Starting phenix.real_space_refine on Fri Mar 6 01:50:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uig_26545/03_2026/7uig_26545.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uig_26545/03_2026/7uig_26545.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uig_26545/03_2026/7uig_26545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uig_26545/03_2026/7uig_26545.map" model { file = "/net/cci-nas-00/data/ceres_data/7uig_26545/03_2026/7uig_26545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uig_26545/03_2026/7uig_26545.cif" } resolution = 4.3 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 107 5.16 5 C 17575 2.51 5 N 4634 2.21 5 O 5264 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 27580 Number of models: 1 Model: "" Number of chains: 17 Chain: "a" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3008 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 356} Chain breaks: 3 Chain: "d" Number of atoms: 1388 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1388 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 6, 'TRANS': 164} Chain breaks: 2 Chain: "f" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1407 Classifications: {'peptide': 169} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 159} Chain breaks: 2 Chain: "g" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1409 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 11, 'TRANS': 157} Chain breaks: 4 Chain: "h" Number of atoms: 1126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1126 Classifications: {'peptide': 136} Link IDs: {'PTRANS': 5, 'TRANS': 130} Chain breaks: 1 Chain: "i" Number of atoms: 709 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 709 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain breaks: 1 Chain: "j" Number of atoms: 1173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1173 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 7, 'TRANS': 138} Chain breaks: 1 Chain: "k" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 876 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 103} Chain breaks: 1 Chain: "n" Number of atoms: 5139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 625, 5139 Classifications: {'peptide': 625} Link IDs: {'PTRANS': 18, 'TRANS': 606} Chain breaks: 6 Chain: "q" Number of atoms: 4182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 515, 4182 Classifications: {'peptide': 515} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 497} Chain breaks: 4 Chain: "r" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 253, 1995 Classifications: {'peptide': 253} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 242} Chain breaks: 1 Chain: "s" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 657 Classifications: {'peptide': 81} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 77} Chain breaks: 1 Chain: "t" Number of atoms: 1609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1609 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 202} Chain: "u" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 978 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain breaks: 2 Chain: "v" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 869 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 1, 'TRANS': 107} Chain breaks: 1 Chain: "w" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 871 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 95} Chain breaks: 1 Chain: "z" Number of atoms: 184 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 184 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 6, 'TRANS': 18} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N PRO z 8 " occ=0.70 ... (5 atoms not shown) pdb=" CD PRO z 8 " occ=0.70 residue: pdb=" N SER z 9 " occ=0.70 ... (4 atoms not shown) pdb=" OG SER z 9 " occ=0.70 Time building chain proxies: 5.93, per 1000 atoms: 0.22 Number of scatterers: 27580 At special positions: 0 Unit cell: (158.7, 253.92, 230.46, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 107 16.00 O 5264 8.00 N 4634 7.00 C 17575 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.49 Conformation dependent library (CDL) restraints added in 1.1 seconds 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6566 Finding SS restraints... Secondary structure from input PDB file: 118 helices and 17 sheets defined 57.3% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.80 Creating SS restraints... Processing helix chain 'a' and resid 6 through 22 Processing helix chain 'a' and resid 27 through 38 Processing helix chain 'a' and resid 102 through 110 Processing helix chain 'a' and resid 114 through 131 Processing helix chain 'a' and resid 163 through 182 removed outlier: 3.801A pdb=" N SER a 172 " --> pdb=" O PHE a 168 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N HIS a 173 " --> pdb=" O THR a 169 " (cutoff:3.500A) Processing helix chain 'a' and resid 279 through 281 No H-bonds generated for 'chain 'a' and resid 279 through 281' Processing helix chain 'a' and resid 297 through 305 Processing helix chain 'a' and resid 331 through 335 Processing helix chain 'a' and resid 336 through 351 removed outlier: 4.257A pdb=" N GLU a 340 " --> pdb=" O ASP a 336 " (cutoff:3.500A) Processing helix chain 'a' and resid 351 through 361 Processing helix chain 'a' and resid 550 through 566 Processing helix chain 'd' and resid 32 through 40 removed outlier: 3.845A pdb=" N VAL d 40 " --> pdb=" O LYS d 36 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 62 removed outlier: 4.029A pdb=" N GLU d 44 " --> pdb=" O VAL d 40 " (cutoff:3.500A) Processing helix chain 'd' and resid 66 through 89 removed outlier: 3.560A pdb=" N ALA d 70 " --> pdb=" O ASN d 66 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA d 88 " --> pdb=" O VAL d 84 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU d 89 " --> pdb=" O LYS d 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 92 through 128 Processing helix chain 'd' and resid 132 through 148 removed outlier: 3.520A pdb=" N ILE d 148 " --> pdb=" O GLN d 144 " (cutoff:3.500A) Processing helix chain 'd' and resid 149 through 165 removed outlier: 3.680A pdb=" N LEU d 153 " --> pdb=" O ASN d 149 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS d 162 " --> pdb=" O THR d 158 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N PHE d 163 " --> pdb=" O LYS d 159 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS d 165 " --> pdb=" O SER d 161 " (cutoff:3.500A) Processing helix chain 'd' and resid 184 through 191 Processing helix chain 'd' and resid 191 through 199 removed outlier: 4.359A pdb=" N MET d 195 " --> pdb=" O GLY d 191 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 20 Processing helix chain 'f' and resid 26 through 33 removed outlier: 4.388A pdb=" N GLU f 33 " --> pdb=" O ASP f 29 " (cutoff:3.500A) Processing helix chain 'f' and resid 41 through 56 removed outlier: 3.718A pdb=" N VAL f 45 " --> pdb=" O SER f 41 " (cutoff:3.500A) Processing helix chain 'f' and resid 89 through 97 removed outlier: 3.876A pdb=" N TYR f 97 " --> pdb=" O ILE f 93 " (cutoff:3.500A) Processing helix chain 'f' and resid 97 through 108 removed outlier: 3.660A pdb=" N MET f 101 " --> pdb=" O TYR f 97 " (cutoff:3.500A) Processing helix chain 'f' and resid 166 through 192 Processing helix chain 'g' and resid 18 through 23 removed outlier: 3.728A pdb=" N PHE g 23 " --> pdb=" O VAL g 20 " (cutoff:3.500A) Processing helix chain 'g' and resid 24 through 43 Proline residue: g 32 - end of helix Processing helix chain 'g' and resid 112 through 140 Processing helix chain 'g' and resid 141 through 143 No H-bonds generated for 'chain 'g' and resid 141 through 143' Processing helix chain 'g' and resid 144 through 166 removed outlier: 3.641A pdb=" N GLU g 149 " --> pdb=" O GLU g 145 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N ASN g 150 " --> pdb=" O ARG g 146 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLU g 164 " --> pdb=" O HIS g 160 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N TYR g 165 " --> pdb=" O LEU g 161 " (cutoff:3.500A) Processing helix chain 'g' and resid 170 through 213 Processing helix chain 'h' and resid 31 through 55 Processing helix chain 'h' and resid 61 through 86 Processing helix chain 'h' and resid 86 through 93 Processing helix chain 'h' and resid 102 through 115 removed outlier: 6.453A pdb=" N SER h 108 " --> pdb=" O THR h 104 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU h 109 " --> pdb=" O SER h 105 " (cutoff:3.500A) Processing helix chain 'h' and resid 119 through 134 Processing helix chain 'h' and resid 144 through 170 removed outlier: 3.818A pdb=" N HIS h 170 " --> pdb=" O GLU h 166 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 79 Processing helix chain 'i' and resid 83 through 108 removed outlier: 3.830A pdb=" N ASN i 108 " --> pdb=" O LEU i 104 " (cutoff:3.500A) Processing helix chain 'i' and resid 108 through 115 removed outlier: 3.628A pdb=" N LYS i 112 " --> pdb=" O ASN i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 120 through 148 removed outlier: 3.500A pdb=" N GLN i 148 " --> pdb=" O TYR i 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 38 Processing helix chain 'j' and resid 42 through 68 Processing helix chain 'j' and resid 80 through 87 Processing helix chain 'j' and resid 94 through 133 Processing helix chain 'j' and resid 136 through 148 Processing helix chain 'k' and resid 3 through 40 removed outlier: 3.523A pdb=" N GLN k 7 " --> pdb=" O PRO k 3 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY k 35 " --> pdb=" O THR k 31 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLU k 36 " --> pdb=" O PHE k 32 " (cutoff:3.500A) Processing helix chain 'k' and resid 44 through 77 removed outlier: 3.531A pdb=" N PHE k 48 " --> pdb=" O VAL k 44 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLU k 49 " --> pdb=" O LYS k 45 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASN k 50 " --> pdb=" O PRO k 46 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N SER k 62 " --> pdb=" O ARG k 58 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N THR k 63 " --> pdb=" O LEU k 59 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU k 75 " --> pdb=" O GLN k 71 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL k 77 " --> pdb=" O LEU k 73 " (cutoff:3.500A) Processing helix chain 'k' and resid 89 through 110 removed outlier: 3.996A pdb=" N ASP k 94 " --> pdb=" O ALA k 90 " (cutoff:3.500A) removed outlier: 5.649A pdb=" N THR k 95 " --> pdb=" O LEU k 91 " (cutoff:3.500A) Processing helix chain 'k' and resid 111 through 114 removed outlier: 3.718A pdb=" N SER k 114 " --> pdb=" O PRO k 111 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 111 through 114' Processing helix chain 'n' and resid 91 through 117 Processing helix chain 'n' and resid 122 through 154 removed outlier: 3.613A pdb=" N LYS n 126 " --> pdb=" O PRO n 122 " (cutoff:3.500A) Processing helix chain 'n' and resid 161 through 191 Processing helix chain 'n' and resid 241 through 260 Processing helix chain 'n' and resid 263 through 267 Processing helix chain 'n' and resid 344 through 359 Processing helix chain 'n' and resid 365 through 393 removed outlier: 3.700A pdb=" N ASN n 391 " --> pdb=" O LEU n 387 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N GLY n 392 " --> pdb=" O LYS n 388 " (cutoff:3.500A) Processing helix chain 'n' and resid 444 through 450 Processing helix chain 'n' and resid 459 through 486 removed outlier: 6.468A pdb=" N GLU n 465 " --> pdb=" O VAL n 461 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLY n 466 " --> pdb=" O SER n 462 " (cutoff:3.500A) Processing helix chain 'n' and resid 530 through 542 Processing helix chain 'n' and resid 545 through 571 Processing helix chain 'n' and resid 684 through 711 removed outlier: 4.010A pdb=" N LEU n 696 " --> pdb=" O GLN n 692 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ASN n 697 " --> pdb=" O ARG n 693 " (cutoff:3.500A) Processing helix chain 'n' and resid 719 through 725 Processing helix chain 'n' and resid 729 through 734 Processing helix chain 'n' and resid 749 through 753 Processing helix chain 'n' and resid 756 through 760 removed outlier: 3.853A pdb=" N LEU n 759 " --> pdb=" O SER n 756 " (cutoff:3.500A) Processing helix chain 'n' and resid 788 through 792 Processing helix chain 'n' and resid 795 through 798 Processing helix chain 'n' and resid 818 through 820 No H-bonds generated for 'chain 'n' and resid 818 through 820' Processing helix chain 'n' and resid 821 through 832 Processing helix chain 'q' and resid 91 through 97 Processing helix chain 'q' and resid 98 through 111 Proline residue: q 104 - end of helix Processing helix chain 'q' and resid 120 through 133 Processing helix chain 'q' and resid 198 through 226 removed outlier: 3.736A pdb=" N GLU q 217 " --> pdb=" O LEU q 213 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N SER q 218 " --> pdb=" O ALA q 214 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LEU q 220 " --> pdb=" O ASN q 216 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA q 221 " --> pdb=" O GLU q 217 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU q 222 " --> pdb=" O SER q 218 " (cutoff:3.500A) Processing helix chain 'q' and resid 226 through 233 removed outlier: 3.823A pdb=" N SER q 230 " --> pdb=" O SER q 226 " (cutoff:3.500A) Processing helix chain 'q' and resid 233 through 239 removed outlier: 4.450A pdb=" N SER q 239 " --> pdb=" O SER q 235 " (cutoff:3.500A) Processing helix chain 'q' and resid 242 through 249 removed outlier: 3.546A pdb=" N VAL q 249 " --> pdb=" O LEU q 245 " (cutoff:3.500A) Processing helix chain 'q' and resid 265 through 316 removed outlier: 4.437A pdb=" N TYR q 269 " --> pdb=" O THR q 265 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE q 270 " --> pdb=" O LYS q 266 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N GLU q 271 " --> pdb=" O LYS q 267 " (cutoff:3.500A) Processing helix chain 'q' and resid 341 through 345 removed outlier: 3.818A pdb=" N GLY q 345 " --> pdb=" O GLU q 342 " (cutoff:3.500A) Processing helix chain 'q' and resid 380 through 386 Processing helix chain 'q' and resid 417 through 422 Processing helix chain 'q' and resid 424 through 450 Processing helix chain 'q' and resid 451 through 455 removed outlier: 4.946A pdb=" N SER q 454 " --> pdb=" O LEU q 451 " (cutoff:3.500A) Processing helix chain 'q' and resid 497 through 526 removed outlier: 3.639A pdb=" N SER q 526 " --> pdb=" O SER q 522 " (cutoff:3.500A) Processing helix chain 'q' and resid 541 through 566 removed outlier: 4.459A pdb=" N ILE q 545 " --> pdb=" O ILE q 541 " (cutoff:3.500A) Processing helix chain 'q' and resid 593 through 605 removed outlier: 3.567A pdb=" N THR q 597 " --> pdb=" O ASP q 593 " (cutoff:3.500A) Processing helix chain 'q' and resid 606 through 611 Processing helix chain 'q' and resid 666 through 686 Processing helix chain 'r' and resid 15 through 28 Processing helix chain 'r' and resid 71 through 75 Processing helix chain 'r' and resid 86 through 93 removed outlier: 3.607A pdb=" N ILE r 89 " --> pdb=" O ASN r 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 101 through 109 Processing helix chain 'r' and resid 199 through 208 Processing helix chain 'r' and resid 225 through 227 No H-bonds generated for 'chain 'r' and resid 225 through 227' Processing helix chain 'r' and resid 264 through 282 removed outlier: 3.865A pdb=" N ILE r 268 " --> pdb=" O ASP r 264 " (cutoff:3.500A) Processing helix chain 's' and resid 41 through 47 Processing helix chain 's' and resid 64 through 68 Processing helix chain 's' and resid 134 through 148 Processing helix chain 't' and resid 15 through 24 Processing helix chain 't' and resid 83 through 87 removed outlier: 3.873A pdb=" N ILE t 87 " --> pdb=" O ALA t 84 " (cutoff:3.500A) Processing helix chain 't' and resid 88 through 95 removed outlier: 3.607A pdb=" N VAL t 92 " --> pdb=" O PRO t 88 " (cutoff:3.500A) Processing helix chain 't' and resid 103 through 111 removed outlier: 3.545A pdb=" N ILE t 107 " --> pdb=" O SER t 103 " (cutoff:3.500A) Processing helix chain 't' and resid 162 through 177 removed outlier: 3.647A pdb=" N ILE t 177 " --> pdb=" O HIS t 173 " (cutoff:3.500A) Processing helix chain 't' and resid 195 through 209 Processing helix chain 'u' and resid 3 through 30 Processing helix chain 'u' and resid 51 through 78 Processing helix chain 'u' and resid 86 through 138 removed outlier: 3.600A pdb=" N GLN u 90 " --> pdb=" O SER u 86 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 29 Processing helix chain 'v' and resid 46 through 87 removed outlier: 4.072A pdb=" N ALA v 51 " --> pdb=" O GLU v 47 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLN v 87 " --> pdb=" O TRP v 83 " (cutoff:3.500A) Processing helix chain 'v' and resid 101 through 119 Processing helix chain 'w' and resid 21 through 33 Processing helix chain 'w' and resid 35 through 45 removed outlier: 3.628A pdb=" N GLN w 45 " --> pdb=" O TYR w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 45 through 51 removed outlier: 4.091A pdb=" N TRP w 49 " --> pdb=" O GLN w 45 " (cutoff:3.500A) Processing helix chain 'w' and resid 51 through 61 removed outlier: 4.167A pdb=" N LYS w 55 " --> pdb=" O SER w 51 " (cutoff:3.500A) Processing helix chain 'w' and resid 62 through 66 removed outlier: 4.136A pdb=" N ASN w 66 " --> pdb=" O TYR w 63 " (cutoff:3.500A) Processing helix chain 'w' and resid 68 through 73 removed outlier: 3.530A pdb=" N ILE w 73 " --> pdb=" O SER w 70 " (cutoff:3.500A) Processing helix chain 'w' and resid 76 through 89 removed outlier: 3.933A pdb=" N PHE w 80 " --> pdb=" O PRO w 76 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS w 83 " --> pdb=" O LEU w 79 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N MET w 89 " --> pdb=" O LEU w 85 " (cutoff:3.500A) Processing helix chain 'w' and resid 105 through 126 Proline residue: w 115 - end of helix Processing sheet with id=AA1, first strand: chain 'a' and resid 41 through 46 removed outlier: 6.789A pdb=" N VAL a 62 " --> pdb=" O LEU a 79 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N LEU a 79 " --> pdb=" O VAL a 62 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N ASP a 64 " --> pdb=" O VAL a 77 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N VAL a 77 " --> pdb=" O ASP a 64 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ASP a 66 " --> pdb=" O GLN a 75 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'a' and resid 187 through 190 removed outlier: 6.381A pdb=" N ILE a 198 " --> pdb=" O LYS a 214 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS a 214 " --> pdb=" O ILE a 198 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N ILE a 200 " --> pdb=" O LEU a 212 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 252 through 258 current: chain 'a' and resid 322 through 329 Processing sheet with id=AA3, first strand: chain 'a' and resid 227 through 229 Processing sheet with id=AA4, first strand: chain 'a' and resid 232 through 234 removed outlier: 3.652A pdb=" N SER a 239 " --> pdb=" O SER a 234 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'a' and resid 312 through 316 Processing sheet with id=AA6, first strand: chain 'f' and resid 113 through 121 removed outlier: 3.887A pdb=" N GLN f 131 " --> pdb=" O GLU f 114 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL f 127 " --> pdb=" O SER f 118 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL f 120 " --> pdb=" O PHE f 125 " (cutoff:3.500A) removed outlier: 7.296A pdb=" N PHE f 125 " --> pdb=" O VAL f 120 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N TRP f 126 " --> pdb=" O TYR f 154 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N TYR f 154 " --> pdb=" O TRP f 126 " (cutoff:3.500A) removed outlier: 8.038A pdb=" N ILE f 128 " --> pdb=" O ASP f 152 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ASP f 152 " --> pdb=" O ILE f 128 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N LYS f 130 " --> pdb=" O LEU f 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 193 through 195 Processing sheet with id=AA8, first strand: chain 'g' and resid 76 through 78 Processing sheet with id=AA9, first strand: chain 'n' and resid 269 through 272 removed outlier: 6.066A pdb=" N SER n 289 " --> pdb=" O PHE n 299 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N PHE n 299 " --> pdb=" O SER n 289 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'n' and resid 400 through 405 removed outlier: 3.786A pdb=" N GLY n 425 " --> pdb=" O TYR n 415 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N LYS n 426 " --> pdb=" O ASP n 443 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'n' and resid 490 through 491 Processing sheet with id=AB3, first strand: chain 'n' and resid 575 through 577 removed outlier: 4.871A pdb=" N PHE n 626 " --> pdb=" O SER n 577 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N ILE n 655 " --> pdb=" O LEU n 670 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LEU n 670 " --> pdb=" O ILE n 655 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS n 657 " --> pdb=" O LYS n 668 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'n' and resid 715 through 717 removed outlier: 6.841A pdb=" N SER n 766 " --> pdb=" O LYS n 783 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N LYS n 783 " --> pdb=" O SER n 766 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'q' and resid 321 through 326 removed outlier: 4.504A pdb=" N VAL q 321 " --> pdb=" O LYS q 338 " (cutoff:3.500A) removed outlier: 14.007A pdb=" N LYS q 333 " --> pdb=" O ASN q 359 " (cutoff:3.500A) removed outlier: 10.211A pdb=" N ASN q 359 " --> pdb=" O LYS q 333 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LEU q 335 " --> pdb=" O ILE q 357 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'q' and resid 403 through 408 removed outlier: 6.011A pdb=" N LEU q 405 " --> pdb=" O THR q 395 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N THR q 395 " --> pdb=" O LEU q 405 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS q 464 " --> pdb=" O GLU q 460 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'q' and resid 574 through 578 Processing sheet with id=AB8, first strand: chain 'r' and resid 2 through 12 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 2 through 12 current: chain 'r' and resid 64 through 68 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 181 through 195 current: chain 'r' and resid 229 through 239 WARNING: can't find start of bonding for strands! previous: chain 'r' and resid 242 through 245 current: chain 't' and resid 56 through 62 WARNING: can't find start of bonding for strands! previous: chain 't' and resid 76 through 81 current: chain 't' and resid 135 through 143 removed outlier: 7.048A pdb=" N THR t 136 " --> pdb=" O LEU t 155 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N LEU t 155 " --> pdb=" O THR t 136 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ARG t 138 " --> pdb=" O ILE t 153 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE t 153 " --> pdb=" O ARG t 138 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N VAL t 140 " --> pdb=" O LEU t 151 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU t 151 " --> pdb=" O VAL t 140 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N LEU t 142 " --> pdb=" O LYS t 149 " (cutoff:3.500A) 1633 hydrogen bonds defined for protein. 4740 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.01 Time building geometry restraints manager: 3.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5275 1.33 - 1.45: 6402 1.45 - 1.57: 16178 1.57 - 1.70: 1 1.70 - 1.82: 183 Bond restraints: 28039 Sorted by residual: bond pdb=" CZ ARG a 189 " pdb=" NH2 ARG a 189 " ideal model delta sigma weight residual 1.330 1.292 0.038 1.30e-02 5.92e+03 8.60e+00 bond pdb=" CZ ARG a 349 " pdb=" NH2 ARG a 349 " ideal model delta sigma weight residual 1.330 1.294 0.036 1.30e-02 5.92e+03 7.76e+00 bond pdb=" CZ ARG a 33 " pdb=" NH2 ARG a 33 " ideal model delta sigma weight residual 1.330 1.296 0.034 1.30e-02 5.92e+03 6.99e+00 bond pdb=" ND1 HIS a 536 " pdb=" CE1 HIS a 536 " ideal model delta sigma weight residual 1.321 1.347 -0.026 1.00e-02 1.00e+04 6.76e+00 bond pdb=" CD2 HIS a 173 " pdb=" NE2 HIS a 173 " ideal model delta sigma weight residual 1.374 1.401 -0.027 1.10e-02 8.26e+03 6.04e+00 ... (remaining 28034 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.49: 36924 2.49 - 4.99: 823 4.99 - 7.48: 77 7.48 - 9.98: 10 9.98 - 12.47: 3 Bond angle restraints: 37837 Sorted by residual: angle pdb=" CA PRO g 16 " pdb=" N PRO g 16 " pdb=" CD PRO g 16 " ideal model delta sigma weight residual 112.00 104.16 7.84 1.40e+00 5.10e-01 3.14e+01 angle pdb=" C PRO a 298 " pdb=" N ILE a 299 " pdb=" CA ILE a 299 " ideal model delta sigma weight residual 120.56 127.50 -6.94 1.26e+00 6.30e-01 3.03e+01 angle pdb=" OE1 GLN a 529 " pdb=" CD GLN a 529 " pdb=" NE2 GLN a 529 " ideal model delta sigma weight residual 122.60 117.16 5.44 1.00e+00 1.00e+00 2.96e+01 angle pdb=" OD1 ASN a 324 " pdb=" CG ASN a 324 " pdb=" ND2 ASN a 324 " ideal model delta sigma weight residual 122.60 117.49 5.11 1.00e+00 1.00e+00 2.61e+01 angle pdb=" C LYS a 22 " pdb=" N PRO a 23 " pdb=" CA PRO a 23 " ideal model delta sigma weight residual 119.56 124.73 -5.17 1.02e+00 9.61e-01 2.56e+01 ... (remaining 37832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.44: 15716 17.44 - 34.87: 1361 34.87 - 52.31: 177 52.31 - 69.75: 30 69.75 - 87.18: 16 Dihedral angle restraints: 17300 sinusoidal: 7267 harmonic: 10033 Sorted by residual: dihedral pdb=" CA SER a 295 " pdb=" C SER a 295 " pdb=" N SER a 296 " pdb=" CA SER a 296 " ideal model delta harmonic sigma weight residual 180.00 154.70 25.30 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" CA ASN j 92 " pdb=" C ASN j 92 " pdb=" N PRO j 93 " pdb=" CA PRO j 93 " ideal model delta harmonic sigma weight residual -180.00 -156.41 -23.59 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA SER q 252 " pdb=" C SER q 252 " pdb=" N SER q 253 " pdb=" CA SER q 253 " ideal model delta harmonic sigma weight residual -180.00 -156.81 -23.19 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 17297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 3256 0.049 - 0.097: 791 0.097 - 0.146: 250 0.146 - 0.194: 37 0.194 - 0.243: 7 Chirality restraints: 4341 Sorted by residual: chirality pdb=" CG LEU i 73 " pdb=" CB LEU i 73 " pdb=" CD1 LEU i 73 " pdb=" CD2 LEU i 73 " both_signs ideal model delta sigma weight residual False -2.59 -2.83 0.24 2.00e-01 2.50e+01 1.47e+00 chirality pdb=" CG LEU a 352 " pdb=" CB LEU a 352 " pdb=" CD1 LEU a 352 " pdb=" CD2 LEU a 352 " both_signs ideal model delta sigma weight residual False -2.59 -2.80 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CG LEU d 53 " pdb=" CB LEU d 53 " pdb=" CD1 LEU d 53 " pdb=" CD2 LEU d 53 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 4338 not shown) Planarity restraints: 4801 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR a 216 " 0.109 2.00e-02 2.50e+03 6.74e-02 9.09e+01 pdb=" CG TYR a 216 " -0.013 2.00e-02 2.50e+03 pdb=" CD1 TYR a 216 " -0.033 2.00e-02 2.50e+03 pdb=" CD2 TYR a 216 " -0.064 2.00e-02 2.50e+03 pdb=" CE1 TYR a 216 " -0.063 2.00e-02 2.50e+03 pdb=" CE2 TYR a 216 " -0.041 2.00e-02 2.50e+03 pdb=" CZ TYR a 216 " -0.011 2.00e-02 2.50e+03 pdb=" OH TYR a 216 " 0.116 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP a 344 " -0.088 2.00e-02 2.50e+03 4.64e-02 5.37e+01 pdb=" CG TRP a 344 " 0.028 2.00e-02 2.50e+03 pdb=" CD1 TRP a 344 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP a 344 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP a 344 " 0.042 2.00e-02 2.50e+03 pdb=" CE2 TRP a 344 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP a 344 " 0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP a 344 " -0.079 2.00e-02 2.50e+03 pdb=" CZ3 TRP a 344 " 0.033 2.00e-02 2.50e+03 pdb=" CH2 TRP a 344 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR a 67 " 0.055 2.00e-02 2.50e+03 4.40e-02 3.87e+01 pdb=" CG TYR a 67 " 0.011 2.00e-02 2.50e+03 pdb=" CD1 TYR a 67 " -0.029 2.00e-02 2.50e+03 pdb=" CD2 TYR a 67 " -0.018 2.00e-02 2.50e+03 pdb=" CE1 TYR a 67 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 TYR a 67 " -0.040 2.00e-02 2.50e+03 pdb=" CZ TYR a 67 " -0.023 2.00e-02 2.50e+03 pdb=" OH TYR a 67 " 0.085 2.00e-02 2.50e+03 ... (remaining 4798 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.15: 14 2.15 - 2.84: 8413 2.84 - 3.52: 40350 3.52 - 4.21: 60383 4.21 - 4.90: 105778 Nonbonded interactions: 214938 Sorted by model distance: nonbonded pdb=" CZ TYR a 21 " pdb=" CE LYS d 71 " model vdw 1.461 3.660 nonbonded pdb=" CE1 TYR a 21 " pdb=" CE LYS d 71 " model vdw 1.614 3.740 nonbonded pdb=" CD2 LEU a 17 " pdb=" CD2 LEU d 67 " model vdw 1.622 3.880 nonbonded pdb=" CE2 TYR a 21 " pdb=" CE LYS d 71 " model vdw 1.664 2.992 nonbonded pdb=" CZ TYR a 21 " pdb=" NZ LYS d 71 " model vdw 1.737 2.672 ... (remaining 214933 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.30 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: 3.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.390 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 24.420 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4689 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 0.580 28040 Z= 0.433 Angle : 0.800 12.469 37837 Z= 0.474 Chirality : 0.048 0.243 4341 Planarity : 0.006 0.147 4801 Dihedral : 12.884 87.182 10734 Min Nonbonded Distance : 1.461 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.12 % Allowed : 1.34 % Favored : 98.54 % Rotamer: Outliers : 0.09 % Allowed : 0.47 % Favored : 99.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 1.54 (0.15), residues: 3294 helix: 1.77 (0.12), residues: 1759 sheet: 0.80 (0.24), residues: 486 loop : -0.06 (0.20), residues: 1049 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG h 130 TYR 0.116 0.003 TYR a 216 PHE 0.055 0.003 PHE a 356 TRP 0.088 0.005 TRP a 344 HIS 0.014 0.001 HIS a 536 Details of bonding type rmsd covalent geometry : bond 0.00492 (28039) covalent geometry : angle 0.79976 (37837) hydrogen bonds : bond 0.12156 ( 1633) hydrogen bonds : angle 5.40320 ( 4740) Misc. bond : bond 0.57972 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 215 time to evaluate : 0.983 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: d 195 MET cc_start: 0.4780 (mpp) cc_final: 0.4212 (mpp) REVERT: k 1 MET cc_start: 0.3740 (tpt) cc_final: 0.2639 (tpt) REVERT: n 510 MET cc_start: 0.0877 (tpt) cc_final: -0.1328 (mmt) REVERT: n 565 LEU cc_start: 0.7462 (pp) cc_final: 0.7168 (pp) REVERT: n 790 MET cc_start: -0.4515 (ppp) cc_final: -0.6643 (tpt) REVERT: t 200 LEU cc_start: 0.6137 (tp) cc_final: 0.5271 (tp) REVERT: u 1 MET cc_start: 0.0534 (pmm) cc_final: -0.0500 (mpp) outliers start: 3 outliers final: 1 residues processed: 218 average time/residue: 0.1881 time to fit residues: 64.3230 Evaluate side-chains 125 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 124 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 40.0000 chunk 298 optimal weight: 20.0000 overall best weight: 3.1590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 118 HIS ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 122 HIS ** h 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN ** n 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 399 ASN n 622 GLN ** n 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 63 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 9 GLN ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.047059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.036191 restraints weight = 443247.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.036370 restraints weight = 374742.247| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.036332 restraints weight = 325043.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.036649 restraints weight = 260295.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.036633 restraints weight = 218815.218| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3294 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3294 r_free = 0.3294 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 28040 Z= 0.136 Angle : 0.566 11.749 37837 Z= 0.297 Chirality : 0.041 0.212 4341 Planarity : 0.004 0.083 4801 Dihedral : 4.067 24.520 3628 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.55 % Favored : 98.42 % Rotamer: Outliers : 0.38 % Allowed : 3.60 % Favored : 96.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 1.88 (0.15), residues: 3294 helix: 2.02 (0.12), residues: 1802 sheet: 0.91 (0.24), residues: 469 loop : 0.09 (0.20), residues: 1023 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG h 130 TYR 0.022 0.001 TYR f 100 PHE 0.037 0.002 PHE d 136 TRP 0.039 0.002 TRP n 181 HIS 0.011 0.001 HIS n 116 Details of bonding type rmsd covalent geometry : bond 0.00285 (28039) covalent geometry : angle 0.56631 (37837) hydrogen bonds : bond 0.03917 ( 1633) hydrogen bonds : angle 4.26799 ( 4740) Misc. bond : bond 0.00985 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.083 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: d 195 MET cc_start: 0.1132 (mpp) cc_final: 0.0707 (mmt) REVERT: f 37 PHE cc_start: 0.8555 (t80) cc_final: 0.7975 (t80) REVERT: h 54 MET cc_start: 0.8711 (ptt) cc_final: 0.8314 (ppp) REVERT: j 49 MET cc_start: -0.1125 (tpt) cc_final: -0.1344 (tpt) REVERT: k 1 MET cc_start: 0.7521 (tpt) cc_final: 0.7175 (tpt) REVERT: n 453 MET cc_start: 0.7534 (tmm) cc_final: 0.6806 (tmm) REVERT: n 472 MET cc_start: 0.9387 (mmp) cc_final: 0.9156 (mmp) REVERT: n 510 MET cc_start: 0.3857 (tpt) cc_final: 0.2438 (mmt) REVERT: n 790 MET cc_start: -0.5471 (ppp) cc_final: -0.5827 (tpt) REVERT: q 238 MET cc_start: 0.8560 (mmp) cc_final: 0.8283 (mmp) REVERT: r 224 MET cc_start: 0.7586 (mmp) cc_final: 0.7325 (mmm) REVERT: t 1 MET cc_start: 0.8030 (tmm) cc_final: 0.7801 (tmm) REVERT: t 57 MET cc_start: 0.8482 (tmm) cc_final: 0.8019 (tmm) REVERT: t 141 ASN cc_start: 0.9490 (p0) cc_final: 0.9090 (p0) REVERT: u 1 MET cc_start: 0.1047 (pmm) cc_final: 0.0520 (mpp) REVERT: v 63 MET cc_start: 0.9117 (ptp) cc_final: 0.8861 (ppp) REVERT: w 38 TYR cc_start: 0.9584 (t80) cc_final: 0.9145 (t80) outliers start: 12 outliers final: 5 residues processed: 153 average time/residue: 0.1908 time to fit residues: 46.3025 Evaluate side-chains 124 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 119 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 48 optimal weight: 7.9990 chunk 188 optimal weight: 4.9990 chunk 210 optimal weight: 30.0000 chunk 229 optimal weight: 4.9990 chunk 32 optimal weight: 30.0000 chunk 217 optimal weight: 30.0000 chunk 270 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 209 optimal weight: 8.9990 chunk 51 optimal weight: 8.9990 chunk 191 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 106 ASN ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 182 ASN ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 150 GLN ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 715 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 53 ASN ** r 245 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 203 GLN ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 45 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.046172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.035763 restraints weight = 446432.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.035940 restraints weight = 374415.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.035777 restraints weight = 294882.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.035895 restraints weight = 231490.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.036101 restraints weight = 213228.490| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3269 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3269 r_free = 0.3269 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.034 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 28040 Z= 0.142 Angle : 0.546 10.666 37837 Z= 0.286 Chirality : 0.040 0.196 4341 Planarity : 0.004 0.068 4801 Dihedral : 3.983 24.608 3628 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.52 % Favored : 98.45 % Rotamer: Outliers : 0.06 % Allowed : 3.57 % Favored : 96.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 1.83 (0.15), residues: 3294 helix: 1.99 (0.12), residues: 1791 sheet: 0.93 (0.25), residues: 455 loop : 0.07 (0.20), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG u 92 TYR 0.025 0.001 TYR f 100 PHE 0.027 0.002 PHE d 136 TRP 0.030 0.002 TRP r 41 HIS 0.009 0.001 HIS n 116 Details of bonding type rmsd covalent geometry : bond 0.00295 (28039) covalent geometry : angle 0.54563 (37837) hydrogen bonds : bond 0.03651 ( 1633) hydrogen bonds : angle 4.15039 ( 4740) Misc. bond : bond 0.00228 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 139 time to evaluate : 1.044 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: d 195 MET cc_start: 0.1469 (mpp) cc_final: 0.1053 (mmt) REVERT: n 453 MET cc_start: 0.7556 (tmm) cc_final: 0.6853 (tmm) REVERT: n 472 MET cc_start: 0.9404 (mmp) cc_final: 0.9197 (mmt) REVERT: n 510 MET cc_start: 0.4338 (tpt) cc_final: 0.2891 (mmt) REVERT: n 790 MET cc_start: -0.5949 (ppp) cc_final: -0.6320 (tpt) REVERT: q 238 MET cc_start: 0.8815 (mmp) cc_final: 0.8393 (mmp) REVERT: r 224 MET cc_start: 0.7702 (mmp) cc_final: 0.7435 (mmm) REVERT: t 1 MET cc_start: 0.8151 (tmm) cc_final: 0.7899 (tmm) REVERT: t 57 MET cc_start: 0.8500 (tmm) cc_final: 0.8053 (tmm) REVERT: t 141 ASN cc_start: 0.9543 (p0) cc_final: 0.9132 (p0) REVERT: u 1 MET cc_start: 0.0954 (pmm) cc_final: 0.0334 (mpp) REVERT: v 63 MET cc_start: 0.9180 (ptp) cc_final: 0.8919 (ptm) REVERT: w 38 TYR cc_start: 0.9630 (t80) cc_final: 0.9227 (t80) outliers start: 2 outliers final: 1 residues processed: 141 average time/residue: 0.1801 time to fit residues: 40.6146 Evaluate side-chains 118 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 117 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 112 optimal weight: 50.0000 chunk 97 optimal weight: 5.9990 chunk 39 optimal weight: 7.9990 chunk 264 optimal weight: 8.9990 chunk 27 optimal weight: 50.0000 chunk 23 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 308 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 40.0000 chunk 221 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 199 HIS ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 ASN n 173 ASN n 360 ASN n 502 GLN n 631 HIS r 53 ASN r 245 GLN t 48 ASN v 4 GLN ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN w 86 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.044661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.034280 restraints weight = 452534.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.034326 restraints weight = 377598.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.034219 restraints weight = 328741.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.034356 restraints weight = 263232.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.034398 restraints weight = 235723.931| |-----------------------------------------------------------------------------| r_work (final): 0.3214 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3193 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3193 r_free = 0.3193 target_work(ls_wunit_k1) = 0.031 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3193 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28040 Z= 0.202 Angle : 0.625 10.588 37837 Z= 0.326 Chirality : 0.041 0.207 4341 Planarity : 0.004 0.064 4801 Dihedral : 4.145 24.436 3628 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.03 % Favored : 97.94 % Rotamer: Outliers : 0.09 % Allowed : 3.83 % Favored : 96.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 1.50 (0.14), residues: 3294 helix: 1.69 (0.12), residues: 1819 sheet: 0.81 (0.24), residues: 448 loop : -0.08 (0.20), residues: 1027 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG j 59 TYR 0.027 0.002 TYR z 17 PHE 0.025 0.002 PHE w 80 TRP 0.016 0.002 TRP r 41 HIS 0.009 0.001 HIS q 646 Details of bonding type rmsd covalent geometry : bond 0.00406 (28039) covalent geometry : angle 0.62458 (37837) hydrogen bonds : bond 0.03716 ( 1633) hydrogen bonds : angle 4.31919 ( 4740) Misc. bond : bond 0.00095 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 134 time to evaluate : 1.152 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: g 70 MET cc_start: 0.6384 (tpp) cc_final: 0.6169 (tpp) REVERT: h 54 MET cc_start: 0.8930 (ppp) cc_final: 0.8674 (ppp) REVERT: k 1 MET cc_start: 0.7429 (tpt) cc_final: 0.6971 (tpt) REVERT: n 453 MET cc_start: 0.6765 (tmm) cc_final: 0.6004 (tmm) REVERT: n 472 MET cc_start: 0.9550 (mmp) cc_final: 0.9110 (mmp) REVERT: n 510 MET cc_start: 0.4328 (tpt) cc_final: 0.2761 (mmt) REVERT: n 703 MET cc_start: 0.9082 (ptp) cc_final: 0.8679 (ppp) REVERT: n 767 MET cc_start: -0.4534 (mpp) cc_final: -0.5235 (mpp) REVERT: n 790 MET cc_start: -0.6170 (ppp) cc_final: -0.6479 (tpt) REVERT: q 207 MET cc_start: 0.9131 (ppp) cc_final: 0.8928 (ppp) REVERT: q 238 MET cc_start: 0.8869 (mmp) cc_final: 0.8588 (mmp) REVERT: r 80 MET cc_start: 0.8332 (mmm) cc_final: 0.7853 (mmm) REVERT: r 182 MET cc_start: 0.9505 (pmm) cc_final: 0.9282 (pmm) REVERT: r 204 MET cc_start: 0.9591 (tpt) cc_final: 0.9298 (mmm) REVERT: t 1 MET cc_start: 0.8089 (tmm) cc_final: 0.7804 (tmm) REVERT: t 39 PHE cc_start: 0.9201 (t80) cc_final: 0.8908 (t80) REVERT: t 57 MET cc_start: 0.8563 (tmm) cc_final: 0.8238 (tmm) REVERT: t 72 ILE cc_start: 0.8602 (tt) cc_final: 0.8214 (tp) REVERT: t 141 ASN cc_start: 0.9481 (p0) cc_final: 0.9009 (p0) REVERT: u 1 MET cc_start: 0.1063 (pmm) cc_final: 0.0859 (pmm) REVERT: u 15 MET cc_start: 0.9683 (tmm) cc_final: 0.9225 (mmt) REVERT: v 63 MET cc_start: 0.9210 (ptp) cc_final: 0.8834 (ptt) REVERT: w 38 TYR cc_start: 0.9547 (t80) cc_final: 0.9154 (t80) outliers start: 3 outliers final: 1 residues processed: 137 average time/residue: 0.1864 time to fit residues: 41.1980 Evaluate side-chains 111 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 289 optimal weight: 7.9990 chunk 188 optimal weight: 7.9990 chunk 10 optimal weight: 0.0980 chunk 239 optimal weight: 6.9990 chunk 313 optimal weight: 20.0000 chunk 230 optimal weight: 2.9990 chunk 184 optimal weight: 30.0000 chunk 124 optimal weight: 2.9990 chunk 193 optimal weight: 0.0570 chunk 185 optimal weight: 7.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.6304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 177 GLN ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 ASN n 173 ASN n 399 ASN ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 245 GLN ** t 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 203 GLN ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN v 68 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.044994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.034349 restraints weight = 448937.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.034736 restraints weight = 378026.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.034409 restraints weight = 293294.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.034707 restraints weight = 250935.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.034740 restraints weight = 202131.719| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 28040 Z= 0.112 Angle : 0.541 8.736 37837 Z= 0.281 Chirality : 0.041 0.200 4341 Planarity : 0.004 0.056 4801 Dihedral : 4.019 24.608 3628 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.43 % Favored : 98.54 % Rotamer: Outliers : 0.03 % Allowed : 1.99 % Favored : 97.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 1.65 (0.15), residues: 3294 helix: 1.83 (0.12), residues: 1820 sheet: 0.83 (0.24), residues: 453 loop : -0.04 (0.20), residues: 1021 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG u 92 TYR 0.028 0.001 TYR t 204 PHE 0.026 0.001 PHE d 81 TRP 0.019 0.001 TRP r 41 HIS 0.008 0.001 HIS n 116 Details of bonding type rmsd covalent geometry : bond 0.00231 (28039) covalent geometry : angle 0.54092 (37837) hydrogen bonds : bond 0.03408 ( 1633) hydrogen bonds : angle 4.16507 ( 4740) Misc. bond : bond 0.00062 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.211 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: g 70 MET cc_start: 0.6123 (tpp) cc_final: 0.5900 (tpp) REVERT: h 54 MET cc_start: 0.8829 (ppp) cc_final: 0.8578 (ppp) REVERT: n 453 MET cc_start: 0.6359 (tmm) cc_final: 0.5697 (tmm) REVERT: n 510 MET cc_start: 0.4369 (tpt) cc_final: 0.4029 (mmt) REVERT: n 767 MET cc_start: -0.4616 (mpp) cc_final: -0.5301 (mpp) REVERT: q 238 MET cc_start: 0.8665 (mmp) cc_final: 0.8333 (mmp) REVERT: r 80 MET cc_start: 0.8307 (mmm) cc_final: 0.7879 (mmm) REVERT: r 203 LEU cc_start: 0.9607 (pp) cc_final: 0.9390 (pp) REVERT: r 224 MET cc_start: 0.9155 (mmp) cc_final: 0.8788 (mmm) REVERT: t 1 MET cc_start: 0.7947 (tmm) cc_final: 0.7662 (tmm) REVERT: t 39 PHE cc_start: 0.9275 (t80) cc_final: 0.8949 (t80) REVERT: t 57 MET cc_start: 0.8667 (tmm) cc_final: 0.8299 (tmm) REVERT: t 72 ILE cc_start: 0.8740 (tt) cc_final: 0.8374 (tp) REVERT: t 141 ASN cc_start: 0.9374 (p0) cc_final: 0.8886 (p0) REVERT: u 1 MET cc_start: 0.1003 (pmm) cc_final: 0.0770 (pmm) REVERT: u 15 MET cc_start: 0.9703 (tmm) cc_final: 0.9221 (mmt) REVERT: v 63 MET cc_start: 0.9188 (ptp) cc_final: 0.8799 (ppp) REVERT: w 38 TYR cc_start: 0.9515 (t80) cc_final: 0.9101 (t80) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.1807 time to fit residues: 38.4855 Evaluate side-chains 110 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 67 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 325 optimal weight: 0.0980 chunk 241 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 261 optimal weight: 3.9990 chunk 271 optimal weight: 50.0000 chunk 322 optimal weight: 7.9990 chunk 43 optimal weight: 0.9980 chunk 174 optimal weight: 7.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 68 HIS ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN n 399 ASN n 715 ASN r 53 ASN ** t 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN w 86 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.044959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.034176 restraints weight = 448159.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.034572 restraints weight = 379257.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.034321 restraints weight = 295124.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.034518 restraints weight = 256775.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.034639 restraints weight = 218707.034| |-----------------------------------------------------------------------------| r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 28040 Z= 0.102 Angle : 0.522 7.477 37837 Z= 0.269 Chirality : 0.041 0.176 4341 Planarity : 0.003 0.051 4801 Dihedral : 3.916 25.043 3628 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 1.67 % Favored : 98.30 % Rotamer: Outliers : 0.09 % Allowed : 1.64 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.82 (0.15), residues: 3294 helix: 1.98 (0.12), residues: 1819 sheet: 0.85 (0.25), residues: 444 loop : 0.07 (0.20), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG u 92 TYR 0.022 0.001 TYR t 204 PHE 0.031 0.001 PHE j 39 TRP 0.014 0.001 TRP r 41 HIS 0.008 0.001 HIS n 116 Details of bonding type rmsd covalent geometry : bond 0.00212 (28039) covalent geometry : angle 0.52158 (37837) hydrogen bonds : bond 0.03279 ( 1633) hydrogen bonds : angle 4.04046 ( 4740) Misc. bond : bond 0.00054 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 126 time to evaluate : 0.876 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: g 70 MET cc_start: 0.6051 (tpp) cc_final: 0.5838 (tpp) REVERT: h 54 MET cc_start: 0.8863 (ppp) cc_final: 0.8622 (ppp) REVERT: n 453 MET cc_start: 0.6435 (tmm) cc_final: 0.5751 (tmm) REVERT: n 510 MET cc_start: 0.4344 (tpt) cc_final: 0.4009 (mmt) REVERT: n 767 MET cc_start: -0.4431 (mpp) cc_final: -0.5129 (mpp) REVERT: q 238 MET cc_start: 0.8689 (mmp) cc_final: 0.8303 (mmp) REVERT: r 80 MET cc_start: 0.8546 (mmm) cc_final: 0.8117 (mmm) REVERT: r 224 MET cc_start: 0.9204 (mmp) cc_final: 0.8880 (mmm) REVERT: t 1 MET cc_start: 0.7960 (tmm) cc_final: 0.7627 (tmm) REVERT: t 39 PHE cc_start: 0.9290 (t80) cc_final: 0.8937 (t80) REVERT: t 57 MET cc_start: 0.8663 (tmm) cc_final: 0.8437 (tmm) REVERT: t 141 ASN cc_start: 0.9363 (p0) cc_final: 0.8875 (p0) REVERT: u 1 MET cc_start: 0.1040 (pmm) cc_final: 0.0795 (pmm) REVERT: u 15 MET cc_start: 0.9694 (tmm) cc_final: 0.9205 (mmt) REVERT: v 63 MET cc_start: 0.9211 (ptp) cc_final: 0.8825 (ppp) REVERT: w 38 TYR cc_start: 0.9518 (t80) cc_final: 0.9102 (t80) outliers start: 3 outliers final: 1 residues processed: 129 average time/residue: 0.1751 time to fit residues: 36.9483 Evaluate side-chains 111 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 103 optimal weight: 9.9990 chunk 237 optimal weight: 9.9990 chunk 84 optimal weight: 20.0000 chunk 206 optimal weight: 8.9990 chunk 290 optimal weight: 6.9990 chunk 130 optimal weight: 9.9990 chunk 164 optimal weight: 9.9990 chunk 148 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 139 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** f 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 180 HIS ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 14 ASN ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 25 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN v 60 ASN w 86 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.043023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.032494 restraints weight = 459731.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.032710 restraints weight = 394926.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.032579 restraints weight = 313320.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.032813 restraints weight = 251590.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.032834 restraints weight = 223235.819| |-----------------------------------------------------------------------------| r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.4310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 28040 Z= 0.223 Angle : 0.688 9.414 37837 Z= 0.360 Chirality : 0.043 0.196 4341 Planarity : 0.005 0.056 4801 Dihedral : 4.340 24.693 3628 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.25 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 1.15 (0.14), residues: 3294 helix: 1.41 (0.12), residues: 1815 sheet: 0.50 (0.24), residues: 435 loop : -0.13 (0.19), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG u 92 TYR 0.029 0.002 TYR z 17 PHE 0.026 0.002 PHE j 39 TRP 0.024 0.003 TRP t 35 HIS 0.018 0.002 HIS g 160 Details of bonding type rmsd covalent geometry : bond 0.00450 (28039) covalent geometry : angle 0.68754 (37837) hydrogen bonds : bond 0.03818 ( 1633) hydrogen bonds : angle 4.55444 ( 4740) Misc. bond : bond 0.00064 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.218 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: g 70 MET cc_start: 0.6746 (tpp) cc_final: 0.6541 (tpp) REVERT: h 54 MET cc_start: 0.8954 (ppp) cc_final: 0.8750 (ppp) REVERT: j 86 TYR cc_start: 0.7694 (m-80) cc_final: 0.7471 (m-10) REVERT: j 116 HIS cc_start: 0.9213 (t70) cc_final: 0.8948 (m90) REVERT: n 453 MET cc_start: 0.6656 (tmm) cc_final: 0.5364 (ppp) REVERT: n 472 MET cc_start: 0.9469 (mmt) cc_final: 0.9165 (mmm) REVERT: n 510 MET cc_start: 0.4319 (tpt) cc_final: 0.3588 (mmt) REVERT: n 767 MET cc_start: -0.4106 (mpp) cc_final: -0.4859 (mpp) REVERT: q 207 MET cc_start: 0.9352 (ppp) cc_final: 0.9147 (ppp) REVERT: q 238 MET cc_start: 0.8911 (mmp) cc_final: 0.8688 (mmp) REVERT: q 241 MET cc_start: 0.7876 (mpp) cc_final: 0.7653 (mpp) REVERT: q 279 TRP cc_start: 0.8345 (m100) cc_final: 0.7180 (m100) REVERT: r 182 MET cc_start: 0.9546 (pmm) cc_final: 0.9277 (pmm) REVERT: r 224 MET cc_start: 0.9210 (mmp) cc_final: 0.8897 (mmm) REVERT: t 1 MET cc_start: 0.8151 (tmm) cc_final: 0.7843 (tmm) REVERT: t 72 ILE cc_start: 0.8728 (tt) cc_final: 0.8421 (tp) REVERT: t 141 ASN cc_start: 0.9470 (p0) cc_final: 0.8981 (p0) REVERT: u 1 MET cc_start: 0.0860 (pmm) cc_final: 0.0385 (pmm) REVERT: v 63 MET cc_start: 0.9135 (ptp) cc_final: 0.8785 (ppp) REVERT: w 38 TYR cc_start: 0.9588 (t80) cc_final: 0.9219 (t80) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1787 time to fit residues: 34.7584 Evaluate side-chains 106 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 120 optimal weight: 0.9990 chunk 208 optimal weight: 10.0000 chunk 266 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 282 optimal weight: 7.9990 chunk 136 optimal weight: 5.9990 chunk 256 optimal weight: 20.0000 chunk 12 optimal weight: 30.0000 chunk 190 optimal weight: 50.0000 chunk 273 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 10 GLN ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 68 HIS ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 25 GLN n 173 ASN n 399 ASN ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 167 GLN ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN ** v 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 86 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.043283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.032699 restraints weight = 456656.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.032846 restraints weight = 397390.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.032713 restraints weight = 312125.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.032807 restraints weight = 260013.073| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.032876 restraints weight = 230539.295| |-----------------------------------------------------------------------------| r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 28040 Z= 0.147 Angle : 0.579 10.000 37837 Z= 0.304 Chirality : 0.042 0.178 4341 Planarity : 0.004 0.070 4801 Dihedral : 4.194 24.424 3628 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.09 % Favored : 97.87 % Rotamer: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 1.31 (0.14), residues: 3294 helix: 1.61 (0.12), residues: 1819 sheet: 0.46 (0.25), residues: 439 loop : -0.17 (0.19), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG g 166 TYR 0.016 0.001 TYR z 17 PHE 0.025 0.002 PHE j 39 TRP 0.020 0.002 TRP w 64 HIS 0.008 0.001 HIS n 116 Details of bonding type rmsd covalent geometry : bond 0.00301 (28039) covalent geometry : angle 0.57850 (37837) hydrogen bonds : bond 0.03518 ( 1633) hydrogen bonds : angle 4.37363 ( 4740) Misc. bond : bond 0.00063 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 0.888 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: h 54 MET cc_start: 0.8958 (ppp) cc_final: 0.8734 (ppp) REVERT: j 116 HIS cc_start: 0.9240 (t70) cc_final: 0.8981 (m90) REVERT: n 453 MET cc_start: 0.6961 (tmm) cc_final: 0.6659 (tmm) REVERT: n 472 MET cc_start: 0.9491 (mmt) cc_final: 0.9271 (mmp) REVERT: n 510 MET cc_start: 0.4143 (tpt) cc_final: 0.3830 (mmt) REVERT: n 767 MET cc_start: -0.4441 (mpp) cc_final: -0.5038 (mpp) REVERT: q 238 MET cc_start: 0.8861 (mmp) cc_final: 0.8571 (mmp) REVERT: q 279 TRP cc_start: 0.8205 (m100) cc_final: 0.6979 (m100) REVERT: r 80 MET cc_start: 0.8311 (mmm) cc_final: 0.8084 (mmm) REVERT: r 182 MET cc_start: 0.9533 (pmm) cc_final: 0.9319 (pmm) REVERT: r 224 MET cc_start: 0.9278 (mmp) cc_final: 0.8613 (mmm) REVERT: t 1 MET cc_start: 0.8029 (tmm) cc_final: 0.7697 (tmm) REVERT: t 72 ILE cc_start: 0.8777 (tt) cc_final: 0.8521 (tp) REVERT: t 141 ASN cc_start: 0.9467 (p0) cc_final: 0.8989 (p0) REVERT: u 1 MET cc_start: 0.0866 (pmm) cc_final: 0.0408 (pmm) REVERT: v 63 MET cc_start: 0.9223 (ptp) cc_final: 0.8841 (ppp) REVERT: w 38 TYR cc_start: 0.9599 (t80) cc_final: 0.9260 (t80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1744 time to fit residues: 34.4433 Evaluate side-chains 104 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 96 optimal weight: 1.9990 chunk 225 optimal weight: 7.9990 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 206 optimal weight: 4.9990 chunk 143 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 16 optimal weight: 30.0000 chunk 60 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: f 10 GLN ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 68 HIS ** j 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 140 GLN n 173 ASN r 53 ASN ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN ** v 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.043221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.032665 restraints weight = 455673.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.032760 restraints weight = 380544.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.032637 restraints weight = 319154.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.032899 restraints weight = 259118.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.033062 restraints weight = 213439.644| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 28040 Z= 0.134 Angle : 0.573 8.221 37837 Z= 0.299 Chirality : 0.041 0.166 4341 Planarity : 0.004 0.107 4801 Dihedral : 4.171 25.043 3628 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.00 % Favored : 97.97 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 1.37 (0.14), residues: 3294 helix: 1.70 (0.12), residues: 1809 sheet: 0.37 (0.25), residues: 437 loop : -0.15 (0.19), residues: 1048 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG u 92 TYR 0.020 0.001 TYR f 100 PHE 0.023 0.002 PHE j 39 TRP 0.016 0.002 TRP h 62 HIS 0.008 0.001 HIS n 116 Details of bonding type rmsd covalent geometry : bond 0.00277 (28039) covalent geometry : angle 0.57257 (37837) hydrogen bonds : bond 0.03445 ( 1633) hydrogen bonds : angle 4.33866 ( 4740) Misc. bond : bond 0.00053 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 121 time to evaluate : 1.178 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: h 54 MET cc_start: 0.9119 (ppp) cc_final: 0.8831 (ppp) REVERT: j 116 HIS cc_start: 0.9240 (t70) cc_final: 0.8966 (m90) REVERT: n 453 MET cc_start: 0.7090 (tmm) cc_final: 0.6635 (tmm) REVERT: n 472 MET cc_start: 0.9504 (mmt) cc_final: 0.9270 (mmp) REVERT: n 510 MET cc_start: 0.4106 (tpt) cc_final: 0.3764 (mmt) REVERT: n 767 MET cc_start: -0.4520 (mpp) cc_final: -0.5099 (mpp) REVERT: q 215 MET cc_start: 0.9517 (mmp) cc_final: 0.9296 (mmp) REVERT: q 238 MET cc_start: 0.8956 (mmp) cc_final: 0.8661 (mmp) REVERT: q 279 TRP cc_start: 0.8279 (m100) cc_final: 0.7023 (m100) REVERT: r 182 MET cc_start: 0.9514 (pmm) cc_final: 0.9305 (pmm) REVERT: r 224 MET cc_start: 0.9320 (mmp) cc_final: 0.8699 (mmm) REVERT: t 1 MET cc_start: 0.8103 (tmm) cc_final: 0.7792 (tmm) REVERT: t 78 MET cc_start: 0.9131 (tpt) cc_final: 0.8560 (mpp) REVERT: t 141 ASN cc_start: 0.9426 (p0) cc_final: 0.8984 (p0) REVERT: u 1 MET cc_start: 0.0556 (pmm) cc_final: 0.0227 (pmm) REVERT: v 63 MET cc_start: 0.9230 (ptp) cc_final: 0.8857 (ppp) REVERT: w 38 TYR cc_start: 0.9642 (t80) cc_final: 0.9318 (t80) outliers start: 0 outliers final: 0 residues processed: 121 average time/residue: 0.1761 time to fit residues: 35.0427 Evaluate side-chains 105 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 292 optimal weight: 10.0000 chunk 294 optimal weight: 7.9990 chunk 210 optimal weight: 6.9990 chunk 12 optimal weight: 30.0000 chunk 165 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 288 optimal weight: 5.9990 chunk 303 optimal weight: 5.9990 chunk 187 optimal weight: 40.0000 chunk 67 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 159 HIS i 68 HIS ** i 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 76 ASN ** n 173 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 177 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 399 ASN ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 226 HIS r 258 ASN ** s 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN ** v 61 GLN ** 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 = 0.3472 r_free = 0.3472 target = 0.041901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.031410 restraints weight = 466580.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.031929 restraints weight = 380100.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.031756 restraints weight = 274687.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.031712 restraints weight = 245623.498| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.031757 restraints weight = 230320.102| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.5603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28040 Z= 0.225 Angle : 0.689 10.044 37837 Z= 0.362 Chirality : 0.044 0.246 4341 Planarity : 0.005 0.100 4801 Dihedral : 4.538 24.640 3628 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.91 % Favored : 97.06 % Rotamer: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 0.82 (0.14), residues: 3294 helix: 1.20 (0.12), residues: 1814 sheet: 0.12 (0.24), residues: 435 loop : -0.27 (0.19), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG q 614 TYR 0.031 0.002 TYR n 637 PHE 0.024 0.002 PHE j 39 TRP 0.037 0.003 TRP t 35 HIS 0.008 0.002 HIS q 646 Details of bonding type rmsd covalent geometry : bond 0.00450 (28039) covalent geometry : angle 0.68867 (37837) hydrogen bonds : bond 0.03969 ( 1633) hydrogen bonds : angle 4.66118 ( 4740) Misc. bond : bond 0.00057 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6588 Ramachandran restraints generated. 3294 Oldfield, 0 Emsley, 3294 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 0.996 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: h 54 MET cc_start: 0.9094 (ppp) cc_final: 0.8812 (ppp) REVERT: n 453 MET cc_start: 0.7801 (tmm) cc_final: 0.7317 (tmm) REVERT: n 510 MET cc_start: 0.4455 (tpt) cc_final: 0.4129 (mmt) REVERT: n 703 MET cc_start: 0.9128 (ptp) cc_final: 0.8803 (ppp) REVERT: n 767 MET cc_start: -0.4554 (mpp) cc_final: -0.4820 (mpp) REVERT: q 238 MET cc_start: 0.9010 (mmp) cc_final: 0.8677 (mmm) REVERT: q 279 TRP cc_start: 0.7966 (m100) cc_final: 0.6913 (m100) REVERT: r 80 MET cc_start: 0.8630 (mmm) cc_final: 0.8094 (mmm) REVERT: r 182 MET cc_start: 0.9583 (pmm) cc_final: 0.9232 (pmm) REVERT: r 204 MET cc_start: 0.9684 (mmm) cc_final: 0.9406 (mmm) REVERT: r 224 MET cc_start: 0.9349 (mmp) cc_final: 0.8747 (mmm) REVERT: t 78 MET cc_start: 0.9218 (tpt) cc_final: 0.8753 (mpp) REVERT: v 63 MET cc_start: 0.9181 (ptp) cc_final: 0.8887 (ppp) REVERT: w 38 TYR cc_start: 0.9715 (t80) cc_final: 0.9506 (t80) outliers start: 0 outliers final: 0 residues processed: 111 average time/residue: 0.1848 time to fit residues: 33.4434 Evaluate side-chains 97 residues out of total 3163 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 331 random chunks: chunk 185 optimal weight: 40.0000 chunk 62 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 288 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 293 optimal weight: 4.9990 chunk 134 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 264 optimal weight: 5.9990 chunk 291 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** g 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 68 HIS ** i 128 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 173 ASN n 177 ASN n 399 ASN ** r 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 26 GLN u 18 GLN ** u 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 45 ASN ** v 61 GLN ** 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 = 0.3477 r_free = 0.3477 target = 0.042031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.031748 restraints weight = 462271.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.031916 restraints weight = 375335.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.031661 restraints weight = 301380.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.031773 restraints weight = 244186.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.031893 restraints weight = 220928.429| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28040 Z= 0.158 Angle : 0.613 15.507 37837 Z= 0.319 Chirality : 0.043 0.366 4341 Planarity : 0.004 0.092 4801 Dihedral : 4.408 24.422 3628 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.31 % Favored : 97.66 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.46 % 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: 1.01 (0.14), residues: 3294 helix: 1.40 (0.12), residues: 1809 sheet: 0.13 (0.25), residues: 430 loop : -0.25 (0.19), residues: 1055 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG u 92 TYR 0.018 0.001 TYR z 17 PHE 0.021 0.002 PHE k 55 TRP 0.026 0.002 TRP w 125 HIS 0.008 0.001 HIS n 116 Details of bonding type rmsd covalent geometry : bond 0.00324 (28039) covalent geometry : angle 0.61300 (37837) hydrogen bonds : bond 0.03653 ( 1633) hydrogen bonds : angle 4.53194 ( 4740) Misc. bond : bond 0.00056 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5193.48 seconds wall clock time: 90 minutes 27.53 seconds (5427.53 seconds total)