Starting phenix.real_space_refine on Sun Jul 5 14:39:12 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rmc_54056/07_2026/9rmc_54056.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rmc_54056/07_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_54056/07_2026/9rmc_54056.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rmc_54056/07_2026/9rmc_54056.map" model { file = "/net/cci-nas-00/data/ceres_data/9rmc_54056/07_2026/9rmc_54056.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rmc_54056/07_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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27953 Number of models: 1 Model: "" Number of chains: 23 Chain: "A" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 783 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 641 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 641 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 844 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2021 Classifications: {'peptide': 331} Incomplete info: {'truncation_to_alanine': 194} Link IDs: {'PTRANS': 10, 'TRANS': 320} Chain breaks: 4 Unresolved non-hydrogen bonds: 778 Unresolved non-hydrogen angles: 999 Unresolved non-hydrogen dihedrals: 669 Unresolved non-hydrogen chiralities: 70 Planarities with less than four sites: {'GLN:plan1': 12, 'GLU:plan': 11, 'ARG:plan': 11, 'HIS:plan': 9, 'TYR:plan': 12, 'ASN:plan1': 12, 'ASP:plan': 5, 'PHE:plan': 8, 'TRP:plan': 6} Unresolved non-hydrogen planarities: 429 Chain: "J" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 1677 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 272} Link IDs: {'PTRANS': 15, 'TRANS': 318} Chain breaks: 4 Unresolved non-hydrogen bonds: 980 Unresolved non-hydrogen angles: 1263 Unresolved non-hydrogen dihedrals: 814 Unresolved non-hydrogen chiralities: 96 Planarities with less than four sites: {'PHE:plan': 15, 'ASP:plan': 18, 'TYR:plan': 12, 'ARG:plan': 15, 'GLU:plan': 18, 'ASN:plan1': 14, 'TRP:plan': 5, 'GLN:plan1': 15, 'HIS:plan': 8} Unresolved non-hydrogen planarities: 562 Chain: "K" Number of atoms: 1600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 1600 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 253} Link IDs: {'PTRANS': 17, 'TRANS': 299} Chain breaks: 3 Unresolved non-hydrogen bonds: 922 Unresolved non-hydrogen angles: 1182 Unresolved non-hydrogen dihedrals: 767 Unresolved non-hydrogen chiralities: 88 Planarities with less than four sites: {'ASP:plan': 21, 'ASN:plan1': 8, 'PHE:plan': 12, 'ARG:plan': 14, 'TRP:plan': 4, 'GLU:plan': 23, 'HIS:plan': 7, 'TYR:plan': 13, 'GLN:plan1': 9} Unresolved non-hydrogen planarities: 519 Chain: "L" Number of atoms: 3671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 466, 3671 Classifications: {'peptide': 466} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 25, 'TRANS': 440} Chain breaks: 4 Chain: "M" Number of atoms: 1488 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 1488 Classifications: {'peptide': 295} Incomplete info: {'truncation_to_alanine': 252} Link IDs: {'PTRANS': 13, 'TRANS': 281} Chain breaks: 2 Unresolved non-hydrogen bonds: 920 Unresolved non-hydrogen angles: 1174 Unresolved non-hydrogen dihedrals: 755 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'PHE:plan': 11, 'GLN:plan1': 13, 'GLU:plan': 27, 'ASP:plan': 21, 'TYR:plan': 8, 'ASN:plan1': 12, 'ARG:plan': 18, 'TRP:plan': 5, 'HIS:plan': 4} Unresolved non-hydrogen planarities: 536 Chain: "N" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 260, 1622 Classifications: {'peptide': 260} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PTRANS': 6, 'TRANS': 253} Chain breaks: 3 Unresolved non-hydrogen bonds: 497 Unresolved non-hydrogen angles: 627 Unresolved non-hydrogen dihedrals: 406 Unresolved non-hydrogen chiralities: 45 Planarities with less than four sites: {'ASN:plan1': 3, 'TYR:plan': 4, 'GLN:plan1': 9, 'ASP:plan': 7, 'GLU:plan': 20, 'TRP:plan': 1, 'HIS:plan': 5, 'ARG:plan': 9, 'PHE:plan': 5} Unresolved non-hydrogen planarities: 283 Chain: "O" Number of atoms: 1605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 315, 1605 Classifications: {'peptide': 315} Incomplete info: {'truncation_to_alanine': 254} Link IDs: {'PTRANS': 19, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 978 Unresolved non-hydrogen angles: 1250 Unresolved non-hydrogen dihedrals: 816 Unresolved non-hydrogen chiralities: 84 Planarities with less than four sites: {'HIS:plan': 11, 'TYR:plan': 12, 'TRP:plan': 4, 'PHE:plan': 12, 'ASP:plan': 13, 'ASN:plan1': 9, 'GLU:plan': 31, 'ARG:plan': 19, 'GLN:plan1': 14} Unresolved non-hydrogen planarities: 588 Chain: "P" Number of atoms: 1315 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1315 Classifications: {'peptide': 235} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 14, 'TRANS': 220} Chain breaks: 3 Unresolved non-hydrogen bonds: 690 Unresolved non-hydrogen angles: 864 Unresolved non-hydrogen dihedrals: 570 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'ASP:plan': 11, 'GLN:plan1': 23, 'ARG:plan': 15, 'GLU:plan': 13, 'TYR:plan': 4, 'PHE:plan': 9, 'HIS:plan': 5, 'TRP:plan': 2, 'ASN:plan1': 4} Unresolved non-hydrogen planarities: 389 Chain: "Q" Number of atoms: 529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 529 Classifications: {'peptide': 105} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 3, 'TRANS': 101} Unresolved non-hydrogen bonds: 340 Unresolved non-hydrogen angles: 425 Unresolved non-hydrogen dihedrals: 274 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'GLN:plan1': 8, 'GLU:plan': 10, 'ASP:plan': 7, 'TYR:plan': 1, 'PHE:plan': 4, 'HIS:plan': 4, 'ARG:plan': 10, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 203 Chain: "R" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 351 Classifications: {'peptide': 70} Incomplete info: {'truncation_to_alanine': 56} Link IDs: {'PTRANS': 3, 'TRANS': 66} Unresolved non-hydrogen bonds: 242 Unresolved non-hydrogen angles: 307 Unresolved non-hydrogen dihedrals: 215 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 4, 'GLN:plan1': 5, 'TYR:plan': 6, 'ASP:plan': 2, 'HIS:plan': 2, 'ASN:plan1': 3, 'ARG:plan': 8, 'PHE:plan': 1, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 167 Chain: "V" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 338 Classifications: {'peptide': 68} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 1, 'TRANS': 66} Unresolved non-hydrogen bonds: 220 Unresolved non-hydrogen angles: 277 Unresolved non-hydrogen dihedrals: 183 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'GLN:plan1': 7, 'GLU:plan': 3, 'PHE:plan': 5, 'ARG:plan': 3, 'TYR:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 107 Chain: "W" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 373 Classifications: {'peptide': 73} Incomplete info: {'truncation_to_alanine': 61} Link IDs: {'PTRANS': 5, 'TRANS': 67} Unresolved non-hydrogen bonds: 263 Unresolved non-hydrogen angles: 323 Unresolved non-hydrogen dihedrals: 233 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'ARG:plan': 10, 'ASN:plan1': 3, 'PHE:plan': 2, 'TRP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 7, 'HIS:plan': 3, 'ASP:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 160 Chain: "X" Number of atoms: 2662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2662 Classifications: {'DNA': 131} Link IDs: {'rna3p': 130} Chain: "Y" Number of atoms: 2706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 2706 Classifications: {'DNA': 131} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 130} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 13612 SG CYS L2094 41.368 78.961 149.543 1.00196.77 S Time building chain proxies: 5.55, per 1000 atoms: 0.20 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: 2.85 Conformation dependent library (CDL) restraints added in 1.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN L2301 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2021 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2019 " pdb="ZN ZN L2301 " - pdb=" NE2 HIS L2090 " pdb="ZN ZN L2301 " - pdb=" SG CYS L2094 " Number of angles added : 3 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6914 Finding SS restraints... Secondary structure from input PDB file: 172 helices and 28 sheets defined 66.1% alpha, 5.0% beta 130 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 3.89 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: 8.89 Time building geometry restraints manager: 3.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 7410 1.33 - 1.45: 5363 1.45 - 1.57: 15496 1.57 - 1.69: 521 1.69 - 1.81: 66 Bond restraints: 28856 Sorted by residual: bond pdb=" C3' DC X 80 " pdb=" O3' DC X 80 " ideal model delta sigma weight residual 1.435 1.377 0.058 1.30e-02 5.92e+03 2.00e+01 bond pdb=" C3' DG X 100 " pdb=" O3' DG X 100 " ideal model delta sigma weight residual 1.435 1.380 0.055 1.30e-02 5.92e+03 1.80e+01 bond pdb=" C1' DC Y 16 " pdb=" N1 DC Y 16 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.60e+01 bond pdb=" C1' DT Y 110 " pdb=" N1 DT Y 110 " ideal model delta sigma weight residual 1.468 1.524 -0.056 1.40e-02 5.10e+03 1.57e+01 bond pdb=" C5' DT Y 13 " pdb=" C4' DT Y 13 " ideal model delta sigma weight residual 1.512 1.539 -0.027 7.00e-03 2.04e+04 1.54e+01 ... (remaining 28851 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 37518 1.37 - 2.73: 2451 2.73 - 4.10: 462 4.10 - 5.47: 156 5.47 - 6.84: 37 Bond angle restraints: 40624 Sorted by residual: angle pdb=" O5' DT X 129 " pdb=" C5' DT X 129 " pdb=" C4' DT X 129 " ideal model delta sigma weight residual 109.40 114.75 -5.35 8.00e-01 1.56e+00 4.46e+01 angle pdb=" O5' DA X 131 " pdb=" C5' DA X 131 " pdb=" C4' DA X 131 " ideal model delta sigma weight residual 109.40 114.08 -4.68 8.00e-01 1.56e+00 3.42e+01 angle pdb=" O5' DC Y 21 " pdb=" C5' DC Y 21 " pdb=" C4' DC Y 21 " ideal model delta sigma weight residual 109.40 113.93 -4.53 8.00e-01 1.56e+00 3.20e+01 angle pdb=" O5' DT Y 13 " pdb=" C5' DT Y 13 " pdb=" C4' DT Y 13 " ideal model delta sigma weight residual 109.40 113.74 -4.34 8.00e-01 1.56e+00 2.94e+01 angle pdb=" O5' DA Y 17 " pdb=" C5' DA Y 17 " pdb=" C4' DA Y 17 " ideal model delta sigma weight residual 109.40 113.62 -4.22 8.00e-01 1.56e+00 2.78e+01 ... (remaining 40619 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 14373 17.68 - 35.37: 1001 35.37 - 53.05: 1111 53.05 - 70.73: 237 70.73 - 88.42: 9 Dihedral angle restraints: 16731 sinusoidal: 6190 harmonic: 10541 Sorted by residual: dihedral pdb=" CA LEU I 807 " pdb=" C LEU I 807 " pdb=" N ILE I 808 " pdb=" CA ILE I 808 " ideal model delta harmonic sigma weight residual 180.00 156.09 23.91 0 5.00e+00 4.00e-02 2.29e+01 dihedral pdb=" CA PHE I 853 " pdb=" C PHE I 853 " pdb=" N ASN I 854 " pdb=" CA ASN I 854 " ideal model delta harmonic sigma weight residual -180.00 -157.49 -22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA SER I 937 " pdb=" C SER I 937 " pdb=" N THR I 938 " pdb=" CA THR I 938 " ideal model delta harmonic sigma weight residual 180.00 157.50 22.50 0 5.00e+00 4.00e-02 2.02e+01 ... (remaining 16728 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 3937 0.067 - 0.134: 732 0.134 - 0.201: 261 0.201 - 0.268: 21 0.268 - 0.335: 1 Chirality restraints: 4952 Sorted by residual: chirality pdb=" CA ASP L1663 " pdb=" N ASP L1663 " pdb=" C ASP L1663 " pdb=" CB ASP L1663 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C3' DG Y 30 " pdb=" C4' DG Y 30 " pdb=" O3' DG Y 30 " pdb=" C2' DG Y 30 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C3' DA Y 24 " pdb=" C4' DA Y 24 " pdb=" O3' DA Y 24 " pdb=" C2' DA Y 24 " both_signs ideal model delta sigma weight residual False -2.73 -2.50 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 4949 not shown) Planarity restraints: 4537 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA X 69 " -0.036 2.00e-02 2.50e+03 1.61e-02 7.15e+00 pdb=" N9 DA X 69 " 0.035 2.00e-02 2.50e+03 pdb=" C8 DA X 69 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA X 69 " 0.000 2.00e-02 2.50e+03 pdb=" C5 DA X 69 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA X 69 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA X 69 " -0.014 2.00e-02 2.50e+03 pdb=" N1 DA X 69 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA X 69 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA X 69 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA X 69 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT X 127 " 0.030 2.00e-02 2.50e+03 1.53e-02 5.89e+00 pdb=" N1 DT X 127 " -0.028 2.00e-02 2.50e+03 pdb=" C2 DT X 127 " -0.007 2.00e-02 2.50e+03 pdb=" O2 DT X 127 " -0.011 2.00e-02 2.50e+03 pdb=" N3 DT X 127 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DT X 127 " 0.007 2.00e-02 2.50e+03 pdb=" O4 DT X 127 " 0.012 2.00e-02 2.50e+03 pdb=" C5 DT X 127 " 0.008 2.00e-02 2.50e+03 pdb=" C7 DT X 127 " -0.016 2.00e-02 2.50e+03 pdb=" C6 DT X 127 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA X 39 " 0.033 2.00e-02 2.50e+03 1.44e-02 5.71e+00 pdb=" N9 DA X 39 " -0.032 2.00e-02 2.50e+03 pdb=" C8 DA X 39 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA X 39 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DA X 39 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA X 39 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA X 39 " 0.012 2.00e-02 2.50e+03 pdb=" N1 DA X 39 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA X 39 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA X 39 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA X 39 " -0.003 2.00e-02 2.50e+03 ... (remaining 4534 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6199 2.79 - 3.31: 27033 3.31 - 3.84: 47527 3.84 - 4.37: 53286 4.37 - 4.90: 81684 Nonbonded interactions: 215729 Sorted by model distance: nonbonded pdb=" N GLU I 454 " pdb=" OE1 GLU I 454 " model vdw 2.258 3.120 nonbonded pdb=" O CYS L1968 " pdb=" OG1 THR L1969 " model vdw 2.278 3.040 nonbonded pdb=" O THR I 859 " pdb=" N ILE I 863 " model vdw 2.373 3.120 nonbonded pdb=" O ALA G 11 " pdb=" NZ LYS H 121 " model vdw 2.382 3.120 nonbonded pdb=" OD2 ASP N 434 " pdb=" OG SER N 437 " model vdw 2.442 3.040 ... (remaining 215724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 34 through 125) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 11.460 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: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 34.760 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6741 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 28860 Z= 0.488 Angle : 0.813 6.835 40627 Z= 0.540 Chirality : 0.061 0.335 4952 Planarity : 0.006 0.096 4537 Dihedral : 20.695 88.418 9817 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 0.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.42 % Favored : 96.49 % Rotamer: Outliers : 0.52 % Allowed : 2.37 % Favored : 97.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.22 (0.13), residues: 3534 helix: 0.18 (0.10), residues: 2215 sheet: -0.33 (0.42), residues: 136 loop : -0.50 (0.18), residues: 1183 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 43 TYR 0.013 0.002 TYR N 435 PHE 0.022 0.001 PHE L1641 TRP 0.013 0.002 TRP N 507 HIS 0.007 0.002 HIS B 76 Details of bonding type rmsd/Z covalent geometry : bond 0.00573 / 0.49 (28856) covalent geometry : angle 0.81259 / 0.54 (40624) hydrogen bonds : bond 0.15363 / 10.55 ( 2106) hydrogen bonds : angle 5.83295 / 4.28 ( 5758) metal coordination : bond 0.00144 / 0.07 ( 4) metal coordination : angle 1.44606 / 0.79 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7068 Ramachandran restraints generated. 3534 Oldfield, 0 Emsley, 3534 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 433 time to evaluate : 0.980 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: 0.2038 time to fit residues: 133.6071 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 : 0.854 ------------------------------------------------------------------------------- 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... D 96 GLN D 110 HIS E 69 GLN E 77 GLN H 96 GLN I 383 GLN L1835 GLN ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 422 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.080734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.060302 restraints weight = 246034.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.061554 restraints weight = 159116.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.062383 restraints weight = 119205.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.062929 restraints weight = 98120.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.063232 restraints weight = 86136.772| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.2507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 28860 Z= 0.202 Angle : 0.706 8.952 40627 Z= 0.383 Chirality : 0.043 0.219 4952 Planarity : 0.005 0.064 4537 Dihedral : 23.736 71.831 6613 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.42 (0.14), residues: 3534 helix: 1.68 (0.11), residues: 2233 sheet: -0.16 (0.45), residues: 137 loop : -0.30 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.001 ARG B 40 TYR 0.032 0.002 TYR C 40 PHE 0.015 0.002 PHE L1859 TRP 0.021 0.002 TRP L2091 HIS 0.010 0.002 HIS L2090 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.20 (28856) covalent geometry : angle 0.70567 / 0.38 (40624) hydrogen bonds : bond 0.05644 / 3.92 ( 2106) hydrogen bonds : angle 4.39279 / 3.25 ( 5758) metal coordination : bond 0.01133 / 0.56 ( 4) metal coordination : angle 2.01072 / 1.75 ( 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 287 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 287 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 82 ASP cc_start: 0.9009 (m-30) cc_final: 0.8802 (m-30) REVERT: A 121 MET cc_start: 0.8956 (mmp) cc_final: 0.8721 (mmm) REVERT: B 64 GLU cc_start: 0.9394 (mm-30) cc_final: 0.8704 (mm-30) REVERT: B 86 ASP cc_start: 0.8946 (m-30) cc_final: 0.8543 (m-30) REVERT: E 77 GLN cc_start: 0.9076 (mt0) cc_final: 0.8857 (mt0) REVERT: F 32 LYS cc_start: 0.9684 (tmtt) cc_final: 0.9480 (tmtt) REVERT: F 60 LYS cc_start: 0.9112 (tttt) cc_final: 0.8285 (tttt) REVERT: F 64 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8793 (mm-30) REVERT: F 75 GLU cc_start: 0.9272 (mt-10) cc_final: 0.9021 (pt0) REVERT: F 78 LYS cc_start: 0.9503 (mttt) cc_final: 0.9121 (mmtt) REVERT: F 85 MET cc_start: 0.9109 (mmm) cc_final: 0.8804 (mmm) REVERT: G 57 GLU cc_start: 0.9223 (tt0) cc_final: 0.8881 (tt0) REVERT: H 60 MET cc_start: 0.9445 (tpp) cc_final: 0.9069 (tpp) REVERT: H 71 PHE cc_start: 0.9324 (t80) cc_final: 0.9097 (t80) REVERT: H 94 GLU cc_start: 0.8975 (mp0) cc_final: 0.8471 (mp0) REVERT: I 423 CYS cc_start: 0.8922 (m) cc_final: 0.8468 (t) REVERT: L 1695 LEU cc_start: 0.9391 (tp) cc_final: 0.9142 (tp) REVERT: L 1961 SER cc_start: 0.6118 (p) cc_final: 0.5232 (t) REVERT: L 2063 THR cc_start: 0.8670 (m) cc_final: 0.8450 (p) REVERT: L 2151 MET cc_start: 0.8798 (mmp) cc_final: 0.8580 (tpp) REVERT: L 2232 ARG cc_start: 0.8771 (ptt180) cc_final: 0.8467 (ptt90) REVERT: N 498 MET cc_start: 0.8873 (tmm) cc_final: 0.8611 (tmm) REVERT: P 475 GLU cc_start: 0.8534 (tp30) cc_final: 0.8024 (tp30) REVERT: P 481 PHE cc_start: 0.8783 (t80) cc_final: 0.8503 (t80) REVERT: P 488 GLN cc_start: 0.8546 (mp10) cc_final: 0.8238 (mp10) REVERT: P 489 GLU cc_start: 0.8314 (tt0) cc_final: 0.8074 (tm-30) REVERT: P 492 CYS cc_start: 0.9180 (m) cc_final: 0.8704 (t) outliers start: 0 outliers final: 0 residues processed: 287 average time/residue: 0.1718 time to fit residues: 77.4409 Evaluate side-chains 217 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 217 time to evaluate : 0.925 ------------------------------------------------------------------------------- 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: 40.0000 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 376 optimal weight: 20.0000 chunk 240 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 193 optimal weight: 1.9990 chunk 315 optimal weight: 0.0170 chunk 359 optimal weight: 10.0000 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 69 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 39 ASN G 111 ASN H 110 HIS L1986 ASN L2018 HIS L2176 GLN ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.079494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.059150 restraints weight = 247645.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.060397 restraints weight = 159381.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.061205 restraints weight = 118822.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.061724 restraints weight = 97794.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.062090 restraints weight = 86037.536| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.3181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 28860 Z= 0.170 Angle : 0.602 9.216 40627 Z= 0.333 Chirality : 0.039 0.206 4952 Planarity : 0.004 0.061 4537 Dihedral : 23.214 76.108 6613 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.22 % Allowed : 2.00 % Favored : 97.78 % 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: 2.13 (0.14), residues: 3534 helix: 2.30 (0.11), residues: 2251 sheet: -0.01 (0.44), residues: 137 loop : -0.18 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 40 TYR 0.027 0.002 TYR F 89 PHE 0.019 0.001 PHE N 468 TRP 0.026 0.002 TRP L2050 HIS 0.006 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (28856) covalent geometry : angle 0.60217 / 0.33 (40624) hydrogen bonds : bond 0.04770 / 3.29 ( 2106) hydrogen bonds : angle 3.90724 / 2.90 ( 5758) metal coordination : bond 0.01292 / 0.64 ( 4) metal coordination : angle 0.77549 / 0.63 ( 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 255 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 252 time to evaluate : 0.710 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: 0.9407 (pt0) cc_final: 0.9110 (pt0) REVERT: A 82 ASP cc_start: 0.8989 (m-30) cc_final: 0.8771 (m-30) REVERT: B 64 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8745 (mm-30) REVERT: C 39 ASN cc_start: 0.7904 (p0) cc_final: 0.7613 (p0) REVERT: E 77 GLN cc_start: 0.9027 (mt0) cc_final: 0.8797 (mt0) REVERT: F 60 LYS cc_start: 0.9214 (tttt) cc_final: 0.8713 (tttp) REVERT: F 64 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8778 (mt-10) REVERT: F 75 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8992 (pt0) REVERT: F 78 LYS cc_start: 0.9548 (mttt) cc_final: 0.9229 (mmtm) REVERT: F 85 MET cc_start: 0.9189 (mmm) cc_final: 0.8956 (mmm) REVERT: G 39 ASN cc_start: 0.8029 (OUTLIER) cc_final: 0.7251 (p0) REVERT: G 57 GLU cc_start: 0.9196 (tt0) cc_final: 0.8886 (tt0) REVERT: H 60 MET cc_start: 0.9421 (tpp) cc_final: 0.9100 (tpp) REVERT: H 94 GLU cc_start: 0.8989 (mp0) cc_final: 0.8623 (mp0) REVERT: L 1674 MET cc_start: 0.8322 (tpp) cc_final: 0.7699 (tpp) REVERT: L 1695 LEU cc_start: 0.9346 (tp) cc_final: 0.9040 (tp) REVERT: L 2151 MET cc_start: 0.8810 (mmp) cc_final: 0.8602 (tpp) REVERT: L 2166 MET cc_start: 0.8714 (mtt) cc_final: 0.8376 (mtt) REVERT: L 2232 ARG cc_start: 0.8881 (ptt180) cc_final: 0.8577 (ptt90) REVERT: N 480 TYR cc_start: 0.8638 (t80) cc_final: 0.8293 (t80) REVERT: N 498 MET cc_start: 0.8792 (tmm) cc_final: 0.8517 (tmm) REVERT: P 481 PHE cc_start: 0.8781 (t80) cc_final: 0.8432 (t80) REVERT: P 488 GLN cc_start: 0.8590 (mp10) cc_final: 0.8323 (mp10) REVERT: P 489 GLU cc_start: 0.8364 (tt0) cc_final: 0.7854 (tm-30) REVERT: P 492 CYS cc_start: 0.9235 (m) cc_final: 0.8713 (t) outliers start: 3 outliers final: 0 residues processed: 255 average time/residue: 0.1682 time to fit residues: 69.7563 Evaluate side-chains 209 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 208 time to evaluate : 0.954 ------------------------------------------------------------------------------- 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: 2.9990 chunk 198 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 189 optimal weight: 0.7980 chunk 115 optimal weight: 50.0000 chunk 98 optimal weight: 1.9990 chunk 291 optimal weight: 3.9990 chunk 271 optimal weight: 20.0000 chunk 125 optimal weight: 8.9990 chunk 242 optimal weight: 9.9990 chunk 266 optimal weight: 9.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 69 GLN ** E 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.078906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.058191 restraints weight = 261239.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.059535 restraints weight = 165891.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.060358 restraints weight = 123512.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.060909 restraints weight = 102186.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.061250 restraints weight = 90343.957| |-----------------------------------------------------------------------------| r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7488 moved from start: 0.3726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 28860 Z= 0.166 Angle : 0.587 9.925 40627 Z= 0.325 Chirality : 0.039 0.168 4952 Planarity : 0.004 0.043 4537 Dihedral : 23.000 69.170 6613 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.07 % Allowed : 2.52 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.14), residues: 3534 helix: 2.49 (0.11), residues: 2252 sheet: 0.07 (0.44), residues: 144 loop : -0.11 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 73 TYR 0.017 0.001 TYR N 429 PHE 0.017 0.001 PHE H 66 TRP 0.016 0.002 TRP L2050 HIS 0.006 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (28856) covalent geometry : angle 0.58684 / 0.33 (40624) hydrogen bonds : bond 0.04397 / 3.04 ( 2106) hydrogen bonds : angle 3.78058 / 2.80 ( 5758) metal coordination : bond 0.01117 / 0.55 ( 4) metal coordination : angle 2.18450 / 1.36 ( 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 248 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 247 time to evaluate : 1.003 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: A 51 GLU cc_start: 0.9370 (pt0) cc_final: 0.9110 (pt0) REVERT: A 82 ASP cc_start: 0.8940 (m-30) cc_final: 0.8735 (m-30) REVERT: A 121 MET cc_start: 0.9283 (mmm) cc_final: 0.8900 (mmm) REVERT: B 28 GLN cc_start: 0.9063 (pp30) cc_final: 0.8795 (pp30) REVERT: B 64 GLU cc_start: 0.9304 (mm-30) cc_final: 0.8875 (mm-30) REVERT: E 121 MET cc_start: 0.8279 (mpp) cc_final: 0.7912 (mpp) REVERT: F 53 GLU cc_start: 0.9190 (mp0) cc_final: 0.8903 (mp0) REVERT: F 60 LYS cc_start: 0.9244 (tttt) cc_final: 0.8737 (tttp) REVERT: F 64 GLU cc_start: 0.9249 (mt-10) cc_final: 0.8778 (mt-10) REVERT: F 75 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8991 (pt0) REVERT: G 57 GLU cc_start: 0.9167 (tt0) cc_final: 0.8699 (tt0) REVERT: H 60 MET cc_start: 0.9384 (tpp) cc_final: 0.9107 (tpp) REVERT: H 94 GLU cc_start: 0.9086 (mp0) cc_final: 0.8502 (mp0) REVERT: L 1674 MET cc_start: 0.8280 (tpp) cc_final: 0.7776 (mmm) REVERT: L 1695 LEU cc_start: 0.9347 (tp) cc_final: 0.9083 (tp) REVERT: L 2151 MET cc_start: 0.8804 (mmp) cc_final: 0.8565 (tpp) REVERT: L 2166 MET cc_start: 0.8666 (mtt) cc_final: 0.8101 (mtt) REVERT: L 2232 ARG cc_start: 0.8844 (ptt180) cc_final: 0.8613 (ptt90) REVERT: N 480 TYR cc_start: 0.8664 (t80) cc_final: 0.8279 (t80) REVERT: N 498 MET cc_start: 0.8807 (tmm) cc_final: 0.8535 (tmm) REVERT: P 489 GLU cc_start: 0.8353 (tt0) cc_final: 0.7830 (tm-30) REVERT: P 492 CYS cc_start: 0.9150 (m) cc_final: 0.8721 (t) outliers start: 1 outliers final: 1 residues processed: 247 average time/residue: 0.1707 time to fit residues: 68.5675 Evaluate side-chains 210 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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: 10.0000 chunk 167 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 212 optimal weight: 0.8980 chunk 195 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 164 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 373 optimal weight: 9.9990 overall best weight: 2.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 76 HIS E 69 GLN E 77 GLN E 126 GLN L2018 HIS ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 506 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.078166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.057511 restraints weight = 263381.607| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.058989 restraints weight = 173907.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.059163 restraints weight = 136842.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.059809 restraints weight = 110274.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.059722 restraints weight = 105502.358| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 28860 Z= 0.166 Angle : 0.573 7.777 40627 Z= 0.321 Chirality : 0.039 0.179 4952 Planarity : 0.004 0.073 4537 Dihedral : 22.868 72.215 6613 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % 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: 2.49 (0.14), residues: 3534 helix: 2.61 (0.11), residues: 2247 sheet: 0.12 (0.44), residues: 138 loop : -0.11 (0.19), residues: 1149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 93 TYR 0.019 0.001 TYR F 52 PHE 0.023 0.001 PHE N 468 TRP 0.012 0.002 TRP L1686 HIS 0.007 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.17 (28856) covalent geometry : angle 0.57235 / 0.32 (40624) hydrogen bonds : bond 0.04153 / 2.87 ( 2106) hydrogen bonds : angle 3.72861 / 2.77 ( 5758) metal coordination : bond 0.01219 / 0.59 ( 4) metal coordination : angle 1.81521 / 1.22 ( 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 240 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.805 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: 0.9217 (pt0) cc_final: 0.9016 (pt0) REVERT: A 60 GLU cc_start: 0.9055 (pm20) cc_final: 0.8836 (pm20) REVERT: A 69 GLN cc_start: 0.9479 (tt0) cc_final: 0.9197 (tp40) REVERT: A 121 MET cc_start: 0.9344 (mmm) cc_final: 0.8992 (mmm) REVERT: B 28 GLN cc_start: 0.9062 (pp30) cc_final: 0.8814 (pp30) REVERT: B 64 GLU cc_start: 0.9268 (mm-30) cc_final: 0.8843 (mm-30) REVERT: F 53 GLU cc_start: 0.9171 (mp0) cc_final: 0.8866 (mp0) REVERT: F 60 LYS cc_start: 0.9302 (tttt) cc_final: 0.8357 (tptt) REVERT: F 64 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8801 (mm-30) REVERT: F 75 GLU cc_start: 0.9173 (mt-10) cc_final: 0.8963 (pt0) REVERT: G 57 GLU cc_start: 0.9098 (tt0) cc_final: 0.8816 (tt0) REVERT: H 60 MET cc_start: 0.9375 (tpp) cc_final: 0.9136 (tpp) REVERT: H 94 GLU cc_start: 0.9093 (mp0) cc_final: 0.8730 (mp0) REVERT: L 1674 MET cc_start: 0.8306 (tpp) cc_final: 0.7886 (tpt) REVERT: L 1695 LEU cc_start: 0.9372 (tp) cc_final: 0.9102 (tp) REVERT: L 2055 MET cc_start: 0.7972 (tpt) cc_final: 0.7748 (tpt) REVERT: L 2151 MET cc_start: 0.8784 (mmp) cc_final: 0.8550 (tpp) REVERT: L 2166 MET cc_start: 0.8784 (mtt) cc_final: 0.8573 (mtt) REVERT: L 2229 ASP cc_start: 0.8834 (t0) cc_final: 0.8372 (t0) REVERT: N 498 MET cc_start: 0.8778 (tmm) cc_final: 0.8553 (tmm) REVERT: P 475 GLU cc_start: 0.8876 (tp30) cc_final: 0.8643 (tm-30) REVERT: P 489 GLU cc_start: 0.8326 (tt0) cc_final: 0.7853 (tm-30) REVERT: P 492 CYS cc_start: 0.9223 (m) cc_final: 0.8772 (t) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1600 time to fit residues: 62.2098 Evaluate side-chains 198 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.965 ------------------------------------------------------------------------------- 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: 0.0270 chunk 347 optimal weight: 0.7980 chunk 158 optimal weight: 0.7980 chunk 192 optimal weight: 0.4980 chunk 202 optimal weight: 0.6980 chunk 206 optimal weight: 2.9990 chunk 196 optimal weight: 0.6980 chunk 59 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 124 optimal weight: 7.9990 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 69 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 451 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.078944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.058376 restraints weight = 261240.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.059699 restraints weight = 166248.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.060543 restraints weight = 123507.589| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.061084 restraints weight = 102193.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.061368 restraints weight = 90708.926| |-----------------------------------------------------------------------------| r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 28860 Z= 0.121 Angle : 0.536 11.120 40627 Z= 0.301 Chirality : 0.038 0.162 4952 Planarity : 0.004 0.075 4537 Dihedral : 22.661 68.625 6613 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.14), residues: 3534 helix: 2.78 (0.11), residues: 2243 sheet: 0.11 (0.44), residues: 135 loop : -0.01 (0.19), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L2232 TYR 0.017 0.001 TYR P 482 PHE 0.020 0.001 PHE N 468 TRP 0.010 0.001 TRP N 432 HIS 0.007 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00212 / 0.12 (28856) covalent geometry : angle 0.53599 / 0.30 (40624) hydrogen bonds : bond 0.03700 / 2.56 ( 2106) hydrogen bonds : angle 3.53172 / 2.61 ( 5758) metal coordination : bond 0.00744 / 0.39 ( 4) metal coordination : angle 2.11752 / 1.47 ( 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 244 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9381 (pt0) cc_final: 0.9147 (pt0) REVERT: A 69 GLN cc_start: 0.9521 (tt0) cc_final: 0.9197 (tp40) REVERT: A 82 ASP cc_start: 0.8937 (m-30) cc_final: 0.8728 (m-30) REVERT: A 106 GLU cc_start: 0.9287 (mm-30) cc_final: 0.8838 (mm-30) REVERT: A 121 MET cc_start: 0.9355 (mmm) cc_final: 0.9015 (mmm) REVERT: B 28 GLN cc_start: 0.9095 (pp30) cc_final: 0.8890 (pp30) REVERT: B 64 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8803 (mm-30) REVERT: B 75 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8823 (tm-30) REVERT: E 63 ILE cc_start: 0.8706 (mm) cc_final: 0.8464 (mm) REVERT: E 74 GLU cc_start: 0.8775 (tt0) cc_final: 0.8206 (tm-30) REVERT: E 94 GLN cc_start: 0.9253 (tt0) cc_final: 0.9015 (tp-100) REVERT: F 53 GLU cc_start: 0.9172 (mp0) cc_final: 0.8837 (mp0) REVERT: F 60 LYS cc_start: 0.9219 (tttt) cc_final: 0.8237 (tptt) REVERT: F 64 GLU cc_start: 0.9232 (mt-10) cc_final: 0.8734 (mm-30) REVERT: F 75 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8945 (pt0) REVERT: G 57 GLU cc_start: 0.9141 (tt0) cc_final: 0.8675 (tt0) REVERT: G 90 ASN cc_start: 0.9484 (m-40) cc_final: 0.9250 (m110) REVERT: H 60 MET cc_start: 0.9379 (tpp) cc_final: 0.9142 (tpp) REVERT: H 72 GLU cc_start: 0.9004 (pp20) cc_final: 0.8660 (pp20) REVERT: H 94 GLU cc_start: 0.9105 (mp0) cc_final: 0.8704 (mp0) REVERT: L 1674 MET cc_start: 0.8390 (tpp) cc_final: 0.7888 (tpt) REVERT: L 1695 LEU cc_start: 0.9353 (tp) cc_final: 0.9126 (tp) REVERT: L 2151 MET cc_start: 0.8856 (mmp) cc_final: 0.8601 (tpp) REVERT: L 2229 ASP cc_start: 0.8730 (t0) cc_final: 0.7959 (t0) REVERT: N 480 TYR cc_start: 0.8725 (t80) cc_final: 0.8521 (t80) REVERT: N 498 MET cc_start: 0.8777 (tmm) cc_final: 0.8482 (tmm) REVERT: P 475 GLU cc_start: 0.8815 (tp30) cc_final: 0.7991 (tm-30) REVERT: P 492 CYS cc_start: 0.9226 (m) cc_final: 0.8807 (t) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1665 time to fit residues: 65.4496 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 : 0.891 ------------------------------------------------------------------------------- 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: 7.9990 chunk 54 optimal weight: 0.9990 chunk 234 optimal weight: 40.0000 chunk 210 optimal weight: 9.9990 chunk 127 optimal weight: 0.9980 chunk 99 optimal weight: 20.0000 chunk 168 optimal weight: 10.0000 chunk 249 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 101 optimal weight: 20.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 69 GLN E 77 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2059 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L2248 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 451 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.075527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.054715 restraints weight = 265013.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.055980 restraints weight = 168858.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.056774 restraints weight = 126807.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.057288 restraints weight = 105572.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.057602 restraints weight = 94035.984| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.120 28860 Z= 0.261 Angle : 0.700 11.138 40627 Z= 0.384 Chirality : 0.041 0.224 4952 Planarity : 0.005 0.071 4537 Dihedral : 22.807 71.842 6613 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.08 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % 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: 2.06 (0.14), residues: 3534 helix: 2.24 (0.11), residues: 2259 sheet: -0.08 (0.42), residues: 144 loop : -0.21 (0.19), residues: 1131 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L2232 TYR 0.043 0.002 TYR P 482 PHE 0.047 0.003 PHE N 468 TRP 0.019 0.002 TRP N 507 HIS 0.013 0.002 HIS L2090 Details of bonding type rmsd/Z covalent geometry : bond 0.00504 / 0.26 (28856) covalent geometry : angle 0.69833 / 0.38 (40624) hydrogen bonds : bond 0.05411 / 3.73 ( 2106) hydrogen bonds : angle 4.06534 / 3.02 ( 5758) metal coordination : bond 0.03407 / 1.64 ( 4) metal coordination : angle 6.35947 / 4.81 ( 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 235 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 235 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 GLN cc_start: 0.9500 (tt0) cc_final: 0.9185 (tp40) REVERT: A 82 ASP cc_start: 0.8993 (m-30) cc_final: 0.8782 (m-30) REVERT: A 121 MET cc_start: 0.9406 (mmm) cc_final: 0.9193 (mmm) REVERT: B 28 GLN cc_start: 0.9102 (pp30) cc_final: 0.8901 (pp30) REVERT: B 64 GLU cc_start: 0.9350 (mm-30) cc_final: 0.8915 (mm-30) REVERT: B 89 TYR cc_start: 0.8758 (m-80) cc_final: 0.8514 (m-80) REVERT: E 121 MET cc_start: 0.8298 (mpp) cc_final: 0.8042 (mpp) REVERT: F 53 GLU cc_start: 0.9173 (mp0) cc_final: 0.8896 (mp0) REVERT: F 60 LYS cc_start: 0.9383 (tttt) cc_final: 0.8806 (tppt) REVERT: F 64 GLU cc_start: 0.9303 (mt-10) cc_final: 0.8897 (mt-10) REVERT: F 85 MET cc_start: 0.9195 (tpt) cc_final: 0.8761 (tpp) REVERT: F 89 TYR cc_start: 0.9489 (m-80) cc_final: 0.9096 (m-80) REVERT: G 57 GLU cc_start: 0.9039 (tt0) cc_final: 0.8732 (tt0) REVERT: H 94 GLU cc_start: 0.9040 (mp0) cc_final: 0.8666 (mp0) REVERT: L 1674 MET cc_start: 0.8508 (tpp) cc_final: 0.8159 (tpt) REVERT: L 1695 LEU cc_start: 0.9441 (tp) cc_final: 0.9125 (tp) REVERT: N 498 MET cc_start: 0.8702 (tmm) cc_final: 0.8401 (tmm) REVERT: P 480 GLU cc_start: 0.8031 (tp30) cc_final: 0.7822 (tp30) REVERT: P 488 GLN cc_start: 0.8829 (mp-120) cc_final: 0.8510 (mp10) REVERT: P 492 CYS cc_start: 0.9211 (m) cc_final: 0.8875 (m) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.1540 time to fit residues: 59.9950 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 : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 382 random chunks: chunk 32 optimal weight: 0.8980 chunk 152 optimal weight: 50.0000 chunk 251 optimal weight: 0.7980 chunk 221 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 279 optimal weight: 20.0000 chunk 359 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 348 optimal weight: 4.9990 chunk 134 optimal weight: 40.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS E 69 GLN E 94 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.075933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.055599 restraints weight = 247075.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.056786 restraints weight = 157377.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.057550 restraints weight = 117836.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.058040 restraints weight = 97556.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.058319 restraints weight = 86389.452| |-----------------------------------------------------------------------------| r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 moved from start: 0.5145 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= 0.152 Angle : 0.580 9.943 40627 Z= 0.324 Chirality : 0.039 0.173 4952 Planarity : 0.004 0.059 4537 Dihedral : 22.767 68.779 6613 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.44 (0.14), residues: 3534 helix: 2.58 (0.11), residues: 2249 sheet: 0.03 (0.44), residues: 135 loop : -0.13 (0.19), residues: 1150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 444 TYR 0.027 0.002 TYR P 482 PHE 0.033 0.002 PHE E 68 TRP 0.015 0.002 TRP N 432 HIS 0.008 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (28856) covalent geometry : angle 0.57950 / 0.32 (40624) hydrogen bonds : bond 0.03858 / 2.67 ( 2106) hydrogen bonds : angle 3.76472 / 2.78 ( 5758) metal coordination : bond 0.01313 / 0.65 ( 4) metal coordination : angle 3.00777 / 1.77 ( 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 232 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9394 (pt0) cc_final: 0.9134 (pt0) REVERT: A 69 GLN cc_start: 0.9513 (tt0) cc_final: 0.9182 (tp40) REVERT: A 82 ASP cc_start: 0.8968 (m-30) cc_final: 0.8745 (m-30) REVERT: A 121 MET cc_start: 0.9430 (mmm) cc_final: 0.9211 (mmm) REVERT: B 64 GLU cc_start: 0.9267 (mm-30) cc_final: 0.8831 (mm-30) REVERT: B 75 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8897 (tm-30) REVERT: B 89 TYR cc_start: 0.8873 (m-80) cc_final: 0.8594 (m-80) REVERT: C 40 TYR cc_start: 0.8970 (m-80) cc_final: 0.8714 (m-80) REVERT: E 74 GLU cc_start: 0.9117 (pp20) cc_final: 0.7975 (tt0) REVERT: F 32 LYS cc_start: 0.9569 (tmtt) cc_final: 0.9228 (tptp) REVERT: F 53 GLU cc_start: 0.9162 (mp0) cc_final: 0.8888 (mp0) REVERT: F 64 GLU cc_start: 0.9273 (mt-10) cc_final: 0.8787 (mm-30) REVERT: F 85 MET cc_start: 0.9219 (tpt) cc_final: 0.8840 (mmm) REVERT: F 89 TYR cc_start: 0.9389 (m-80) cc_final: 0.8920 (m-80) REVERT: G 57 GLU cc_start: 0.8969 (tt0) cc_final: 0.8630 (tt0) REVERT: G 100 ARG cc_start: 0.7563 (tmm-80) cc_final: 0.7352 (tmm-80) REVERT: H 72 GLU cc_start: 0.8964 (pp20) cc_final: 0.8627 (pp20) REVERT: L 1674 MET cc_start: 0.8481 (tpp) cc_final: 0.8122 (tpt) REVERT: L 1695 LEU cc_start: 0.9418 (tp) cc_final: 0.9177 (tp) REVERT: L 2231 MET cc_start: 0.7904 (mtt) cc_final: 0.7255 (mmm) REVERT: P 492 CYS cc_start: 0.9211 (m) cc_final: 0.8825 (t) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.1489 time to fit residues: 56.6936 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 : 0.628 ------------------------------------------------------------------------------- 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: 10.0000 chunk 124 optimal weight: 8.9990 chunk 191 optimal weight: 0.9980 chunk 281 optimal weight: 0.0770 chunk 209 optimal weight: 0.9990 chunk 164 optimal weight: 20.0000 chunk 321 optimal weight: 4.9990 chunk 227 optimal weight: 6.9990 chunk 367 optimal weight: 50.0000 chunk 172 optimal weight: 3.9990 chunk 264 optimal weight: 20.0000 overall best weight: 2.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS E 69 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 ASN L2194 ASN ** 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 = 0.3863 r_free = 0.3863 target = 0.075523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.055090 restraints weight = 254222.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.056285 restraints weight = 161071.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.057081 restraints weight = 120412.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.057576 restraints weight = 99347.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.057885 restraints weight = 88216.509| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.5413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 28860 Z= 0.163 Angle : 0.594 10.997 40627 Z= 0.330 Chirality : 0.039 0.174 4952 Planarity : 0.004 0.107 4537 Dihedral : 22.674 68.475 6613 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.14), residues: 3534 helix: 2.57 (0.11), residues: 2257 sheet: 0.06 (0.45), residues: 138 loop : -0.12 (0.19), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG I 448 TYR 0.022 0.002 TYR P 482 PHE 0.025 0.002 PHE P 481 TRP 0.012 0.002 TRP L1686 HIS 0.009 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (28856) covalent geometry : angle 0.59350 / 0.33 (40624) hydrogen bonds : bond 0.03957 / 2.73 ( 2106) hydrogen bonds : angle 3.79941 / 2.80 ( 5758) metal coordination : bond 0.01666 / 0.81 ( 4) metal coordination : angle 3.13722 / 1.86 ( 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 227 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 0.874 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9370 (pt0) cc_final: 0.9118 (pt0) REVERT: A 69 GLN cc_start: 0.9519 (tt0) cc_final: 0.9141 (tp40) REVERT: A 82 ASP cc_start: 0.8963 (m-30) cc_final: 0.8747 (m-30) REVERT: A 121 MET cc_start: 0.9447 (mmm) cc_final: 0.9236 (mmm) REVERT: B 28 GLN cc_start: 0.9086 (pp30) cc_final: 0.8856 (tm-30) REVERT: B 64 GLU cc_start: 0.9286 (mm-30) cc_final: 0.8847 (mm-30) REVERT: B 89 TYR cc_start: 0.8863 (m-80) cc_final: 0.8599 (m-80) REVERT: C 40 TYR cc_start: 0.8921 (m-80) cc_final: 0.8647 (m-80) REVERT: F 32 LYS cc_start: 0.9572 (tmtt) cc_final: 0.9214 (tptp) REVERT: F 53 GLU cc_start: 0.9156 (mp0) cc_final: 0.8886 (mp0) REVERT: F 64 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8833 (mm-30) REVERT: F 85 MET cc_start: 0.9192 (tpt) cc_final: 0.8805 (mmm) REVERT: F 89 TYR cc_start: 0.9382 (m-80) cc_final: 0.8890 (m-80) REVERT: G 57 GLU cc_start: 0.8994 (tt0) cc_final: 0.8685 (tt0) REVERT: G 100 ARG cc_start: 0.7676 (tmm-80) cc_final: 0.7363 (tmm-80) REVERT: H 94 GLU cc_start: 0.9086 (mp0) cc_final: 0.8820 (mp0) REVERT: L 1661 MET cc_start: 0.8088 (tmm) cc_final: 0.7803 (tmm) REVERT: L 1674 MET cc_start: 0.8482 (tpp) cc_final: 0.8151 (tpt) REVERT: L 1695 LEU cc_start: 0.9422 (tp) cc_final: 0.9190 (tp) REVERT: L 2231 MET cc_start: 0.7955 (mtt) cc_final: 0.7648 (mmm) REVERT: P 476 GLU cc_start: 0.8251 (mp0) cc_final: 0.7725 (mp0) REVERT: P 492 CYS cc_start: 0.9236 (m) cc_final: 0.8839 (t) outliers start: 0 outliers final: 0 residues processed: 227 average time/residue: 0.1504 time to fit residues: 56.7384 Evaluate side-chains 196 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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: 8.9990 chunk 207 optimal weight: 0.6980 chunk 76 optimal weight: 0.8980 chunk 292 optimal weight: 0.3980 chunk 139 optimal weight: 20.0000 chunk 206 optimal weight: 2.9990 chunk 300 optimal weight: 9.9990 chunk 122 optimal weight: 6.9990 chunk 380 optimal weight: 20.0000 chunk 285 optimal weight: 9.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS E 69 GLN ** 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 = 0.3872 r_free = 0.3872 target = 0.075842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.055467 restraints weight = 254880.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.056700 restraints weight = 160894.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.057500 restraints weight = 119536.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.058012 restraints weight = 98775.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.058300 restraints weight = 87483.548| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7564 moved from start: 0.5573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 28860 Z= 0.133 Angle : 0.559 9.362 40627 Z= 0.314 Chirality : 0.039 0.185 4952 Planarity : 0.004 0.047 4537 Dihedral : 22.578 68.074 6613 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.07 % Allowed : 0.22 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.66 (0.15), residues: 3534 helix: 2.73 (0.11), residues: 2263 sheet: 0.12 (0.45), residues: 138 loop : -0.04 (0.19), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 36 TYR 0.025 0.002 TYR P 482 PHE 0.021 0.001 PHE H 71 TRP 0.013 0.002 TRP N 432 HIS 0.007 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (28856) covalent geometry : angle 0.55884 / 0.31 (40624) hydrogen bonds : bond 0.03557 / 2.45 ( 2106) hydrogen bonds : angle 3.66315 / 2.70 ( 5758) metal coordination : bond 0.01051 / 0.53 ( 4) metal coordination : angle 2.73767 / 1.65 ( 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 227 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 226 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 GLU cc_start: 0.9373 (pt0) cc_final: 0.9110 (pt0) REVERT: A 69 GLN cc_start: 0.9516 (tt0) cc_final: 0.9128 (tp40) REVERT: A 82 ASP cc_start: 0.8926 (m-30) cc_final: 0.8710 (m-30) REVERT: A 121 MET cc_start: 0.9439 (mmm) cc_final: 0.9238 (mmm) REVERT: B 28 GLN cc_start: 0.9078 (pp30) cc_final: 0.8678 (tm-30) REVERT: B 64 GLU cc_start: 0.9257 (mm-30) cc_final: 0.8832 (mm-30) REVERT: B 75 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8898 (tm-30) REVERT: B 89 TYR cc_start: 0.8814 (m-80) cc_final: 0.8530 (m-80) REVERT: C 40 TYR cc_start: 0.8909 (m-80) cc_final: 0.8680 (m-80) REVERT: C 96 LYS cc_start: 0.9401 (ptpp) cc_final: 0.9089 (ptmm) REVERT: E 47 VAL cc_start: 0.8692 (t) cc_final: 0.8431 (t) REVERT: F 32 LYS cc_start: 0.9572 (tmtt) cc_final: 0.9186 (tptp) REVERT: F 53 GLU cc_start: 0.9142 (mp0) cc_final: 0.8858 (mp0) REVERT: F 64 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8834 (mm-30) REVERT: F 85 MET cc_start: 0.9189 (tpt) cc_final: 0.8701 (mmm) REVERT: F 89 TYR cc_start: 0.9375 (m-80) cc_final: 0.8824 (m-80) REVERT: G 42 GLU cc_start: 0.8986 (pm20) cc_final: 0.8729 (pm20) REVERT: G 57 GLU cc_start: 0.8991 (tt0) cc_final: 0.8673 (tt0) REVERT: G 100 ARG cc_start: 0.7717 (tmm-80) cc_final: 0.7398 (tmm-80) REVERT: H 60 MET cc_start: 0.9473 (tpp) cc_final: 0.9171 (tpp) REVERT: H 72 GLU cc_start: 0.8862 (pp20) cc_final: 0.8527 (pp20) REVERT: H 94 GLU cc_start: 0.9076 (mp0) cc_final: 0.8806 (mp0) REVERT: L 1661 MET cc_start: 0.7985 (tmm) cc_final: 0.7703 (tmm) REVERT: L 1674 MET cc_start: 0.8386 (tpp) cc_final: 0.7943 (tpt) REVERT: L 1695 LEU cc_start: 0.9397 (tp) cc_final: 0.9125 (tp) REVERT: L 2231 MET cc_start: 0.7956 (mtt) cc_final: 0.7497 (mmm) REVERT: N 429 TYR cc_start: 0.8480 (p90) cc_final: 0.8212 (p90) REVERT: P 475 GLU cc_start: 0.8707 (tp30) cc_final: 0.8464 (tp30) REVERT: P 476 GLU cc_start: 0.8180 (mp0) cc_final: 0.7893 (pm20) REVERT: P 492 CYS cc_start: 0.9232 (m) cc_final: 0.8823 (t) outliers start: 1 outliers final: 0 residues processed: 226 average time/residue: 0.1633 time to fit residues: 60.7456 Evaluate side-chains 194 residues out of total 3161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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: 7.9990 chunk 195 optimal weight: 0.7980 chunk 252 optimal weight: 0.0010 chunk 139 optimal weight: 5.9990 chunk 287 optimal weight: 10.0000 chunk 214 optimal weight: 0.9990 chunk 107 optimal weight: 40.0000 chunk 165 optimal weight: 7.9990 chunk 194 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 69 GLN F 26 ASN 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 = 0.3881 r_free = 0.3881 target = 0.076363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.056474 restraints weight = 265070.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.057427 restraints weight = 175751.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.057392 restraints weight = 151132.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.057668 restraints weight = 127338.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.057719 restraints weight = 111111.159| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 28860 Z= 0.125 Angle : 0.556 10.536 40627 Z= 0.310 Chirality : 0.039 0.187 4952 Planarity : 0.004 0.112 4537 Dihedral : 22.458 67.418 6613 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % 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: 2.78 (0.15), residues: 3534 helix: 2.84 (0.11), residues: 2254 sheet: -0.00 (0.44), residues: 148 loop : 0.03 (0.20), residues: 1132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG I 448 TYR 0.025 0.001 TYR E 55 PHE 0.031 0.001 PHE N 468 TRP 0.010 0.001 TRP L1670 HIS 0.007 0.001 HIS L2248 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.12 (28856) covalent geometry : angle 0.55597 / 0.31 (40624) hydrogen bonds : bond 0.03491 / 2.41 ( 2106) hydrogen bonds : angle 3.57098 / 2.62 ( 5758) metal coordination : bond 0.00789 / 0.41 ( 4) metal coordination : angle 2.20241 / 1.35 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5858.34 seconds wall clock time: 100 minutes 51.09 seconds (6051.09 seconds total)