A pdb=" N VAL K 10 " --> pdb=" O THR K 106 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 176 through 178 removed outlier: 6.086A pdb=" N ILE K 151 " --> pdb=" O VAL K 298 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N SER K 300 " --> pdb=" O ILE K 151 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N MET K 153 " --> pdb=" O SER K 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 239 through 241 Processing sheet with id=AC2, first strand: chain 'L' and resid 1814 through 1816 Processing sheet with id=AC3, first strand: chain 'M' and resid 17 through 18 Processing sheet with id=AC4, first strand: chain 'M' and resid 186 through 195 Processing sheet with id=AC5, first strand: chain 'M' and resid 261 through 270 Processing sheet with id=AC6, first strand: chain 'N' and resid 424 through 426 removed outlier: 6.555A pdb=" N ILE N 424 " --> pdb=" O LEU O 534 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'N' and resid 437 through 439 removed outlier: 6.670A pdb=" N VAL N 438 " --> pdb=" O LEU R 71 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'O' and resid 523 through 524 Processing sheet with id=AC9, first strand: chain 'P' and resid 309 through 311 Processing sheet with id=AD1, first strand: chain 'P' and resid 336 through 338 1776 hydrogen bonds defined for protein. 5094 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 332 hydrogen bonds 664 hydrogen bond angles 0 basepair planarities 130 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 8.44 Time building geometry restraints manager: 3.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7410 1.33 - 1.45: 5363 1.45 - 1.57: 15496 1.57 - 1.69: 521 1.69 - 1.81: 66 Bond restraints: 28856 Sorted by residual: bond pdb=" C3' DC X 80 " pdb=" O3' DC X 80 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 2.00e+01 bond pdb=" C3' DG X 100 " pdb=" O3' DG X 100 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.80e+01 bond pdb=" C1' DC Y 16 " pdb=" N1 DC Y 16 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.60e+01 bond pdb=" C1' DT Y 110 " pdb=" N1 DT Y 110 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.57e+01 bond pdb=" C5' DT Y 13 " pdb=" C4' DT Y 13 " ideal model delta sigma weight residual 1.512 1.539 -0.027 7.00e-03 2.04e+04 1.54e+01 ... (remaining 28851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 37465 1.37 - 2.73: 2492 2.73 - 4.10: 469 4.10 - 5.47: 161 5.47 - 6.84: 37 Bond angle restraints: 40624 Sorted by residual: angle pdb=" O5' DT X 129 " pdb=" C5' DT X 129 " pdb=" C4' DT X 129 " ideal model delta sigma weight residual 109.40 114.75 -5.35 8.00e-01 1.56e+00 4.46e+01 angle pdb=" O5' DA X 131 " pdb=" C5' DA X 131 " pdb=" C4' DA X 131 " ideal model delta sigma weight residual 109.40 114.08 -4.68 8.00e-01 1.56e+00 3.42e+01 angle pdb=" O5' DC Y 21 " pdb=" C5' DC Y 21 " pdb=" C4' DC Y 21 " ideal model delta sigma weight residual 109.40 113.93 -4.53 8.00e-01 1.56e+00 3.20e+01 angle pdb=" O5' DT Y 13 " pdb=" C5' DT Y 13 " pdb=" C4' DT Y 13 " ideal model delta sigma weight residual 109.40 113.74 -4.34 8.00e-01 1.56e+00 2.94e+01 angle pdb=" O5' DA Y 17 " pdb=" C5' DA Y 17 " pdb=" C4' DA Y 17 " ideal model delta sigma weight residual 109.40 113.62 -4.22 8.00e-01 1.56e+00 2.78e+01 ... (remaining 40619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 14373 17.68 - 35.37: 1001 35.37 - 53.05: 1111 53.05 - 70.73: 237 70.73 - 88.42: 9 Dihedral angle restraints: 16731 sinusoidal: 6190 harmonic: 10541 Sorted by residual: dihedral pdb=" CA LEU I 807 " pdb=" C LEU I 807 " pdb=" N ILE I 808 " pdb=" CA ILE I 808 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA PHE I 853 " pdb=" C PHE I 853 " pdb=" N ASN I 854 " pdb=" CA ASN I 854 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA SER I 937 " pdb=" C SER I 937 " pdb=" N THR I 938 " pdb=" CA THR I 938 " ideal model delta harmonic sigma weight residual 180.00 157.50 22.50 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 16728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3937 0.067 - 0.134: 732 0.134 - 0.201: 261 0.201 - 0.268: 21 0.268 - 0.335: 1 Chirality restraints: 4952 Sorted by residual: chirality pdb=" CA ASP L1663 " pdb=" N ASP L1663 " pdb=" C ASP L1663 " pdb=" CB ASP L1663 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C3' DG Y 30 " pdb=" C4' DG Y 30 " pdb=" O3' DG Y 30 " pdb=" C2' DG Y 30 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C3' DA Y 24 " pdb=" C4' DA Y 24 " pdb=" O3' DA Y 24 " pdb=" C2' DA Y 24 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 4949 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA X 69 " -0.036 2.00e-02 2.50e+03 1.61e-02 7.15e+00 pdb=" N9 DA X 69 " 0.035 2.00e-02 2.50e+03 pdb=" C8 DA X 69 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA X 69 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA X 69 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA X 69 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA X 69 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DA X 69 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA X 69 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA X 69 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA X 69 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT X 127 " 0.030 2.00e-02 2.50e+03 1.53e-02 5.89e+00 pdb=" N1 DT X 127 " -0.028 2.00e-02 2.50e+03 pdb=" C2 DT X 127 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT X 127 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DT X 127 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT X 127 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT X 127 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DT X 127 " 0.008 2.00e-02 2.50e+03 pdb=" C7 DT X 127 " -0.016 2.00e-02 2.50e+03 pdb=" C6 DT X 127 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA X 39 " 0.033 2.00e-02 2.50e+03 1.44e-02 5.71e+00 pdb=" N9 DA X 39 " -0.032 2.00e-02 2.50e+03 pdb=" C8 DA X 39 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA X 39 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA X 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA X 39 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA X 39 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DA X 39 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA X 39 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA X 39 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA X 39 " -0.003 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6199 2.79 - 3.31: 27033 3.31 - 3.84: 47527 3.84 - 4.37: 53286 4.37 - 4.90: 81684 Nonbonded interactions: 215729 Sorted by model distance: nonbonded pdb=" N GLU I 454 " pdb=" OE1 GLU I 454 " model vdw 2.258 3.120 nonbonded pdb=" O CYS L1968 " pdb=" OG1 THR L1969 " model vdw 2.278 3.040 nonbonded pdb=" O THR I 859 " pdb=" N ILE I 863 " model vdw 2.373 3.120 nonbonded pdb=" O ALA G 11 " pdb=" NZ LYS H 121 " model vdw 2.382 3.120 nonbonded pdb=" OD2 ASP N 434 " pdb=" OG SER N 437 " model vdw 2.442 3.040 ... (remaining 215724 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 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 125) selection = chain 'H' } 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 group one per residue 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: 9.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 34.810 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 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 : 0.006 0.058 28860 Z= 0.489 Angle : 0.819 6.835 40627 Z= 0.546 Chirality : 0.061 0.335 4952 Planarity : 0.006 0.096 4537 Dihedral : 20.695 88.418 9817 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.42 % Favored : 96.49 % Rotamer: Outliers : 0.52 % Allowed : 2.37 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.13), residues: 3534 helix: 0.18 (0.10), residues: 2215 sheet: -0.33 (0.42), residues: 136 loop : -0.50 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 43 TYR 0.013 0.002 TYR N 435 PHE 0.022 0.001 PHE L1641 TRP 0.013 0.002 TRP N 507 HIS 0.007 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.49 (28856) covalent geometry : angle 0.81867 / 0.55 (40624) hydrogen bonds : bond 0.15363 / 10.55 ( 2106) hydrogen bonds : angle 5.83295 / 4.28 ( 5758) metal coordination : bond 0.00144 / 0.07 ( 4) metal coordination : angle 1.44606 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 433 time to evaluate : 0.814 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 69 GLN cc_start: 0.8717 (tt0) cc_final: 0.8234 (tm-30) REVERT: F 60 LYS cc_start: 0.9234 (tttt) cc_final: 0.8622 (tttt) REVERT: F 64 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8559 (mt-10) REVERT: F 85 MET cc_start: 0.8395 (mmm) cc_final: 0.8136 (mmm) REVERT: F 93 ARG cc_start: 0.8890 (mtp-110) cc_final: 0.8257 (tpt-90) REVERT: G 57 GLU cc_start: 0.8934 (tt0) cc_final: 0.8693 (tt0) REVERT: H 41 TYR cc_start: 0.8985 (m-80) cc_final: 0.8596 (m-10) REVERT: H 48 GLN cc_start: 0.9009 (mt0) cc_final: 0.8683 (tm-30) REVERT: H 60 MET cc_start: 0.9431 (tpp) cc_final: 0.9206 (tpp) REVERT: I 423 CYS cc_start: 0.9176 (m) cc_final: 0.8735 (t) REVERT: I 427 ASP cc_start: 0.8583 (m-30) cc_final: 0.7819 (p0) REVERT: L 1674 MET cc_start: 0.8485 (mmm) cc_final: 0.7949 (tpp) REVERT: L 1695 LEU cc_start: 0.9693 (tp) cc_final: 0.9463 (tp) REVERT: L 1730 ILE cc_start: 0.9365 (tp) cc_final: 0.9156 (pt) REVERT: L 1956 GLU cc_start: 0.8813 (mt-10) cc_final: 0.8265 (mm-30) REVERT: L 2001 MET cc_start: 0.9157 (mtp) cc_final: 0.8735 (mtp) REVERT: L 2054 GLU cc_start: 0.8590 (mt-10) cc_final: 0.8351 (tm-30) REVERT: L 2063 THR cc_start: 0.8526 (m) cc_final: 0.8265 (p) REVERT: L 2130 ASN cc_start: 0.9330 (m-40) cc_final: 0.9123 (p0) REVERT: L 2151 MET cc_start: 0.9438 (mmp) cc_final: 0.9200 (mmp) REVERT: N 425 ILE cc_start: 0.9255 (mt) cc_final: 0.8891 (tp) REVERT: N 429 TYR cc_start: 0.8891 (p90) cc_final: 0.8457 (p90) REVERT: N 505 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8465 (mm-30) REVERT: P 482 TYR cc_start: 0.7755 (m-80) cc_final: 0.7412 (m-80) REVERT: P 492 CYS cc_start: 0.9251 (m) cc_final: 0.8841 (t) outliers start: 7 outliers final: 1 residues processed: 438 average time/residue: 0.2199 time to fit residues: 144.1095 Evaluate side-chains 242 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 241 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 0.6980 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 7.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 0.7980 chunk 298 optimal weight: 6.9990 overall best weight: 2.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 96 GLN D 110 HIS E 69 GLN E 77 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN I 383 GLN L1835 GLN ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 422 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.080646 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.060137 restraints weight = 245563.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.061401 restraints weight = 159342.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.062224 restraints weight = 118993.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.062763 restraints weight = 98074.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.063116 restraints weight = 86253.441| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 28860 Z= 0.211 Angle : 0.724 8.994 40627 Z= 0.392 Chirality : 0.043 0.225 4952 Planarity : 0.005 0.065 4537 Dihedral : 23.678 71.662 6613 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.07 % Allowed : 2.59 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.14), residues: 3534 helix: 1.64 (0.11), residues: 2236 sheet: -0.16 (0.44), residues: 138 loop : -0.29 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 40 TYR 0.025 0.002 TYR C 40 PHE 0.016 0.002 PHE L1859 TRP 0.021 0.002 TRP L2091 HIS 0.010 0.002 HIS L2090 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.21 (28856) covalent geometry : angle 0.72429 / 0.39 (40624) hydrogen bonds : bond 0.05706 / 3.95 ( 2106) hydrogen bonds : angle 4.41398 / 3.26 ( 5758) metal coordination : bond 0.01295 / 0.63 ( 4) metal coordination : angle 2.10893 / 1.89 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 283 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.9020 (m-30) cc_final: 0.8812 (m-30) REVERT: A 121 MET cc_start: 0.8931 (mmp) cc_final: 0.8677 (mmm) REVERT: B 64 GLU cc_start: 0.9399 (mm-30) cc_final: 0.9105 (mm-30) REVERT: B 86 ASP cc_start: 0.8950 (m-30) cc_final: 0.8545 (m-30) REVERT: F 60 LYS cc_start: 0.9116 (tttt) cc_final: 0.8289 (tttt) REVERT: F 64 GLU cc_start: 0.9213 (mt-10) cc_final: 0.8796 (mm-30) REVERT: F 75 GLU cc_start: 0.9276 (mt-10) cc_final: 0.9018 (pt0) REVERT: F 78 LYS cc_start: 0.9512 (mttt) cc_final: 0.9129 (mmtt) REVERT: F 85 MET cc_start: 0.9126 (mmm) cc_final: 0.8834 (mmm) REVERT: G 57 GLU cc_start: 0.9223 (tt0) cc_final: 0.8883 (tt0) REVERT: H 60 MET cc_start: 0.9444 (tpp) cc_final: 0.9070 (tpp) REVERT: H 94 GLU cc_start: 0.8977 (mp0) cc_final: 0.8470 (mp0) REVERT: I 423 CYS cc_start: 0.8913 (m) cc_final: 0.8471 (t) REVERT: L 1695 LEU cc_start: 0.9401 (tp) cc_final: 0.9154 (tp) REVERT: L 1961 SER cc_start: 0.6136 (p) cc_final: 0.5245 (t) REVERT: L 2063 THR cc_start: 0.8683 (m) cc_final: 0.8463 (p) REVERT: L 2151 MET cc_start: 0.8797 (mmp) cc_final: 0.8581 (tpp) REVERT: L 2232 ARG cc_start: 0.8773 (ptt180) cc_final: 0.8481 (ptt90) REVERT: N 462 TYR cc_start: 0.8287 (t80) cc_final: 0.7943 (t80) REVERT: N 498 MET cc_start: 0.8880 (tmm) cc_final: 0.8628 (tmm) REVERT: P 475 GLU cc_start: 0.8568 (tp30) cc_final: 0.8051 (tp30) REVERT: P 481 PHE cc_start: 0.8782 (t80) cc_final: 0.8453 (t80) REVERT: P 488 GLN cc_start: 0.8557 (mp10) cc_final: 0.8242 (mp10) REVERT: P 489 GLU cc_start: 0.8311 (tt0) cc_final: 0.8092 (tm-30) REVERT: P 492 CYS cc_start: 0.9188 (m) cc_final: 0.8704 (t) outliers start: 1 outliers final: 0 residues processed: 284 average time/residue: 0.1862 time to fit residues: 83.1261 Evaluate side-chains 216 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 270 optimal weight: 10.0000 chunk 106 optimal weight: 20.0000 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 4.9990 chunk 376 optimal weight: 20.0000 chunk 240 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 114 optimal weight: 6.9990 chunk 193 optimal weight: 3.9990 chunk 315 optimal weight: 8.9990 chunk 359 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN E 77 GLN E 126 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN H 110 HIS I 460 GLN ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.075257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.054615 restraints weight = 253513.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.055785 restraints weight = 162774.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.056534 restraints weight = 122206.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.057022 restraints weight = 101689.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.057276 restraints weight = 90348.804| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.4390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.129 28860 Z= 0.323 Angle : 0.829 14.926 40627 Z= 0.449 Chirality : 0.045 0.315 4952 Planarity : 0.006 0.076 4537 Dihedral : 23.460 80.754 6613 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.40 % Favored : 96.58 % Rotamer: Outliers : 0.30 % Allowed : 4.15 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.14), residues: 3534 helix: 1.39 (0.10), residues: 2249 sheet: -0.10 (0.43), residues: 144 loop : -0.60 (0.18), residues: 1141 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.001 ARG B 40 TYR 0.089 0.003 TYR B 89 PHE 0.034 0.003 PHE N 468 TRP 0.033 0.005 TRP L2050 HIS 0.014 0.003 HIS L2090 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.32 (28856) covalent geometry : angle 0.82769 / 0.45 (40624) hydrogen bonds : bond 0.06648 / 4.58 ( 2106) hydrogen bonds : angle 4.65727 / 3.47 ( 5758) metal coordination : bond 0.03981 / 1.90 ( 4) metal coordination : angle 6.14541 / 5.68 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 249 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9519 (tt0) cc_final: 0.9263 (tp-100) REVERT: A 82 ASP cc_start: 0.9073 (m-30) cc_final: 0.8850 (m-30) REVERT: B 28 GLN cc_start: 0.9055 (pp30) cc_final: 0.8841 (pp30) REVERT: B 45 LYS cc_start: 0.9397 (tmtt) cc_final: 0.9169 (tptp) REVERT: B 64 GLU cc_start: 0.9399 (mm-30) cc_final: 0.8840 (mm-30) REVERT: B 89 TYR cc_start: 0.8845 (m-10) cc_final: 0.8581 (m-80) REVERT: E 77 GLN cc_start: 0.9181 (mt0) cc_final: 0.8967 (mt0) REVERT: E 94 GLN cc_start: 0.9350 (tt0) cc_final: 0.9083 (tt0) REVERT: F 60 LYS cc_start: 0.9387 (tttt) cc_final: 0.9025 (tttt) REVERT: F 64 GLU cc_start: 0.9325 (mt-10) cc_final: 0.8922 (mt-10) REVERT: G 57 GLU cc_start: 0.9033 (tt0) cc_final: 0.8726 (tt0) REVERT: H 94 GLU cc_start: 0.8987 (mp0) cc_final: 0.8705 (mp0) REVERT: I 423 CYS cc_start: 0.8999 (m) cc_final: 0.8743 (t) REVERT: L 1674 MET cc_start: 0.8540 (tpp) cc_final: 0.8087 (tpt) REVERT: L 1695 LEU cc_start: 0.9447 (tp) cc_final: 0.9033 (tp) REVERT: L 2229 ASP cc_start: 0.8772 (t0) cc_final: 0.8315 (t0) REVERT: N 480 TYR cc_start: 0.8793 (t80) cc_final: 0.8558 (t80) REVERT: N 505 GLU cc_start: 0.8662 (mm-30) cc_final: 0.8413 (mm-30) REVERT: P 492 CYS cc_start: 0.9335 (m) cc_final: 0.9006 (m) outliers start: 4 outliers final: 3 residues processed: 251 average time/residue: 0.1740 time to fit residues: 71.4494 Evaluate side-chains 211 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 208 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 38 optimal weight: 7.9990 chunk 198 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 189 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 291 optimal weight: 9.9990 chunk 271 optimal weight: 7.9990 chunk 125 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 chunk 266 optimal weight: 9.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 76 HIS ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.076364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055469 restraints weight = 262547.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.056726 restraints weight = 166929.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.057520 restraints weight = 124746.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.058021 restraints weight = 103851.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.058340 restraints weight = 92805.588| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 28860 Z= 0.184 Angle : 0.623 9.008 40627 Z= 0.343 Chirality : 0.040 0.176 4952 Planarity : 0.004 0.054 4537 Dihedral : 23.326 68.779 6613 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.14), residues: 3534 helix: 2.07 (0.11), residues: 2252 sheet: 0.01 (0.45), residues: 144 loop : -0.36 (0.18), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 73 TYR 0.021 0.002 TYR P 482 PHE 0.018 0.002 PHE E 68 TRP 0.017 0.002 TRP L2049 HIS 0.008 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.18 (28856) covalent geometry : angle 0.62231 / 0.34 (40624) hydrogen bonds : bond 0.04513 / 3.11 ( 2106) hydrogen bonds : angle 4.08175 / 3.03 ( 5758) metal coordination : bond 0.01414 / 0.71 ( 4) metal coordination : angle 3.19122 / 1.91 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.838 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9508 (tt0) cc_final: 0.9206 (tp40) REVERT: A 121 MET cc_start: 0.9324 (mmm) cc_final: 0.8979 (mmm) REVERT: B 45 LYS cc_start: 0.9357 (tmtt) cc_final: 0.9142 (tptp) REVERT: B 64 GLU cc_start: 0.9292 (mm-30) cc_final: 0.8895 (mm-30) REVERT: B 89 TYR cc_start: 0.9024 (m-10) cc_final: 0.8776 (m-10) REVERT: C 40 TYR cc_start: 0.9113 (m-80) cc_final: 0.8824 (m-80) REVERT: E 121 MET cc_start: 0.8111 (mpp) cc_final: 0.7882 (mpp) REVERT: F 53 GLU cc_start: 0.9068 (mp0) cc_final: 0.8818 (mp0) REVERT: F 64 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8792 (mm-30) REVERT: G 57 GLU cc_start: 0.9025 (tt0) cc_final: 0.8620 (tt0) REVERT: H 87 ARG cc_start: 0.8786 (mmt90) cc_final: 0.8571 (mmm-85) REVERT: H 94 GLU cc_start: 0.9100 (mp0) cc_final: 0.8748 (mp0) REVERT: L 1674 MET cc_start: 0.8385 (tpp) cc_final: 0.8035 (tpt) REVERT: L 1695 LEU cc_start: 0.9391 (tp) cc_final: 0.9133 (tp) REVERT: L 2151 MET cc_start: 0.8882 (mmp) cc_final: 0.8626 (tpp) REVERT: N 505 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8355 (mm-30) REVERT: P 488 GLN cc_start: 0.8786 (mp-120) cc_final: 0.8537 (mp10) REVERT: P 489 GLU cc_start: 0.8371 (tm-30) cc_final: 0.8127 (tm-30) REVERT: P 492 CYS cc_start: 0.9188 (m) cc_final: 0.8826 (t) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1729 time to fit residues: 69.3873 Evaluate side-chains 200 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 111 optimal weight: 30.0000 chunk 167 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 212 optimal weight: 1.9990 chunk 195 optimal weight: 0.5980 chunk 200 optimal weight: 1.9990 chunk 78 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 125 optimal weight: 7.9990 chunk 373 optimal weight: 20.0000 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 484 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.075649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.054991 restraints weight = 250627.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.056201 restraints weight = 160562.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.056966 restraints weight = 120202.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.057450 restraints weight = 99938.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.057766 restraints weight = 88950.260| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7591 moved from start: 0.4955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.089 28860 Z= 0.176 Angle : 0.606 10.613 40627 Z= 0.332 Chirality : 0.040 0.178 4952 Planarity : 0.004 0.084 4537 Dihedral : 23.108 70.247 6613 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.07 % Allowed : 0.81 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.05 (0.14), residues: 3534 helix: 2.29 (0.11), residues: 2245 sheet: -0.13 (0.45), residues: 133 loop : -0.31 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 93 TYR 0.022 0.002 TYR P 482 PHE 0.028 0.002 PHE E 68 TRP 0.020 0.002 TRP L2049 HIS 0.007 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 (28856) covalent geometry : angle 0.60552 / 0.33 (40624) hydrogen bonds : bond 0.04344 / 3.00 ( 2106) hydrogen bonds : angle 3.97070 / 2.95 ( 5758) metal coordination : bond 0.01777 / 0.86 ( 4) metal coordination : angle 3.41542 / 2.03 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 236 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9528 (tt0) cc_final: 0.9166 (tp40) REVERT: A 82 ASP cc_start: 0.9028 (m-30) cc_final: 0.8804 (m-30) REVERT: A 121 MET cc_start: 0.9378 (mmm) cc_final: 0.9048 (mmm) REVERT: B 28 GLN cc_start: 0.9192 (pp30) cc_final: 0.8973 (tm-30) REVERT: B 64 GLU cc_start: 0.9307 (mm-30) cc_final: 0.8895 (mm-30) REVERT: C 40 TYR cc_start: 0.9111 (m-80) cc_final: 0.8813 (m-80) REVERT: E 121 MET cc_start: 0.8158 (mpp) cc_final: 0.7953 (mpp) REVERT: F 53 GLU cc_start: 0.9052 (mp0) cc_final: 0.8797 (mp0) REVERT: F 64 GLU cc_start: 0.9287 (mt-10) cc_final: 0.8932 (mt-10) REVERT: F 85 MET cc_start: 0.9348 (tpt) cc_final: 0.9131 (mmm) REVERT: F 89 TYR cc_start: 0.9378 (m-80) cc_final: 0.9107 (m-80) REVERT: G 57 GLU cc_start: 0.9035 (tt0) cc_final: 0.8748 (tt0) REVERT: H 71 PHE cc_start: 0.9383 (t80) cc_final: 0.9157 (t80) REVERT: H 94 GLU cc_start: 0.9101 (mp0) cc_final: 0.8720 (mp0) REVERT: I 424 MET cc_start: 0.8794 (ttt) cc_final: 0.8429 (ttm) REVERT: L 1674 MET cc_start: 0.8506 (tpp) cc_final: 0.8147 (tpt) REVERT: L 1695 LEU cc_start: 0.9418 (tp) cc_final: 0.9166 (tp) REVERT: L 1845 ARG cc_start: 0.8498 (tpm170) cc_final: 0.8234 (tpp-160) REVERT: L 1999 PHE cc_start: 0.8579 (t80) cc_final: 0.8353 (t80) REVERT: N 505 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8364 (mm-30) REVERT: P 476 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8140 (mt-10) REVERT: P 488 GLN cc_start: 0.8791 (mp-120) cc_final: 0.8557 (mp10) REVERT: P 489 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8113 (tm-30) REVERT: P 492 CYS cc_start: 0.9192 (m) cc_final: 0.8813 (t) outliers start: 1 outliers final: 0 residues processed: 237 average time/residue: 0.1774 time to fit residues: 69.4022 Evaluate side-chains 206 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 49 optimal weight: 0.8980 chunk 171 optimal weight: 0.5980 chunk 347 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 202 optimal weight: 0.7980 chunk 206 optimal weight: 0.7980 chunk 196 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 50 HIS E 69 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2194 ASN ** L2248 HIS ** 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 = 0.3879 r_free = 0.3879 target = 0.076395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.055848 restraints weight = 249912.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.057086 restraints weight = 158907.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.057873 restraints weight = 118343.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.058373 restraints weight = 98023.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.058646 restraints weight = 86841.745| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.5064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 28860 Z= 0.127 Angle : 0.558 8.008 40627 Z= 0.309 Chirality : 0.039 0.184 4952 Planarity : 0.004 0.048 4537 Dihedral : 22.854 69.111 6613 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.07 % Allowed : 1.48 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.14), residues: 3534 helix: 2.58 (0.11), residues: 2254 sheet: -0.10 (0.44), residues: 135 loop : -0.15 (0.19), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG F 93 TYR 0.021 0.001 TYR P 482 PHE 0.022 0.001 PHE E 68 TRP 0.012 0.001 TRP L1686 HIS 0.007 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.13 (28856) covalent geometry : angle 0.55782 / 0.31 (40624) hydrogen bonds : bond 0.03794 / 2.63 ( 2106) hydrogen bonds : angle 3.67278 / 2.72 ( 5758) metal coordination : bond 0.00703 / 0.37 ( 4) metal coordination : angle 2.61039 / 1.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 237 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9285 (pt0) cc_final: 0.9075 (pt0) REVERT: A 69 GLN cc_start: 0.9529 (tt0) cc_final: 0.9163 (tp40) REVERT: A 82 ASP cc_start: 0.8961 (m-30) cc_final: 0.8733 (m-30) REVERT: A 121 MET cc_start: 0.9400 (mmm) cc_final: 0.9081 (mmm) REVERT: B 64 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8854 (mm-30) REVERT: B 75 GLU cc_start: 0.9155 (tm-30) cc_final: 0.8909 (tm-30) REVERT: C 40 TYR cc_start: 0.9059 (m-80) cc_final: 0.8804 (m-80) REVERT: C 96 LYS cc_start: 0.9496 (ptmt) cc_final: 0.9116 (pttt) REVERT: D 102 LEU cc_start: 0.9388 (mt) cc_final: 0.9105 (mt) REVERT: E 68 PHE cc_start: 0.9004 (t80) cc_final: 0.8636 (t80) REVERT: E 74 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8718 (tt0) REVERT: E 121 MET cc_start: 0.8119 (mpp) cc_final: 0.7723 (mpp) REVERT: F 53 GLU cc_start: 0.9008 (mp0) cc_final: 0.8762 (mp0) REVERT: F 64 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8770 (mm-30) REVERT: F 85 MET cc_start: 0.9289 (tpt) cc_final: 0.9050 (mmm) REVERT: G 57 GLU cc_start: 0.9043 (tt0) cc_final: 0.8747 (tt0) REVERT: H 71 PHE cc_start: 0.9334 (t80) cc_final: 0.9103 (t80) REVERT: H 94 GLU cc_start: 0.9104 (mp0) cc_final: 0.8711 (mp0) REVERT: I 424 MET cc_start: 0.8897 (ttt) cc_final: 0.8595 (ttm) REVERT: L 1674 MET cc_start: 0.8335 (tpp) cc_final: 0.7973 (tpt) REVERT: L 1695 LEU cc_start: 0.9380 (tp) cc_final: 0.9117 (tp) REVERT: L 1845 ARG cc_start: 0.8460 (tpm170) cc_final: 0.8181 (tpp-160) REVERT: P 475 GLU cc_start: 0.8840 (tp30) cc_final: 0.8493 (tp30) REVERT: P 476 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7957 (mt-10) REVERT: P 489 GLU cc_start: 0.8427 (tm-30) cc_final: 0.8092 (tm-30) REVERT: P 492 CYS cc_start: 0.9162 (m) cc_final: 0.8816 (t) outliers start: 1 outliers final: 1 residues processed: 238 average time/residue: 0.1698 time to fit residues: 66.9738 Evaluate side-chains 205 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 204 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 63 optimal weight: 6.9990 chunk 54 optimal weight: 8.9990 chunk 234 optimal weight: 9.9990 chunk 210 optimal weight: 9.9990 chunk 127 optimal weight: 50.0000 chunk 99 optimal weight: 20.0000 chunk 168 optimal weight: 50.0000 chunk 249 optimal weight: 0.9980 chunk 33 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 101 optimal weight: 10.0000 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS E 69 GLN E 77 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN ** L2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 451 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.071842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.051575 restraints weight = 257716.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.053030 restraints weight = 174465.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.053121 restraints weight = 127313.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.053584 restraints weight = 109457.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.053627 restraints weight = 100768.342| |-----------------------------------------------------------------------------| r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.6139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.172 28860 Z= 0.388 Angle : 0.864 17.386 40627 Z= 0.466 Chirality : 0.046 0.241 4952 Planarity : 0.006 0.081 4537 Dihedral : 23.192 76.431 6613 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.68 % Favored : 96.26 % Rotamer: Outliers : 0.07 % Allowed : 1.63 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.14), residues: 3534 helix: 1.40 (0.11), residues: 2256 sheet: -0.34 (0.43), residues: 140 loop : -0.72 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 73 TYR 0.029 0.003 TYR H 41 PHE 0.052 0.004 PHE N 468 TRP 0.030 0.004 TRP L2091 HIS 0.017 0.003 HIS L2090 Details of bonding type rmsd/Z covalent geometry : bond 0.00755 / 0.39 (28856) covalent geometry : angle 0.85923 / 0.47 (40624) hydrogen bonds : bond 0.06994 / 4.86 ( 2106) hydrogen bonds : angle 4.82510 / 3.57 ( 5758) metal coordination : bond 0.06301 / 3.06 ( 4) metal coordination : angle 10.21197 / 7.40 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 217 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9061 (pm20) cc_final: 0.8820 (pm20) REVERT: A 69 GLN cc_start: 0.9487 (tt0) cc_final: 0.9285 (tt0) REVERT: A 82 ASP cc_start: 0.9029 (m-30) cc_final: 0.8792 (m-30) REVERT: A 106 GLU cc_start: 0.9370 (mm-30) cc_final: 0.9146 (mm-30) REVERT: B 64 GLU cc_start: 0.9386 (mm-30) cc_final: 0.9019 (mm-30) REVERT: B 89 TYR cc_start: 0.8683 (m-80) cc_final: 0.8360 (m-80) REVERT: D 72 GLU cc_start: 0.8736 (mt-10) cc_final: 0.8247 (mt-10) REVERT: E 69 GLN cc_start: 0.9558 (OUTLIER) cc_final: 0.8854 (tm-30) REVERT: E 74 GLU cc_start: 0.9293 (tm-30) cc_final: 0.9040 (tm-30) REVERT: F 53 GLU cc_start: 0.9068 (mp0) cc_final: 0.8830 (mp0) REVERT: F 64 GLU cc_start: 0.9370 (mt-10) cc_final: 0.9097 (mt-10) REVERT: G 57 GLU cc_start: 0.8824 (tt0) cc_final: 0.8538 (tt0) REVERT: H 72 GLU cc_start: 0.9050 (mt-10) cc_final: 0.8837 (pt0) REVERT: H 94 GLU cc_start: 0.9030 (mp0) cc_final: 0.8650 (mp0) REVERT: I 424 MET cc_start: 0.8955 (ttt) cc_final: 0.8698 (ttm) REVERT: L 1674 MET cc_start: 0.8549 (tpp) cc_final: 0.8332 (tpt) REVERT: L 1695 LEU cc_start: 0.9421 (tp) cc_final: 0.9187 (tp) REVERT: L 1845 ARG cc_start: 0.8550 (tpm170) cc_final: 0.8259 (tpp-160) REVERT: L 1999 PHE cc_start: 0.8578 (t80) cc_final: 0.8368 (t80) REVERT: N 505 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8218 (mm-30) REVERT: P 476 GLU cc_start: 0.8467 (mt-10) cc_final: 0.8047 (mt-10) REVERT: P 488 GLN cc_start: 0.8886 (mp10) cc_final: 0.8568 (mp10) REVERT: P 492 CYS cc_start: 0.9300 (m) cc_final: 0.8988 (m) outliers start: 1 outliers final: 0 residues processed: 217 average time/residue: 0.1674 time to fit residues: 59.9494 Evaluate side-chains 192 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 32 optimal weight: 0.8980 chunk 152 optimal weight: 5.9990 chunk 251 optimal weight: 0.9990 chunk 221 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 279 optimal weight: 9.9990 chunk 359 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 348 optimal weight: 6.9990 chunk 134 optimal weight: 8.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS E 69 GLN E 77 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** 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 = 0.3835 r_free = 0.3835 target = 0.074009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.053642 restraints weight = 245289.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.054794 restraints weight = 157622.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.055527 restraints weight = 118422.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.056008 restraints weight = 98323.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.056299 restraints weight = 87494.824| |-----------------------------------------------------------------------------| r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.6095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 28860 Z= 0.138 Angle : 0.591 8.927 40627 Z= 0.326 Chirality : 0.040 0.198 4952 Planarity : 0.004 0.060 4537 Dihedral : 23.061 69.469 6613 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.03 (0.14), residues: 3534 helix: 2.29 (0.11), residues: 2259 sheet: -0.25 (0.44), residues: 138 loop : -0.38 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L1742 TYR 0.021 0.002 TYR H 41 PHE 0.016 0.001 PHE A 105 TRP 0.018 0.002 TRP N 432 HIS 0.009 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (28856) covalent geometry : angle 0.58960 / 0.33 (40624) hydrogen bonds : bond 0.03989 / 2.75 ( 2106) hydrogen bonds : angle 3.94073 / 2.91 ( 5758) metal coordination : bond 0.01287 / 0.65 ( 4) metal coordination : angle 4.18518 / 2.46 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9530 (tt0) cc_final: 0.9297 (tt0) REVERT: A 82 ASP cc_start: 0.9021 (m-30) cc_final: 0.8805 (m-30) REVERT: B 64 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8869 (mm-30) REVERT: B 75 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8987 (tm-30) REVERT: B 89 TYR cc_start: 0.8885 (m-80) cc_final: 0.8406 (m-80) REVERT: C 40 TYR cc_start: 0.9144 (m-80) cc_final: 0.8913 (m-80) REVERT: C 96 LYS cc_start: 0.9531 (ptmt) cc_final: 0.9103 (pttm) REVERT: E 74 GLU cc_start: 0.9258 (tm-30) cc_final: 0.8489 (tt0) REVERT: F 53 GLU cc_start: 0.9009 (mp0) cc_final: 0.8801 (mp0) REVERT: F 64 GLU cc_start: 0.9335 (mt-10) cc_final: 0.9016 (mt-10) REVERT: F 85 MET cc_start: 0.9253 (tpt) cc_final: 0.8913 (tpp) REVERT: G 42 GLU cc_start: 0.9013 (pm20) cc_final: 0.8795 (pm20) REVERT: G 57 GLU cc_start: 0.8933 (tt0) cc_final: 0.8648 (tt0) REVERT: H 60 MET cc_start: 0.9530 (tpp) cc_final: 0.9270 (tpp) REVERT: H 63 MET cc_start: 0.9555 (mmm) cc_final: 0.9342 (mmm) REVERT: H 72 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8810 (pt0) REVERT: H 94 GLU cc_start: 0.9058 (mp0) cc_final: 0.8663 (mp0) REVERT: I 424 MET cc_start: 0.8970 (ttt) cc_final: 0.8689 (ttm) REVERT: L 1674 MET cc_start: 0.8449 (tpp) cc_final: 0.8171 (tpt) REVERT: L 1695 LEU cc_start: 0.9423 (tp) cc_final: 0.9145 (tp) REVERT: L 1845 ARG cc_start: 0.8617 (tpm170) cc_final: 0.8404 (tpp-160) REVERT: L 1999 PHE cc_start: 0.8604 (t80) cc_final: 0.8381 (t80) REVERT: N 505 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8343 (mm-30) REVERT: P 475 GLU cc_start: 0.8879 (tp30) cc_final: 0.8520 (tm-30) REVERT: P 476 GLU cc_start: 0.8344 (mt-10) cc_final: 0.8008 (mt-10) REVERT: P 492 CYS cc_start: 0.9217 (m) cc_final: 0.8821 (t) outliers start: 0 outliers final: 0 residues processed: 226 average time/residue: 0.1583 time to fit residues: 58.7319 Evaluate side-chains 194 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 375 optimal weight: 20.0000 chunk 124 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 281 optimal weight: 9.9990 chunk 209 optimal weight: 1.9990 chunk 164 optimal weight: 8.9990 chunk 321 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 chunk 367 optimal weight: 50.0000 chunk 172 optimal weight: 0.0070 chunk 264 optimal weight: 6.9990 overall best weight: 1.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 39 ASN E 69 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN ** L2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 436 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.074483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.053969 restraints weight = 265763.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.055235 restraints weight = 167303.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.056011 restraints weight = 125068.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.056520 restraints weight = 104392.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.056763 restraints weight = 92996.032| |-----------------------------------------------------------------------------| r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.6233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 28860 Z= 0.143 Angle : 0.582 9.513 40627 Z= 0.321 Chirality : 0.039 0.195 4952 Planarity : 0.004 0.052 4537 Dihedral : 22.814 70.826 6613 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.07 % Allowed : 0.44 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.14), residues: 3534 helix: 2.53 (0.11), residues: 2256 sheet: -0.14 (0.46), residues: 132 loop : -0.34 (0.19), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 36 TYR 0.015 0.002 TYR P 482 PHE 0.016 0.001 PHE A 105 TRP 0.015 0.002 TRP L2050 HIS 0.010 0.001 HIS C 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.14 (28856) covalent geometry : angle 0.58114 / 0.32 (40624) hydrogen bonds : bond 0.03839 / 2.65 ( 2106) hydrogen bonds : angle 3.80288 / 2.82 ( 5758) metal coordination : bond 0.01294 / 0.64 ( 4) metal coordination : angle 2.80696 / 1.66 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 218 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9528 (tt0) cc_final: 0.9282 (tt0) REVERT: A 82 ASP cc_start: 0.9003 (m-30) cc_final: 0.8778 (m-30) REVERT: B 64 GLU cc_start: 0.9273 (mm-30) cc_final: 0.8876 (mm-30) REVERT: B 89 TYR cc_start: 0.8831 (m-80) cc_final: 0.8430 (m-80) REVERT: E 74 GLU cc_start: 0.9216 (tm-30) cc_final: 0.8740 (tm-30) REVERT: F 53 GLU cc_start: 0.9017 (mp0) cc_final: 0.8800 (mp0) REVERT: F 64 GLU cc_start: 0.9334 (mt-10) cc_final: 0.9023 (mt-10) REVERT: F 85 MET cc_start: 0.9234 (tpt) cc_final: 0.8899 (tpp) REVERT: G 42 GLU cc_start: 0.9033 (pm20) cc_final: 0.8816 (pm20) REVERT: H 60 MET cc_start: 0.9536 (tpp) cc_final: 0.9293 (tpp) REVERT: H 72 GLU cc_start: 0.9094 (mt-10) cc_final: 0.8801 (pt0) REVERT: H 94 GLU cc_start: 0.9046 (mp0) cc_final: 0.8653 (mp0) REVERT: I 424 MET cc_start: 0.8953 (ttt) cc_final: 0.8620 (ttm) REVERT: L 1674 MET cc_start: 0.8508 (tpp) cc_final: 0.8212 (tpt) REVERT: L 1695 LEU cc_start: 0.9453 (tp) cc_final: 0.9206 (tp) REVERT: L 1999 PHE cc_start: 0.8624 (t80) cc_final: 0.8403 (t80) REVERT: L 2166 MET cc_start: 0.8410 (mtp) cc_final: 0.8004 (mtp) REVERT: L 2231 MET cc_start: 0.8063 (mtt) cc_final: 0.7693 (mmm) REVERT: P 475 GLU cc_start: 0.8811 (tp30) cc_final: 0.8571 (tp30) REVERT: P 476 GLU cc_start: 0.8305 (mt-10) cc_final: 0.7831 (mt-10) REVERT: P 492 CYS cc_start: 0.9213 (m) cc_final: 0.8856 (t) outliers start: 1 outliers final: 0 residues processed: 219 average time/residue: 0.1643 time to fit residues: 59.5301 Evaluate side-chains 186 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 71 optimal weight: 0.9980 chunk 261 optimal weight: 6.9990 chunk 207 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 292 optimal weight: 6.9990 chunk 139 optimal weight: 20.0000 chunk 206 optimal weight: 1.9990 chunk 300 optimal weight: 9.9990 chunk 122 optimal weight: 50.0000 chunk 380 optimal weight: 20.0000 chunk 285 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 48 GLN D 50 HIS E 69 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 506 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.074562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.054819 restraints weight = 265227.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.055478 restraints weight = 180995.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.056752 restraints weight = 141961.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.056536 restraints weight = 116899.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.056422 restraints weight = 104039.166| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.6380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28860 Z= 0.136 Angle : 0.576 10.406 40627 Z= 0.320 Chirality : 0.039 0.199 4952 Planarity : 0.004 0.105 4537 Dihedral : 22.698 69.868 6613 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.43 (0.15), residues: 3534 helix: 2.61 (0.11), residues: 2257 sheet: -0.09 (0.47), residues: 132 loop : -0.24 (0.19), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 448 TYR 0.017 0.002 TYR N 429 PHE 0.029 0.001 PHE H 71 TRP 0.020 0.002 TRP L2050 HIS 0.008 0.001 HIS N 501 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (28856) covalent geometry : angle 0.57511 / 0.32 (40624) hydrogen bonds : bond 0.03698 / 2.56 ( 2106) hydrogen bonds : angle 3.72307 / 2.75 ( 5758) metal coordination : bond 0.01097 / 0.56 ( 4) metal coordination : angle 3.23357 / 1.93 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 216 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9480 (tt0) cc_final: 0.9225 (tt0) REVERT: A 82 ASP cc_start: 0.8927 (m-30) cc_final: 0.8717 (m-30) REVERT: B 64 GLU cc_start: 0.9245 (mm-30) cc_final: 0.8844 (mm-30) REVERT: B 75 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8898 (tm-30) REVERT: B 89 TYR cc_start: 0.8770 (m-80) cc_final: 0.8370 (m-80) REVERT: C 40 TYR cc_start: 0.9145 (m-80) cc_final: 0.8810 (m-80) REVERT: C 96 LYS cc_start: 0.9530 (ptmt) cc_final: 0.9126 (pttm) REVERT: D 72 GLU cc_start: 0.8684 (mt-10) cc_final: 0.8162 (mt-10) REVERT: E 74 GLU cc_start: 0.9165 (tm-30) cc_final: 0.8726 (tm-30) REVERT: F 53 GLU cc_start: 0.8985 (mp0) cc_final: 0.8754 (mp0) REVERT: F 64 GLU cc_start: 0.9343 (mt-10) cc_final: 0.9036 (mt-10) REVERT: F 85 MET cc_start: 0.9123 (tpt) cc_final: 0.8833 (tpp) REVERT: G 42 GLU cc_start: 0.8968 (pm20) cc_final: 0.8740 (pm20) REVERT: G 57 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8939 (tt0) REVERT: H 72 GLU cc_start: 0.9033 (mt-10) cc_final: 0.8774 (pt0) REVERT: I 424 MET cc_start: 0.8930 (ttt) cc_final: 0.8625 (ttm) REVERT: L 1695 LEU cc_start: 0.9402 (tp) cc_final: 0.9159 (tp) REVERT: L 1845 ARG cc_start: 0.8502 (mmm160) cc_final: 0.8261 (mmm160) REVERT: L 1999 PHE cc_start: 0.8467 (t80) cc_final: 0.8236 (t80) REVERT: L 2166 MET cc_start: 0.8462 (mtp) cc_final: 0.7996 (mtp) REVERT: L 2231 MET cc_start: 0.8077 (mtt) cc_final: 0.7422 (mmm) REVERT: P 475 GLU cc_start: 0.8849 (tp30) cc_final: 0.8520 (tp30) REVERT: P 476 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7774 (mt-10) REVERT: P 492 CYS cc_start: 0.9172 (m) cc_final: 0.8849 (t) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1612 time to fit residues: 58.0893 Evaluate side-chains 189 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 189 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 7 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 195 optimal weight: 1.9990 chunk 252 optimal weight: 0.0270 chunk 139 optimal weight: 6.9990 chunk 287 optimal weight: 4.9990 chunk 214 optimal weight: 0.9990 chunk 107 optimal weight: 40.0000 chunk 165 optimal weight: 0.0970 chunk 194 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 overall best weight: 1.4242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 50 HIS E 69 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2176 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 436 ASN ** 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 = 0.3845 r_free = 0.3845 target = 0.074569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.054191 restraints weight = 265659.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055465 restraints weight = 167147.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.056259 restraints weight = 124244.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.056712 restraints weight = 103283.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.057080 restraints weight = 92097.245| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 28860 Z= 0.131 Angle : 0.555 10.818 40627 Z= 0.308 Chirality : 0.039 0.184 4952 Planarity : 0.004 0.051 4537 Dihedral : 22.570 70.001 6613 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.58 (0.15), residues: 3534 helix: 2.73 (0.11), residues: 2265 sheet: -0.02 (0.47), residues: 132 loop : -0.20 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 448 TYR 0.019 0.002 TYR H 41 PHE 0.013 0.001 PHE A 68 TRP 0.017 0.002 TRP L2050 HIS 0.007 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.13 (28856) covalent geometry : angle 0.55405 / 0.31 (40624) hydrogen bonds : bond 0.03540 / 2.44 ( 2106) hydrogen bonds : angle 3.63767 / 2.69 ( 5758) metal coordination : bond 0.01215 / 0.60 ( 4) metal coordination : angle 2.82356 / 1.66 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5949.95 seconds wall clock time: 102 minutes 17.22 seconds (6137.22 seconds total)