Starting phenix.real_space_refine on Fri Mar 6 05:30:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rmc_54056/03_2026/9rmc_54056.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rmc_54056/03_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_54056/03_2026/9rmc_54056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rmc_54056/03_2026/9rmc_54056.map" model { file = "/net/cci-nas-00/data/ceres_data/9rmc_54056/03_2026/9rmc_54056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rmc_54056/03_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-dev-5986/lib/python3.9/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: 6.18, 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: 2.49 Conformation dependent library (CDL) restraints added in 1.2 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: 3.77 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: 8.35 Time building geometry restraints manager: 3.37 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=" N GLY C 9 " pdb=" CA GLY C 9 " ideal model delta sigma weight residual 1.451 1.494 -0.043 1.60e-02 3.91e+03 7.18e+00 bond pdb=" N GLY G 9 " pdb=" CA GLY G 9 " ideal model delta sigma weight residual 1.451 1.493 -0.042 1.60e-02 3.91e+03 6.78e+00 bond pdb=" N GLY J 12 " pdb=" CA GLY J 12 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.72e+00 bond pdb=" N GLY R 13 " pdb=" CA GLY R 13 " ideal model delta sigma weight residual 1.451 1.492 -0.041 1.60e-02 3.91e+03 6.46e+00 bond pdb=" N GLU N 414 " pdb=" CA GLU N 414 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.90e-02 2.77e+03 3.43e+00 ... (remaining 28851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.30: 37410 1.30 - 2.60: 2622 2.60 - 3.91: 532 3.91 - 5.21: 56 5.21 - 6.51: 4 Bond angle restraints: 40624 Sorted by residual: angle pdb=" N LYS C 37 " pdb=" CA LYS C 37 " pdb=" C LYS C 37 " ideal model delta sigma weight residual 110.33 105.19 5.14 1.29e+00 6.01e-01 1.59e+01 angle pdb=" O3' DA X 59 " pdb=" C3' DA X 59 " pdb=" C2' DA X 59 " ideal model delta sigma weight residual 111.50 116.24 -4.74 1.50e+00 4.44e-01 9.97e+00 angle pdb=" O3' DG X 99 " pdb=" C3' DG X 99 " pdb=" C2' DG X 99 " ideal model delta sigma weight residual 111.50 116.11 -4.61 1.50e+00 4.44e-01 9.43e+00 angle pdb=" C3' DT X 126 " pdb=" C2' DT X 126 " pdb=" C1' DT X 126 " ideal model delta sigma weight residual 101.60 106.18 -4.58 1.50e+00 4.44e-01 9.30e+00 angle pdb=" C3' DA Y 22 " pdb=" C2' DA Y 22 " pdb=" C1' DA Y 22 " ideal model delta sigma weight residual 101.60 106.15 -4.55 1.50e+00 4.44e-01 9.19e+00 ... (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: 3996 0.067 - 0.134: 846 0.134 - 0.201: 107 0.201 - 0.268: 2 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=" CA HIS L2018 " pdb=" N HIS L2018 " pdb=" C HIS L2018 " pdb=" CB HIS L2018 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE P 307 " pdb=" N ILE P 307 " pdb=" C ILE P 307 " pdb=" CB ILE P 307 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.06e+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: 7.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.570 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 33.890 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 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 : 0.005 0.045 28860 Z= 0.228 Angle : 0.753 6.512 40627 Z= 0.459 Chirality : 0.054 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 covalent geometry : bond 0.00462 (28856) covalent geometry : angle 0.75268 (40624) hydrogen bonds : bond 0.15363 ( 2106) hydrogen bonds : angle 5.83295 ( 5758) metal coordination : bond 0.00144 ( 4) metal coordination : angle 1.44606 ( 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 : 1.069 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: symmetry clash REVERT: E 69 GLN cc_start: 0.8717 (tt0) cc_final: 0.8221 (tm-30) REVERT: F 60 LYS cc_start: 0.9234 (tttt) cc_final: 0.8619 (tttt) REVERT: F 64 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8561 (mt-10) REVERT: F 85 MET cc_start: 0.8395 (mmm) cc_final: 0.8128 (mmm) REVERT: F 93 ARG cc_start: 0.8890 (mtp-110) cc_final: 0.8255 (tpt-90) REVERT: G 57 GLU cc_start: 0.8934 (tt0) cc_final: 0.8695 (tt0) REVERT: H 41 TYR cc_start: 0.8985 (m-80) cc_final: 0.8595 (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: 0.9207 (tpp) REVERT: I 423 CYS cc_start: 0.9176 (m) cc_final: 0.8736 (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: 0.7948 (tpp) REVERT: L 1695 LEU cc_start: 0.9693 (tp) cc_final: 0.9462 (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: 0.8266 (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: 0.8890 (tp) REVERT: N 429 TYR cc_start: 0.8891 (p90) cc_final: 0.8458 (p90) REVERT: N 505 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8464 (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: 0.2341 time to fit residues: 151.6858 Evaluate side-chains 241 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 240 time to evaluate : 0.917 ------------------------------------------------------------------------------- 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: 1.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 40.0000 chunk 244 optimal weight: 8.9990 chunk 183 optimal weight: 6.9990 chunk 298 optimal weight: 6.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 96 GLN D 110 HIS E 69 GLN E 77 GLN G 111 ASN H 96 GLN H 110 HIS L1835 GLN ** L2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 422 HIS P 484 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.079981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.059687 restraints weight = 240313.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.060908 restraints weight = 156471.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.061708 restraints weight = 117343.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.062154 restraints weight = 96613.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.062575 restraints weight = 85600.542| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 28860 Z= 0.216 Angle : 0.627 8.341 40627 Z= 0.351 Chirality : 0.040 0.163 4952 Planarity : 0.005 0.056 4537 Dihedral : 23.158 75.275 6613 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: 1.61 (0.14), residues: 3534 helix: 1.81 (0.11), residues: 2238 sheet: -0.01 (0.45), residues: 140 loop : -0.18 (0.18), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG F 36 TYR 0.020 0.002 TYR C 40 PHE 0.020 0.002 PHE P 481 TRP 0.019 0.002 TRP L2091 HIS 0.007 0.001 HIS L2090 Details of bonding type rmsd covalent geometry : bond 0.00441 (28856) covalent geometry : angle 0.62631 (40624) hydrogen bonds : bond 0.05330 ( 2106) hydrogen bonds : angle 4.23123 ( 5758) metal coordination : bond 0.01744 ( 4) metal coordination : angle 2.23009 ( 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 283 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 283 time to evaluate : 0.923 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 82 ASP cc_start: 0.9027 (m-30) cc_final: 0.8808 (m-30) REVERT: B 64 GLU cc_start: 0.9409 (mm-30) cc_final: 0.9042 (mm-30) REVERT: B 86 ASP cc_start: 0.9014 (m-30) cc_final: 0.8603 (m-30) REVERT: C 39 ASN cc_start: 0.8000 (p0) cc_final: 0.7778 (p0) REVERT: E 77 GLN cc_start: 0.9140 (mt0) cc_final: 0.8737 (mt0) REVERT: E 94 GLN cc_start: 0.9190 (tt0) cc_final: 0.8973 (tt0) REVERT: F 60 LYS cc_start: 0.9161 (tttt) cc_final: 0.8344 (tttt) REVERT: F 64 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8766 (mm-30) REVERT: F 75 GLU cc_start: 0.9268 (mt-10) cc_final: 0.9035 (pt0) REVERT: F 78 LYS cc_start: 0.9539 (mttt) cc_final: 0.9198 (mmtm) REVERT: F 85 MET cc_start: 0.9118 (mmm) cc_final: 0.8904 (mmm) REVERT: G 57 GLU cc_start: 0.9206 (tt0) cc_final: 0.8688 (tt0) REVERT: H 94 GLU cc_start: 0.9010 (mp0) cc_final: 0.8491 (mp0) REVERT: L 1695 LEU cc_start: 0.9371 (tp) cc_final: 0.9082 (tp) REVERT: L 1961 SER cc_start: 0.6210 (p) cc_final: 0.5566 (t) REVERT: L 2001 MET cc_start: 0.8947 (mtp) cc_final: 0.8634 (mtm) REVERT: L 2063 THR cc_start: 0.8656 (m) cc_final: 0.8425 (p) REVERT: L 2232 ARG cc_start: 0.8804 (ptt180) cc_final: 0.8502 (ptt90) REVERT: N 498 MET cc_start: 0.8857 (tmm) cc_final: 0.8597 (tmm) REVERT: P 488 GLN cc_start: 0.8563 (mp10) cc_final: 0.8281 (mp10) REVERT: P 489 GLU cc_start: 0.8315 (tt0) cc_final: 0.7741 (tm-30) REVERT: P 492 CYS cc_start: 0.9222 (m) cc_final: 0.8729 (t) outliers start: 0 outliers final: 0 residues processed: 283 average time/residue: 0.1992 time to fit residues: 87.9689 Evaluate side-chains 215 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 215 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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: 20.0000 chunk 106 optimal weight: 50.0000 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.9980 chunk 376 optimal weight: 4.9990 chunk 240 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 114 optimal weight: 20.0000 chunk 193 optimal weight: 4.9990 chunk 315 optimal weight: 7.9990 chunk 359 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN L1960 HIS ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L2018 HIS L2176 GLN ** L2207 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.078174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.057605 restraints weight = 250293.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.058854 restraints weight = 160028.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.059667 restraints weight = 119430.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.060189 restraints weight = 98816.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 52)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.060529 restraints weight = 87343.009| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7414 moved from start: 0.3761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 28860 Z= 0.196 Angle : 0.589 12.875 40627 Z= 0.329 Chirality : 0.038 0.175 4952 Planarity : 0.004 0.053 4537 Dihedral : 22.715 74.202 6613 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.07 % Allowed : 2.37 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.20 (0.14), residues: 3534 helix: 2.34 (0.11), residues: 2254 sheet: 0.05 (0.44), residues: 141 loop : -0.13 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 87 TYR 0.031 0.002 TYR H 41 PHE 0.020 0.001 PHE N 468 TRP 0.015 0.002 TRP L2050 HIS 0.012 0.002 HIS L2021 Details of bonding type rmsd covalent geometry : bond 0.00417 (28856) covalent geometry : angle 0.58892 (40624) hydrogen bonds : bond 0.04489 ( 2106) hydrogen bonds : angle 3.86644 ( 5758) metal coordination : bond 0.01345 ( 4) metal coordination : angle 1.42741 ( 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 258 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 257 time to evaluate : 1.138 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 51 GLU cc_start: 0.9375 (pt0) cc_final: 0.9132 (pt0) REVERT: A 82 ASP cc_start: 0.8989 (m-30) cc_final: 0.8779 (m-30) REVERT: B 28 GLN cc_start: 0.9022 (pp30) cc_final: 0.8781 (pp30) REVERT: B 64 GLU cc_start: 0.9314 (mm-30) cc_final: 0.8849 (mm-30) REVERT: C 39 ASN cc_start: 0.7944 (p0) cc_final: 0.7102 (p0) REVERT: F 60 LYS cc_start: 0.9254 (tttt) cc_final: 0.8813 (tttp) REVERT: F 64 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8807 (mt-10) REVERT: F 75 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8990 (pt0) REVERT: F 78 LYS cc_start: 0.9609 (mttt) cc_final: 0.9297 (mmtm) REVERT: G 39 ASN cc_start: 0.7258 (t0) cc_final: 0.6717 (t0) REVERT: H 94 GLU cc_start: 0.9031 (mp0) cc_final: 0.8675 (mp0) REVERT: L 1674 MET cc_start: 0.8285 (tpp) cc_final: 0.7800 (tpt) REVERT: L 1695 LEU cc_start: 0.9398 (tp) cc_final: 0.9101 (tp) REVERT: L 2063 THR cc_start: 0.8660 (m) cc_final: 0.8420 (p) REVERT: L 2151 MET cc_start: 0.8859 (tpp) cc_final: 0.8657 (tpp) REVERT: L 2166 MET cc_start: 0.8594 (mtt) cc_final: 0.7963 (mtt) REVERT: L 2229 ASP cc_start: 0.8849 (t0) cc_final: 0.8380 (t0) REVERT: L 2232 ARG cc_start: 0.8887 (ptt180) cc_final: 0.8675 (ptt90) REVERT: N 469 MET cc_start: 0.8843 (mtp) cc_final: 0.8576 (mtp) REVERT: N 480 TYR cc_start: 0.8675 (t80) cc_final: 0.8177 (t80) REVERT: N 498 MET cc_start: 0.8826 (tmm) cc_final: 0.8579 (tmm) REVERT: P 475 GLU cc_start: 0.8946 (tp30) cc_final: 0.8348 (tm-30) REVERT: P 489 GLU cc_start: 0.8439 (tt0) cc_final: 0.7883 (tm-30) REVERT: P 492 CYS cc_start: 0.9218 (m) cc_final: 0.8735 (t) outliers start: 1 outliers final: 1 residues processed: 258 average time/residue: 0.1903 time to fit residues: 78.6999 Evaluate side-chains 214 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 213 time to evaluate : 1.178 ------------------------------------------------------------------------------- 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: 5.9990 chunk 198 optimal weight: 0.2980 chunk 68 optimal weight: 2.9990 chunk 189 optimal weight: 1.9990 chunk 115 optimal weight: 30.0000 chunk 98 optimal weight: 0.6980 chunk 291 optimal weight: 3.9990 chunk 271 optimal weight: 20.0000 chunk 125 optimal weight: 20.0000 chunk 242 optimal weight: 20.0000 chunk 266 optimal weight: 9.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 76 HIS E 69 GLN E 77 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN ** L1960 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1986 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.077819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.057033 restraints weight = 261722.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.058468 restraints weight = 171628.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.058661 restraints weight = 133498.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.059627 restraints weight = 111946.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.059422 restraints weight = 97655.634| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 28860 Z= 0.169 Angle : 0.543 10.274 40627 Z= 0.304 Chirality : 0.037 0.140 4952 Planarity : 0.004 0.047 4537 Dihedral : 22.378 67.831 6613 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.14), residues: 3534 helix: 2.61 (0.11), residues: 2249 sheet: 0.03 (0.45), residues: 133 loop : -0.04 (0.19), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 130 TYR 0.014 0.001 TYR F 89 PHE 0.021 0.001 PHE H 71 TRP 0.012 0.002 TRP L2091 HIS 0.008 0.001 HIS L2248 Details of bonding type rmsd covalent geometry : bond 0.00354 (28856) covalent geometry : angle 0.54273 (40624) hydrogen bonds : bond 0.03877 ( 2106) hydrogen bonds : angle 3.65556 ( 5758) metal coordination : bond 0.01362 ( 4) metal coordination : angle 2.76666 ( 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 249 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 1.045 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 51 GLU cc_start: 0.9240 (pt0) cc_final: 0.9020 (pt0) REVERT: A 69 GLN cc_start: 0.9492 (tt0) cc_final: 0.9185 (tp40) REVERT: A 82 ASP cc_start: 0.8931 (m-30) cc_final: 0.8723 (m-30) REVERT: A 121 MET cc_start: 0.9291 (mmm) cc_final: 0.8901 (mmm) REVERT: B 64 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8824 (mm-30) REVERT: C 39 ASN cc_start: 0.7975 (p0) cc_final: 0.7083 (p0) REVERT: E 121 MET cc_start: 0.8356 (mpp) cc_final: 0.7868 (mpp) REVERT: F 24 ARG cc_start: 0.6881 (mmt180) cc_final: 0.6369 (mmp80) REVERT: F 60 LYS cc_start: 0.9327 (tttt) cc_final: 0.8352 (tptt) REVERT: F 64 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8760 (mm-30) REVERT: G 39 ASN cc_start: 0.7393 (t0) cc_final: 0.6869 (t0) REVERT: H 60 MET cc_start: 0.9475 (tpp) cc_final: 0.9169 (tpp) REVERT: H 94 GLU cc_start: 0.9099 (mp0) cc_final: 0.8719 (mp0) REVERT: L 1674 MET cc_start: 0.8290 (tpp) cc_final: 0.7817 (tpt) REVERT: L 1695 LEU cc_start: 0.9339 (tp) cc_final: 0.9056 (tp) REVERT: L 2229 ASP cc_start: 0.8813 (t0) cc_final: 0.8399 (t0) REVERT: N 476 ASN cc_start: 0.9089 (p0) cc_final: 0.8386 (p0) REVERT: N 498 MET cc_start: 0.8774 (tmm) cc_final: 0.8522 (tmm) REVERT: N 505 GLU cc_start: 0.8532 (mm-30) cc_final: 0.8329 (mm-30) REVERT: P 475 GLU cc_start: 0.8884 (tp30) cc_final: 0.8452 (tm-30) REVERT: P 489 GLU cc_start: 0.8375 (tt0) cc_final: 0.7938 (tm-30) REVERT: P 492 CYS cc_start: 0.9191 (m) cc_final: 0.8789 (t) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1826 time to fit residues: 72.9206 Evaluate side-chains 202 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.926 ------------------------------------------------------------------------------- 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: 5.9990 chunk 167 optimal weight: 0.0470 chunk 244 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 212 optimal weight: 1.9990 chunk 195 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 125 optimal weight: 4.9990 chunk 373 optimal weight: 5.9990 overall best weight: 1.3282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 HIS E 69 GLN E 77 GLN E 126 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.077467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.056905 restraints weight = 250144.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.058168 restraints weight = 159011.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.058984 restraints weight = 118568.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.059472 restraints weight = 97550.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.059828 restraints weight = 86507.996| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 28860 Z= 0.144 Angle : 0.530 10.376 40627 Z= 0.294 Chirality : 0.037 0.207 4952 Planarity : 0.004 0.046 4537 Dihedral : 22.212 67.814 6613 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % 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: 2.70 (0.14), residues: 3534 helix: 2.75 (0.11), residues: 2263 sheet: 0.10 (0.45), residues: 135 loop : 0.00 (0.19), residues: 1136 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 100 TYR 0.018 0.001 TYR H 41 PHE 0.024 0.001 PHE E 68 TRP 0.010 0.001 TRP L1670 HIS 0.007 0.001 HIS L2248 Details of bonding type rmsd covalent geometry : bond 0.00305 (28856) covalent geometry : angle 0.52994 (40624) hydrogen bonds : bond 0.03564 ( 2106) hydrogen bonds : angle 3.51734 ( 5758) metal coordination : bond 0.00754 ( 4) metal coordination : angle 1.57920 ( 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 245 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 245 time to evaluate : 0.939 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 51 GLU cc_start: 0.9396 (pt0) cc_final: 0.9113 (pt0) REVERT: A 60 GLU cc_start: 0.9162 (pm20) cc_final: 0.8960 (pm20) REVERT: A 82 ASP cc_start: 0.8929 (m-30) cc_final: 0.8703 (m-30) REVERT: A 121 MET cc_start: 0.9358 (mmm) cc_final: 0.9002 (mmm) REVERT: B 64 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8824 (mm-30) REVERT: B 75 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8875 (tm-30) REVERT: C 39 ASN cc_start: 0.7924 (p0) cc_final: 0.6977 (p0) REVERT: F 32 LYS cc_start: 0.9639 (tmtt) cc_final: 0.9412 (tmtt) REVERT: F 60 LYS cc_start: 0.9303 (tttt) cc_final: 0.8517 (tppt) REVERT: F 64 GLU cc_start: 0.9276 (mt-10) cc_final: 0.8751 (mm-30) REVERT: G 39 ASN cc_start: 0.7396 (t0) cc_final: 0.6875 (t0) REVERT: H 72 GLU cc_start: 0.9009 (mt-10) cc_final: 0.8768 (pt0) REVERT: H 94 GLU cc_start: 0.9079 (mp0) cc_final: 0.8657 (mp0) REVERT: L 1674 MET cc_start: 0.8384 (tpp) cc_final: 0.7930 (tpt) REVERT: L 1695 LEU cc_start: 0.9390 (tp) cc_final: 0.9102 (tp) REVERT: L 1999 PHE cc_start: 0.8454 (t80) cc_final: 0.8245 (t80) REVERT: L 2166 MET cc_start: 0.8106 (mtt) cc_final: 0.7896 (mtt) REVERT: N 498 MET cc_start: 0.8809 (tmm) cc_final: 0.8517 (tmm) REVERT: P 472 ASN cc_start: 0.8671 (t0) cc_final: 0.8231 (t0) REVERT: P 475 GLU cc_start: 0.8863 (tp30) cc_final: 0.8371 (tm-30) REVERT: P 489 GLU cc_start: 0.8320 (tt0) cc_final: 0.7867 (tm-30) REVERT: P 492 CYS cc_start: 0.9189 (m) cc_final: 0.8771 (t) outliers start: 0 outliers final: 0 residues processed: 245 average time/residue: 0.1900 time to fit residues: 74.5616 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 : 0.921 ------------------------------------------------------------------------------- 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: 0.7980 chunk 171 optimal weight: 0.0470 chunk 347 optimal weight: 0.9980 chunk 158 optimal weight: 4.9990 chunk 192 optimal weight: 0.3980 chunk 202 optimal weight: 0.8980 chunk 206 optimal weight: 6.9990 chunk 196 optimal weight: 0.9990 chunk 59 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 124 optimal weight: 5.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN E 77 GLN F 26 ASN G 111 ASN L2194 ASN ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.078271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.058014 restraints weight = 260839.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.059532 restraints weight = 177433.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.059491 restraints weight = 135471.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.060451 restraints weight = 112729.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.060163 restraints weight = 100053.229| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.4868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 28860 Z= 0.126 Angle : 0.513 9.109 40627 Z= 0.286 Chirality : 0.036 0.211 4952 Planarity : 0.004 0.061 4537 Dihedral : 22.009 63.866 6613 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % 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: 2.85 (0.15), residues: 3534 helix: 2.88 (0.11), residues: 2249 sheet: 0.19 (0.45), residues: 138 loop : 0.09 (0.19), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 33 TYR 0.016 0.001 TYR C 40 PHE 0.023 0.001 PHE N 468 TRP 0.010 0.001 TRP L1670 HIS 0.007 0.001 HIS L2248 Details of bonding type rmsd covalent geometry : bond 0.00262 (28856) covalent geometry : angle 0.51315 (40624) hydrogen bonds : bond 0.03340 ( 2106) hydrogen bonds : angle 3.40638 ( 5758) metal coordination : bond 0.00687 ( 4) metal coordination : angle 1.42131 ( 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 239 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 239 time to evaluate : 0.983 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: 0.9508 (tt0) cc_final: 0.8983 (tp40) REVERT: A 121 MET cc_start: 0.9381 (mmm) cc_final: 0.9028 (mmm) REVERT: B 64 GLU cc_start: 0.9258 (mm-30) cc_final: 0.8801 (mm-30) REVERT: B 75 GLU cc_start: 0.9150 (tm-30) cc_final: 0.8864 (tm-30) REVERT: C 39 ASN cc_start: 0.7677 (p0) cc_final: 0.6802 (p0) REVERT: C 96 LYS cc_start: 0.9392 (pttm) cc_final: 0.9186 (pttm) REVERT: E 68 PHE cc_start: 0.8773 (t80) cc_final: 0.8414 (t80) REVERT: F 24 ARG cc_start: 0.6771 (mmt180) cc_final: 0.6401 (mmp80) REVERT: F 60 LYS cc_start: 0.9242 (tttt) cc_final: 0.8486 (tppt) REVERT: F 64 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8771 (mm-30) REVERT: F 85 MET cc_start: 0.9225 (tpt) cc_final: 0.8654 (tpt) REVERT: F 89 TYR cc_start: 0.9281 (m-80) cc_final: 0.9005 (m-80) REVERT: G 39 ASN cc_start: 0.7331 (t0) cc_final: 0.6853 (t0) REVERT: H 60 MET cc_start: 0.9533 (tpp) cc_final: 0.9249 (tpp) REVERT: H 72 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8769 (pt0) REVERT: H 94 GLU cc_start: 0.9069 (mp0) cc_final: 0.8643 (mp0) REVERT: L 1674 MET cc_start: 0.8384 (tpp) cc_final: 0.7980 (tpt) REVERT: L 1695 LEU cc_start: 0.9370 (tp) cc_final: 0.9115 (tp) REVERT: L 1999 PHE cc_start: 0.8433 (t80) cc_final: 0.8206 (t80) REVERT: L 2232 ARG cc_start: 0.8900 (ptt-90) cc_final: 0.8442 (ptt90) REVERT: N 498 MET cc_start: 0.8787 (tmm) cc_final: 0.8496 (tmm) REVERT: P 475 GLU cc_start: 0.8905 (tp30) cc_final: 0.8455 (tp30) REVERT: P 476 GLU cc_start: 0.8377 (pm20) cc_final: 0.8126 (mp0) REVERT: P 489 GLU cc_start: 0.8400 (tt0) cc_final: 0.7781 (tp30) REVERT: P 492 CYS cc_start: 0.9213 (m) cc_final: 0.8802 (t) outliers start: 0 outliers final: 0 residues processed: 239 average time/residue: 0.1882 time to fit residues: 72.2979 Evaluate side-chains 203 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.993 ------------------------------------------------------------------------------- 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: 0.5980 chunk 54 optimal weight: 0.8980 chunk 234 optimal weight: 40.0000 chunk 210 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 99 optimal weight: 20.0000 chunk 168 optimal weight: 9.9990 chunk 249 optimal weight: 0.5980 chunk 33 optimal weight: 10.0000 chunk 14 optimal weight: 6.9990 chunk 101 optimal weight: 40.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 451 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 = 0.3865 r_free = 0.3865 target = 0.075566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.055230 restraints weight = 246065.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.056401 restraints weight = 157606.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.057157 restraints weight = 118119.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.057653 restraints weight = 98073.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.057914 restraints weight = 86839.942| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.5454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 28860 Z= 0.192 Angle : 0.567 12.059 40627 Z= 0.317 Chirality : 0.038 0.194 4952 Planarity : 0.004 0.053 4537 Dihedral : 22.008 66.637 6613 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.15), residues: 3534 helix: 2.69 (0.11), residues: 2261 sheet: 0.11 (0.43), residues: 144 loop : 0.03 (0.19), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG N 444 TYR 0.024 0.002 TYR C 51 PHE 0.031 0.002 PHE E 68 TRP 0.020 0.002 TRP N 507 HIS 0.012 0.002 HIS N 501 Details of bonding type rmsd covalent geometry : bond 0.00403 (28856) covalent geometry : angle 0.56531 (40624) hydrogen bonds : bond 0.04084 ( 2106) hydrogen bonds : angle 3.64451 ( 5758) metal coordination : bond 0.02052 ( 4) metal coordination : angle 4.51071 ( 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 230 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 230 time to evaluate : 0.999 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: 0.9370 (pt0) cc_final: 0.9120 (pt0) REVERT: A 69 GLN cc_start: 0.9505 (tt0) cc_final: 0.9083 (tp40) REVERT: A 82 ASP cc_start: 0.9024 (m-30) cc_final: 0.8790 (m-30) REVERT: A 121 MET cc_start: 0.9439 (mmm) cc_final: 0.9209 (mmm) REVERT: B 28 GLN cc_start: 0.9094 (pp30) cc_final: 0.8718 (tm-30) REVERT: B 64 GLU cc_start: 0.9296 (mm-30) cc_final: 0.8836 (mm-30) REVERT: B 75 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8924 (tm-30) REVERT: C 39 ASN cc_start: 0.8031 (p0) cc_final: 0.7161 (p0) REVERT: C 40 TYR cc_start: 0.9201 (m-80) cc_final: 0.8940 (m-80) REVERT: D 72 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8191 (mt-10) REVERT: D 102 LEU cc_start: 0.9216 (mt) cc_final: 0.8993 (mt) REVERT: F 32 LYS cc_start: 0.9673 (tmtt) cc_final: 0.9430 (tmtt) REVERT: F 53 GLU cc_start: 0.9036 (mp0) cc_final: 0.8826 (mp0) REVERT: F 64 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8830 (mm-30) REVERT: F 85 MET cc_start: 0.9275 (tpt) cc_final: 0.8784 (mmm) REVERT: F 89 TYR cc_start: 0.9335 (m-80) cc_final: 0.8809 (m-80) REVERT: G 39 ASN cc_start: 0.7556 (t0) cc_final: 0.6968 (t0) REVERT: G 57 GLU cc_start: 0.9352 (tt0) cc_final: 0.8950 (mt-10) REVERT: H 72 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8749 (pt0) REVERT: L 1674 MET cc_start: 0.8502 (tpp) cc_final: 0.8029 (tpt) REVERT: L 1695 LEU cc_start: 0.9443 (tp) cc_final: 0.9184 (tp) REVERT: L 1999 PHE cc_start: 0.8569 (t80) cc_final: 0.8304 (t80) REVERT: L 2145 GLU cc_start: 0.8863 (tp30) cc_final: 0.8603 (tm-30) REVERT: L 2232 ARG cc_start: 0.8945 (ptt-90) cc_final: 0.8514 (ptt90) REVERT: N 498 MET cc_start: 0.8777 (tmm) cc_final: 0.8494 (tmm) REVERT: N 505 GLU cc_start: 0.8273 (mp0) cc_final: 0.8061 (pm20) REVERT: P 472 ASN cc_start: 0.8540 (t0) cc_final: 0.8323 (t0) REVERT: P 475 GLU cc_start: 0.8945 (tp30) cc_final: 0.8416 (tm-30) REVERT: P 476 GLU cc_start: 0.8409 (pm20) cc_final: 0.8195 (mp0) REVERT: P 492 CYS cc_start: 0.9272 (m) cc_final: 0.8909 (t) outliers start: 0 outliers final: 0 residues processed: 230 average time/residue: 0.1883 time to fit residues: 70.6737 Evaluate side-chains 201 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.007 ------------------------------------------------------------------------------- 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: 0.7980 chunk 152 optimal weight: 50.0000 chunk 251 optimal weight: 0.8980 chunk 221 optimal weight: 0.0020 chunk 36 optimal weight: 5.9990 chunk 33 optimal weight: 0.0670 chunk 279 optimal weight: 20.0000 chunk 359 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 chunk 348 optimal weight: 8.9990 chunk 134 optimal weight: 30.0000 overall best weight: 0.4926 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 HIS E 69 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 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 = 0.3901 r_free = 0.3901 target = 0.077328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.056779 restraints weight = 263829.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.058103 restraints weight = 166090.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.058944 restraints weight = 123222.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.059484 restraints weight = 101921.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.059814 restraints weight = 90348.311| |-----------------------------------------------------------------------------| r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7495 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 28860 Z= 0.122 Angle : 0.518 12.785 40627 Z= 0.288 Chirality : 0.036 0.159 4952 Planarity : 0.004 0.051 4537 Dihedral : 21.944 63.679 6613 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % 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: 2.98 (0.15), residues: 3534 helix: 2.97 (0.11), residues: 2248 sheet: 0.18 (0.45), residues: 138 loop : 0.16 (0.20), residues: 1148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG N 444 TYR 0.014 0.001 TYR P 494 PHE 0.025 0.001 PHE N 468 TRP 0.015 0.001 TRP P 486 HIS 0.005 0.001 HIS L2248 Details of bonding type rmsd covalent geometry : bond 0.00252 (28856) covalent geometry : angle 0.51787 (40624) hydrogen bonds : bond 0.03229 ( 2106) hydrogen bonds : angle 3.40357 ( 5758) metal coordination : bond 0.00988 ( 4) metal coordination : angle 1.55412 ( 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 233 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 233 time to evaluate : 1.057 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: 0.9503 (tt0) cc_final: 0.8974 (tp40) REVERT: A 82 ASP cc_start: 0.8928 (m-30) cc_final: 0.8719 (m-30) REVERT: A 106 GLU cc_start: 0.9345 (mm-30) cc_final: 0.9057 (mm-30) REVERT: A 121 MET cc_start: 0.9445 (mmm) cc_final: 0.9214 (mmm) REVERT: B 28 GLN cc_start: 0.9087 (pp30) cc_final: 0.8742 (tm-30) REVERT: B 54 GLU cc_start: 0.9498 (mm-30) cc_final: 0.9043 (tt0) REVERT: B 64 GLU cc_start: 0.9256 (mm-30) cc_final: 0.8798 (mm-30) REVERT: B 75 GLU cc_start: 0.9151 (tm-30) cc_final: 0.8870 (tm-30) REVERT: C 39 ASN cc_start: 0.7872 (p0) cc_final: 0.7090 (p0) REVERT: C 40 TYR cc_start: 0.9085 (m-80) cc_final: 0.8817 (m-80) REVERT: D 102 LEU cc_start: 0.9213 (mt) cc_final: 0.8986 (mt) REVERT: F 53 GLU cc_start: 0.9005 (mp0) cc_final: 0.8799 (mp0) REVERT: F 64 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8744 (mm-30) REVERT: F 85 MET cc_start: 0.9267 (tpt) cc_final: 0.8731 (mmm) REVERT: F 89 TYR cc_start: 0.9383 (m-80) cc_final: 0.8715 (m-80) REVERT: G 39 ASN cc_start: 0.7419 (t0) cc_final: 0.6820 (t0) REVERT: G 57 GLU cc_start: 0.9322 (tt0) cc_final: 0.9113 (tt0) REVERT: H 60 MET cc_start: 0.9547 (tpp) cc_final: 0.9324 (tpp) REVERT: H 72 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8676 (pt0) REVERT: H 94 GLU cc_start: 0.9052 (mp0) cc_final: 0.8761 (mp0) REVERT: L 1674 MET cc_start: 0.8365 (tpp) cc_final: 0.7927 (tpt) REVERT: L 1695 LEU cc_start: 0.9394 (tp) cc_final: 0.9126 (tp) REVERT: L 1999 PHE cc_start: 0.8501 (t80) cc_final: 0.8284 (t80) REVERT: L 2145 GLU cc_start: 0.8690 (tp30) cc_final: 0.8345 (tp30) REVERT: L 2232 ARG cc_start: 0.8916 (ptt-90) cc_final: 0.8439 (ptt90) REVERT: N 476 ASN cc_start: 0.8722 (p0) cc_final: 0.8463 (p0) REVERT: N 505 GLU cc_start: 0.8274 (mp0) cc_final: 0.8010 (mp0) REVERT: P 475 GLU cc_start: 0.8838 (tp30) cc_final: 0.8541 (tp30) REVERT: P 492 CYS cc_start: 0.9159 (m) cc_final: 0.8858 (t) outliers start: 0 outliers final: 0 residues processed: 233 average time/residue: 0.1791 time to fit residues: 68.2590 Evaluate side-chains 207 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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: 5.9990 chunk 124 optimal weight: 6.9990 chunk 191 optimal weight: 0.8980 chunk 281 optimal weight: 0.0040 chunk 209 optimal weight: 4.9990 chunk 164 optimal weight: 6.9990 chunk 321 optimal weight: 3.9990 chunk 227 optimal weight: 0.9990 chunk 367 optimal weight: 10.0000 chunk 172 optimal weight: 0.0040 chunk 264 optimal weight: 7.9990 overall best weight: 1.1808 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.076891 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.056373 restraints weight = 260995.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.057688 restraints weight = 165782.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.058475 restraints weight = 123475.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.058901 restraints weight = 102476.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.059279 restraints weight = 91678.076| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 28860 Z= 0.135 Angle : 0.521 10.765 40627 Z= 0.289 Chirality : 0.036 0.174 4952 Planarity : 0.004 0.053 4537 Dihedral : 21.800 64.504 6613 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: 3.00 (0.15), residues: 3534 helix: 2.98 (0.11), residues: 2250 sheet: 0.20 (0.45), residues: 138 loop : 0.18 (0.20), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 50 TYR 0.022 0.001 TYR L1734 PHE 0.020 0.001 PHE N 468 TRP 0.041 0.003 TRP L2049 HIS 0.007 0.001 HIS L2248 Details of bonding type rmsd covalent geometry : bond 0.00282 (28856) covalent geometry : angle 0.52026 (40624) hydrogen bonds : bond 0.03300 ( 2106) hydrogen bonds : angle 3.39435 ( 5758) metal coordination : bond 0.00809 ( 4) metal coordination : angle 2.24295 ( 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 228 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 228 time to evaluate : 1.001 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: 0.9502 (tt0) cc_final: 0.9085 (tp40) REVERT: A 82 ASP cc_start: 0.8932 (m-30) cc_final: 0.8725 (m-30) REVERT: A 106 GLU cc_start: 0.9365 (mm-30) cc_final: 0.9072 (mm-30) REVERT: A 121 MET cc_start: 0.9449 (mmm) cc_final: 0.9229 (mmm) REVERT: B 28 GLN cc_start: 0.9078 (pp30) cc_final: 0.8778 (tm-30) REVERT: B 54 GLU cc_start: 0.9549 (mm-30) cc_final: 0.9053 (tt0) REVERT: B 64 GLU cc_start: 0.9270 (mm-30) cc_final: 0.8814 (mm-30) REVERT: B 75 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8873 (tm-30) REVERT: C 39 ASN cc_start: 0.7912 (p0) cc_final: 0.7135 (p0) REVERT: C 40 TYR cc_start: 0.9084 (m-80) cc_final: 0.8755 (m-80) REVERT: E 47 VAL cc_start: 0.8763 (t) cc_final: 0.8448 (t) REVERT: E 74 GLU cc_start: 0.9134 (pp20) cc_final: 0.8760 (pp20) REVERT: F 24 ARG cc_start: 0.7048 (mmt180) cc_final: 0.6502 (mmp80) REVERT: F 32 LYS cc_start: 0.9676 (tmtt) cc_final: 0.9266 (tptp) REVERT: F 53 GLU cc_start: 0.8980 (mp0) cc_final: 0.8778 (mp0) REVERT: F 64 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8816 (mm-30) REVERT: F 75 GLU cc_start: 0.9075 (pt0) cc_final: 0.8866 (pp20) REVERT: F 85 MET cc_start: 0.9227 (tpt) cc_final: 0.8986 (mmm) REVERT: G 39 ASN cc_start: 0.7394 (t0) cc_final: 0.6732 (t0) REVERT: G 57 GLU cc_start: 0.9303 (tt0) cc_final: 0.9090 (tt0) REVERT: G 73 ASP cc_start: 0.9127 (m-30) cc_final: 0.8926 (m-30) REVERT: H 60 MET cc_start: 0.9546 (tpp) cc_final: 0.9297 (tpp) REVERT: H 72 GLU cc_start: 0.9047 (mt-10) cc_final: 0.8673 (pt0) REVERT: H 94 GLU cc_start: 0.9056 (mp0) cc_final: 0.8791 (mp0) REVERT: L 1674 MET cc_start: 0.8404 (tpp) cc_final: 0.7879 (tpt) REVERT: L 1695 LEU cc_start: 0.9414 (tp) cc_final: 0.9157 (tp) REVERT: L 2145 GLU cc_start: 0.8756 (tp30) cc_final: 0.8384 (tp30) REVERT: L 2232 ARG cc_start: 0.8903 (ptt-90) cc_final: 0.8434 (ptt90) REVERT: N 429 TYR cc_start: 0.8458 (p90) cc_final: 0.8114 (p90) REVERT: N 505 GLU cc_start: 0.8290 (mp0) cc_final: 0.7977 (mp0) REVERT: P 475 GLU cc_start: 0.8800 (tp30) cc_final: 0.8411 (tp30) REVERT: P 476 GLU cc_start: 0.8563 (mp0) cc_final: 0.8052 (mp0) REVERT: P 492 CYS cc_start: 0.9204 (m) cc_final: 0.8877 (t) outliers start: 0 outliers final: 0 residues processed: 228 average time/residue: 0.1752 time to fit residues: 65.6230 Evaluate side-chains 204 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 204 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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: 1.9990 chunk 261 optimal weight: 0.0030 chunk 207 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 292 optimal weight: 10.0000 chunk 139 optimal weight: 40.0000 chunk 206 optimal weight: 1.9990 chunk 300 optimal weight: 10.0000 chunk 122 optimal weight: 0.4980 chunk 380 optimal weight: 7.9990 chunk 285 optimal weight: 9.9990 overall best weight: 1.0996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 69 GLN E 77 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 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 = 0.3894 r_free = 0.3894 target = 0.076928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.056467 restraints weight = 260639.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.057723 restraints weight = 164610.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.058508 restraints weight = 122840.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.058937 restraints weight = 102090.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.059315 restraints weight = 91226.199| |-----------------------------------------------------------------------------| r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.5963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 28860 Z= 0.129 Angle : 0.517 10.226 40627 Z= 0.286 Chirality : 0.036 0.171 4952 Planarity : 0.004 0.053 4537 Dihedral : 21.766 63.924 6613 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 3.07 (0.15), residues: 3534 helix: 3.03 (0.11), residues: 2242 sheet: 0.22 (0.45), residues: 143 loop : 0.23 (0.20), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG B 24 TYR 0.018 0.001 TYR E 55 PHE 0.027 0.001 PHE N 468 TRP 0.009 0.001 TRP L1670 HIS 0.006 0.001 HIS L2248 Details of bonding type rmsd covalent geometry : bond 0.00269 (28856) covalent geometry : angle 0.51729 (40624) hydrogen bonds : bond 0.03108 ( 2106) hydrogen bonds : angle 3.34196 ( 5758) metal coordination : bond 0.00587 ( 4) metal coordination : angle 1.74019 ( 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 224 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 224 time to evaluate : 0.885 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: 0.9366 (pt0) cc_final: 0.9162 (pt0) REVERT: A 69 GLN cc_start: 0.9514 (tt0) cc_final: 0.9098 (tp40) REVERT: A 82 ASP cc_start: 0.8919 (m-30) cc_final: 0.8707 (m-30) REVERT: A 106 GLU cc_start: 0.9384 (mm-30) cc_final: 0.9102 (mm-30) REVERT: B 28 GLN cc_start: 0.9101 (pp30) cc_final: 0.8795 (tm-30) REVERT: B 54 GLU cc_start: 0.9546 (mm-30) cc_final: 0.9085 (tt0) REVERT: B 64 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8805 (mm-30) REVERT: B 75 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8882 (tm-30) REVERT: C 39 ASN cc_start: 0.7900 (p0) cc_final: 0.7132 (p0) REVERT: C 40 TYR cc_start: 0.9047 (m-80) cc_final: 0.8673 (m-80) REVERT: C 96 LYS cc_start: 0.9342 (ptpp) cc_final: 0.9122 (ptmm) REVERT: E 54 ARG cc_start: 0.8897 (tpm170) cc_final: 0.8474 (tpp-160) REVERT: F 32 LYS cc_start: 0.9614 (tmtt) cc_final: 0.9167 (tptp) REVERT: F 64 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8802 (mm-30) REVERT: F 75 GLU cc_start: 0.9095 (pt0) cc_final: 0.8866 (pp20) REVERT: G 39 ASN cc_start: 0.7344 (t0) cc_final: 0.6670 (t0) REVERT: G 57 GLU cc_start: 0.9298 (tt0) cc_final: 0.9090 (tt0) REVERT: H 72 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8634 (pt0) REVERT: H 94 GLU cc_start: 0.9084 (mp0) cc_final: 0.8806 (mp0) REVERT: L 1674 MET cc_start: 0.8458 (tpp) cc_final: 0.7947 (tpt) REVERT: L 1695 LEU cc_start: 0.9412 (tp) cc_final: 0.9173 (tp) REVERT: L 2145 GLU cc_start: 0.8771 (tp30) cc_final: 0.8382 (tp30) REVERT: L 2166 MET cc_start: 0.7398 (mtp) cc_final: 0.7155 (mtp) REVERT: L 2231 MET cc_start: 0.8065 (mtt) cc_final: 0.7608 (mmm) REVERT: L 2232 ARG cc_start: 0.8917 (ptt-90) cc_final: 0.8685 (ptt90) REVERT: N 429 TYR cc_start: 0.8494 (p90) cc_final: 0.8154 (p90) REVERT: N 476 ASN cc_start: 0.8895 (p0) cc_final: 0.8603 (p0) REVERT: N 505 GLU cc_start: 0.8255 (mp0) cc_final: 0.7937 (mp0) REVERT: P 475 GLU cc_start: 0.8803 (tp30) cc_final: 0.8408 (tp30) REVERT: P 476 GLU cc_start: 0.8635 (mp0) cc_final: 0.8058 (mp0) REVERT: P 492 CYS cc_start: 0.9237 (m) cc_final: 0.8828 (t) outliers start: 0 outliers final: 0 residues processed: 224 average time/residue: 0.1783 time to fit residues: 65.4224 Evaluate side-chains 203 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 203 time to evaluate : 0.920 ------------------------------------------------------------------------------- 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: 9.9990 chunk 121 optimal weight: 20.0000 chunk 195 optimal weight: 0.7980 chunk 252 optimal weight: 0.8980 chunk 139 optimal weight: 40.0000 chunk 287 optimal weight: 7.9990 chunk 214 optimal weight: 0.9980 chunk 107 optimal weight: 40.0000 chunk 165 optimal weight: 4.9990 chunk 194 optimal weight: 6.9990 chunk 27 optimal weight: 40.0000 overall best weight: 2.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN F 26 ASN ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 436 ASN ** N 451 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 = 0.3840 r_free = 0.3840 target = 0.074261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.053852 restraints weight = 267408.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.055105 restraints weight = 169894.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.055882 restraints weight = 127067.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.056374 restraints weight = 105969.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.056691 restraints weight = 94401.919| |-----------------------------------------------------------------------------| r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.6566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 28860 Z= 0.213 Angle : 0.598 11.766 40627 Z= 0.332 Chirality : 0.039 0.185 4952 Planarity : 0.005 0.061 4537 Dihedral : 21.979 71.085 6613 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.15), residues: 3534 helix: 2.68 (0.11), residues: 2253 sheet: -0.06 (0.44), residues: 154 loop : 0.09 (0.20), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 50 TYR 0.048 0.002 TYR E 55 PHE 0.022 0.002 PHE N 468 TRP 0.022 0.002 TRP P 486 HIS 0.010 0.002 HIS L2248 Details of bonding type rmsd covalent geometry : bond 0.00441 (28856) covalent geometry : angle 0.59657 (40624) hydrogen bonds : bond 0.04297 ( 2106) hydrogen bonds : angle 3.69953 ( 5758) metal coordination : bond 0.02747 ( 4) metal coordination : angle 5.53834 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6798.23 seconds wall clock time: 116 minutes 47.62 seconds (7007.62 seconds total)