Starting phenix.real_space_refine on Mon Sep 14 02:03:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7c7a_30297/09_2026/7c7a_30297.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c7a_30297/09_2026/7c7a_30297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7c7a_30297/09_2026/7c7a_30297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c7a_30297/09_2026/7c7a_30297.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7c7a_30297/09_2026/7c7a_30297.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7c7a_30297/09_2026/7c7a_30297.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7c7a_30297/09_2026/7c7a_30297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c7a_30297/09_2026/7c7a_30297.map" } resolution = 2.8 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= 0.001 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 339 5.49 5 Mg 3 5.21 5 S 108 5.16 5 C 16101 2.51 5 N 4847 2.21 5 O 6101 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27500 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 6988 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 6988 Classifications: {'RNAv2': 330} Modifications used: {'rna2p_pur': 21, 'rna2p_pyr': 23, 'rna3p_pur': 139, 'rna3p_pyr': 147} Link IDs: {'rna2p': 44, 'rna3p': 285} Chain breaks: 1 Chain: "B" Number of atoms: 6453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 793, 6453 Classifications: {'peptide': 793} Link IDs: {'PTRANS': 37, 'TRANS': 755} Chain breaks: 3 Chain: "C" Number of atoms: 1246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1246 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 11, 'TRANS': 140} Chain: "D" Number of atoms: 2086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 251, 2086 Classifications: {'peptide': 251} Link IDs: {'PTRANS': 8, 'TRANS': 242} Chain breaks: 1 Chain: "E" Number of atoms: 1135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 1135 Classifications: {'peptide': 145} Link IDs: {'PTRANS': 4, 'TRANS': 140} Chain: "F" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1271 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 3, 'TRANS': 153} Chain: "G" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 960 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 2, 'TRANS': 118} Chain breaks: 1 Chain: "H" Number of atoms: 1079 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1079 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 1, 'TRANS': 129} Chain: "I" Number of atoms: 1881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1881 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 9, 'TRANS': 232} Chain: "J" Number of atoms: 2253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2253 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "K" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 840 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain breaks: 1 Chain: "L" Number of atoms: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1110 Classifications: {'peptide': 131} Link IDs: {'TRANS': 130} Chain: "R" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 194 Classifications: {'RNAv2': 9} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 6, 'rna3p_pyr': 1} Link IDs: {'rna2p': 2, 'rna3p': 6} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 25888 SG CYS K 64 52.147 52.393 52.779 1.00130.63 S ATOM 26117 SG CYS K 109 49.422 50.218 54.715 1.00152.26 S Time building chain proxies: 4.88, per 1000 atoms: 0.18 Number of scatterers: 27500 At special positions: 0 Unit cell: (140.8, 133.1, 211.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 108 16.00 P 339 15.00 Mg 3 11.99 O 6101 8.00 N 4847 7.00 C 16101 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.08 Conformation dependent library (CDL) restraints added in 741.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 200 " pdb="ZN ZN K 200 " - pdb=" SG CYS K 109 " pdb="ZN ZN K 200 " - pdb=" SG CYS K 64 " 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4800 Finding SS restraints... Secondary structure from input PDB file: 92 helices and 18 sheets defined 45.9% alpha, 17.4% beta 43 base pairs and 131 stacking pairs defined. Time for finding SS restraints: 2.91 Creating SS restraints... Processing helix chain 'B' and resid 59 through 66 removed outlier: 3.619A pdb=" N ARG B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 78 Processing helix chain 'B' and resid 109 through 122 Processing helix chain 'B' and resid 143 through 163 removed outlier: 3.738A pdb=" N TYR B 148 " --> pdb=" O ALA B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 170 removed outlier: 3.525A pdb=" N LYS B 167 " --> pdb=" O SER B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 180 Processing helix chain 'B' and resid 180 through 195 removed outlier: 3.628A pdb=" N LYS B 184 " --> pdb=" O HIS B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 Processing helix chain 'B' and resid 227 through 235 removed outlier: 3.515A pdb=" N ARG B 233 " --> pdb=" O LYS B 229 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLN B 234 " --> pdb=" O TYR B 230 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N LYS B 235 " --> pdb=" O THR B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 249 Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.662A pdb=" N HIS B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 318 removed outlier: 3.691A pdb=" N SER B 312 " --> pdb=" O ASP B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 330 Processing helix chain 'B' and resid 371 through 384 removed outlier: 4.302A pdb=" N GLN B 377 " --> pdb=" O SER B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 416 removed outlier: 3.697A pdb=" N SER B 411 " --> pdb=" O LYS B 407 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 432 removed outlier: 3.923A pdb=" N MET B 430 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 452 through 456 Processing helix chain 'B' and resid 471 through 479 removed outlier: 4.196A pdb=" N ILE B 475 " --> pdb=" O ASN B 471 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N HIS B 479 " --> pdb=" O ILE B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 483 through 496 Processing helix chain 'B' and resid 496 through 503 Processing helix chain 'B' and resid 509 through 520 Processing helix chain 'B' and resid 564 through 574 removed outlier: 3.735A pdb=" N LEU B 568 " --> pdb=" O TRP B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 582 through 594 removed outlier: 3.615A pdb=" N ASN B 593 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS B 594 " --> pdb=" O GLN B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 597 through 602 Processing helix chain 'B' and resid 605 through 627 removed outlier: 3.533A pdb=" N TYR B 609 " --> pdb=" O THR B 605 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N LYS B 627 " --> pdb=" O LYS B 623 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 678 removed outlier: 4.128A pdb=" N LEU B 664 " --> pdb=" O ASP B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 702 through 718 removed outlier: 3.684A pdb=" N VAL B 706 " --> pdb=" O CYS B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 738 Processing helix chain 'B' and resid 788 through 798 removed outlier: 4.228A pdb=" N TRP B 792 " --> pdb=" O ASP B 788 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU B 793 " --> pdb=" O LEU B 789 " (cutoff:3.500A) Processing helix chain 'B' and resid 844 through 850 Processing helix chain 'C' and resid 40 through 57 removed outlier: 4.492A pdb=" N HIS C 57 " --> pdb=" O ASN C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 64 removed outlier: 3.628A pdb=" N ASN C 63 " --> pdb=" O GLN C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 80 Processing helix chain 'C' and resid 101 through 106 Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 130 through 136 Processing helix chain 'C' and resid 147 through 155 Processing helix chain 'D' and resid 3 through 17 removed outlier: 4.231A pdb=" N LYS D 15 " --> pdb=" O CYS D 11 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS D 16 " --> pdb=" O LEU D 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 27 Processing helix chain 'D' and resid 68 through 111 removed outlier: 3.726A pdb=" N ILE D 87 " --> pdb=" O LYS D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 126 removed outlier: 3.969A pdb=" N HIS D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 133 removed outlier: 3.813A pdb=" N TYR D 130 " --> pdb=" O HIS D 126 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU D 131 " --> pdb=" O PRO D 127 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N SER D 132 " --> pdb=" O THR D 128 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 140 Processing helix chain 'D' and resid 140 through 155 Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 251 through 253 No H-bonds generated for 'chain 'D' and resid 251 through 253' Processing helix chain 'D' and resid 273 through 279 removed outlier: 3.901A pdb=" N ILE D 277 " --> pdb=" O MET D 273 " (cutoff:3.500A) Processing helix chain 'E' and resid 27 through 36 removed outlier: 3.766A pdb=" N ILE E 31 " --> pdb=" O SER E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 60 removed outlier: 3.544A pdb=" N ILE E 48 " --> pdb=" O SER E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 69 removed outlier: 3.585A pdb=" N CYS E 68 " --> pdb=" O GLY E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 102 Processing helix chain 'E' and resid 122 through 145 removed outlier: 3.677A pdb=" N ILE E 126 " --> pdb=" O THR E 122 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ASN E 139 " --> pdb=" O SER E 135 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ILE E 140 " --> pdb=" O LYS E 136 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 141 " --> pdb=" O ILE E 137 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 removed outlier: 4.112A pdb=" N CYS F 22 " --> pdb=" O SER F 18 " (cutoff:3.500A) Processing helix chain 'F' and resid 54 through 66 removed outlier: 3.939A pdb=" N LYS F 64 " --> pdb=" O ASN F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 86 through 104 removed outlier: 4.529A pdb=" N LYS F 90 " --> pdb=" O PRO F 86 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LYS F 104 " --> pdb=" O LYS F 100 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 59 removed outlier: 4.817A pdb=" N HIS G 56 " --> pdb=" O LEU G 52 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N LYS G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) Processing helix chain 'G' and resid 71 through 85 removed outlier: 3.783A pdb=" N ASP G 84 " --> pdb=" O CYS G 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 27 Processing helix chain 'H' and resid 30 through 46 Processing helix chain 'H' and resid 47 through 52 Processing helix chain 'H' and resid 73 through 82 removed outlier: 3.866A pdb=" N SER H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 114 through 133 removed outlier: 3.571A pdb=" N ASP H 129 " --> pdb=" O GLU H 125 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 37 Processing helix chain 'I' and resid 64 through 69 Processing helix chain 'I' and resid 69 through 76 Processing helix chain 'I' and resid 99 through 104 removed outlier: 3.896A pdb=" N ALA I 103 " --> pdb=" O LYS I 99 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N PHE I 104 " --> pdb=" O ILE I 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 99 through 104' Processing helix chain 'I' and resid 113 through 123 Processing helix chain 'I' and resid 142 through 151 removed outlier: 3.637A pdb=" N ILE I 146 " --> pdb=" O LYS I 142 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N SER I 148 " --> pdb=" O LYS I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 165 removed outlier: 3.655A pdb=" N ARG I 165 " --> pdb=" O TYR I 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 168 through 185 removed outlier: 4.265A pdb=" N GLN I 172 " --> pdb=" O GLN I 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 201 removed outlier: 4.015A pdb=" N CYS I 201 " --> pdb=" O PRO I 198 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 215 Processing helix chain 'I' and resid 217 through 242 removed outlier: 3.610A pdb=" N SER I 222 " --> pdb=" O SER I 218 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ALA I 229 " --> pdb=" O MET I 225 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 37 removed outlier: 3.588A pdb=" N VAL J 23 " --> pdb=" O THR J 19 " (cutoff:3.500A) Processing helix chain 'J' and resid 68 through 77 removed outlier: 4.467A pdb=" N ASP J 74 " --> pdb=" O GLY J 70 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG J 75 " --> pdb=" O GLU J 71 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 104 removed outlier: 3.776A pdb=" N ILE J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N GLN J 102 " --> pdb=" O SER J 98 " (cutoff:3.500A) Processing helix chain 'J' and resid 113 through 123 Processing helix chain 'J' and resid 142 through 153 removed outlier: 4.065A pdb=" N ILE J 146 " --> pdb=" O LYS J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 165 removed outlier: 3.718A pdb=" N LEU J 164 " --> pdb=" O GLY J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 167 through 185 removed outlier: 4.456A pdb=" N ARG J 171 " --> pdb=" O VAL J 167 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLN J 172 " --> pdb=" O GLN J 168 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ARG J 185 " --> pdb=" O ILE J 181 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 201 removed outlier: 3.632A pdb=" N CYS J 201 " --> pdb=" O PRO J 198 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 215 Processing helix chain 'J' and resid 217 through 239 removed outlier: 3.599A pdb=" N LEU J 228 " --> pdb=" O ALA J 224 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ALA J 229 " --> pdb=" O MET J 225 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER J 230 " --> pdb=" O GLY J 226 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY J 236 " --> pdb=" O VAL J 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 21 removed outlier: 3.853A pdb=" N LYS K 8 " --> pdb=" O ASP K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 29 Processing helix chain 'K' and resid 29 through 47 removed outlier: 3.613A pdb=" N ARG K 46 " --> pdb=" O ASN K 42 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N TYR K 47 " --> pdb=" O SER K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 58 removed outlier: 4.526A pdb=" N GLY K 58 " --> pdb=" O GLN K 54 " (cutoff:3.500A) Processing helix chain 'L' and resid 4 through 29 removed outlier: 3.686A pdb=" N ARG L 24 " --> pdb=" O LEU L 20 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N ASN L 27 " --> pdb=" O HIS L 23 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN L 28 " --> pdb=" O ARG L 24 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N HIS L 29 " --> pdb=" O ASN L 25 " (cutoff:3.500A) Processing helix chain 'L' and resid 32 through 59 removed outlier: 3.634A pdb=" N GLY L 36 " --> pdb=" O ALA L 32 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER L 37 " --> pdb=" O SER L 33 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ASN L 44 " --> pdb=" O GLU L 40 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU L 51 " --> pdb=" O GLN L 47 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG L 55 " --> pdb=" O LEU L 51 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG L 56 " --> pdb=" O PHE L 52 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA L 59 " --> pdb=" O ARG L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 75 removed outlier: 4.181A pdb=" N GLN L 75 " --> pdb=" O HIS L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 95 removed outlier: 3.936A pdb=" N ILE L 93 " --> pdb=" O PHE L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 131 removed outlier: 3.822A pdb=" N THR L 104 " --> pdb=" O THR L 100 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA L 114 " --> pdb=" O ALA L 110 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU L 115 " --> pdb=" O ASN L 111 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR L 125 " --> pdb=" O GLU L 121 " (cutoff:3.500A) removed outlier: 5.204A pdb=" N GLU L 126 " --> pdb=" O ILE L 122 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLY L 131 " --> pdb=" O PHE L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 48 through 50 Processing sheet with id=AA2, first strand: chain 'B' and resid 250 through 254 removed outlier: 6.517A pdb=" N HIS B 251 " --> pdb=" O TRP B 262 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 445 through 450 Processing sheet with id=AA4, first strand: chain 'B' and resid 336 through 340 removed outlier: 5.940A pdb=" N SER B 340 " --> pdb=" O PRO B 352 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR B 295 " --> pdb=" O CYS B 394 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 762 through 769 removed outlier: 4.760A pdb=" N GLY B 836 " --> pdb=" O LEU B 769 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ASN B 835 " --> pdb=" O TYR B 829 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR B 829 " --> pdb=" O ASN B 835 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N MET B 837 " --> pdb=" O GLY B 827 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N GLY B 827 " --> pdb=" O MET B 837 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE B 839 " --> pdb=" O THR B 825 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N PHE B 823 " --> pdb=" O PHE B 841 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N ILE B 821 " --> pdb=" O ASP B 843 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N ILE B 781 " --> pdb=" O ILE B 821 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N PHE B 823 " --> pdb=" O ALA B 779 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ALA B 779 " --> pdb=" O PHE B 823 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 68 through 69 Processing sheet with id=AA7, first strand: chain 'D' and resid 197 through 199 removed outlier: 8.044A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 187 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 246 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 234 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 197 through 199 removed outlier: 8.044A pdb=" N LEU D 183 " --> pdb=" O GLU D 233 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N GLU D 233 " --> pdb=" O LEU D 183 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL D 185 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N GLN D 231 " --> pdb=" O VAL D 185 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS D 187 " --> pdb=" O VAL D 229 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N TYR D 246 " --> pdb=" O PHE D 232 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE D 234 " --> pdb=" O LEU D 244 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 202 through 203 removed outlier: 4.627A pdb=" N TRP D 202 " --> pdb=" O ILE D 209 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE D 209 " --> pdb=" O TRP D 202 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 73 through 78 removed outlier: 6.781A pdb=" N ILE E 85 " --> pdb=" O LYS E 75 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N PHE E 77 " --> pdb=" O THR E 83 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N THR E 83 " --> pdb=" O PHE E 77 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS E 118 " --> pdb=" O LEU E 10 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N GLU E 12 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE E 14 " --> pdb=" O VAL E 114 " (cutoff:3.500A) removed outlier: 5.275A pdb=" N VAL E 114 " --> pdb=" O ILE E 14 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.094A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU F 138 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER F 83 " --> pdb=" O LEU F 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 10 through 12 removed outlier: 4.094A pdb=" N VAL F 5 " --> pdb=" O ARG F 12 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N GLY F 4 " --> pdb=" O LYS F 121 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 15 through 17 Processing sheet with id=AB5, first strand: chain 'H' and resid 55 through 61 removed outlier: 9.028A pdb=" N TYR H 55 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ASN H 70 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE H 57 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG H 68 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N HIS H 59 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR H 66 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 55 through 61 removed outlier: 9.028A pdb=" N TYR H 55 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 8.951A pdb=" N ASN H 70 " --> pdb=" O TYR H 55 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N PHE H 57 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ARG H 68 " --> pdb=" O PHE H 57 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N HIS H 59 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N TYR H 66 " --> pdb=" O HIS H 59 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU H 64 " --> pdb=" O ASP H 61 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER H 103 " --> pdb=" O TYR H 11 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 3 through 8 removed outlier: 4.537A pdb=" N VAL I 3 " --> pdb=" O HIS I 40 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N ALA I 42 " --> pdb=" O VAL I 3 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N LEU I 5 " --> pdb=" O ALA I 42 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASN I 44 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 5.819A pdb=" N VAL I 7 " --> pdb=" O ASN I 44 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N THR I 46 " --> pdb=" O VAL I 7 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N VAL I 47 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N ILE I 106 " --> pdb=" O LEU I 80 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N SER I 82 " --> pdb=" O ILE I 106 " (cutoff:3.500A) removed outlier: 8.330A pdb=" N ALA I 108 " --> pdb=" O SER I 82 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ILE I 84 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N LEU I 110 " --> pdb=" O ILE I 84 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU I 86 " --> pdb=" O LEU I 110 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL I 107 " --> pdb=" O LEU I 128 " (cutoff:3.500A) removed outlier: 8.291A pdb=" N THR I 130 " --> pdb=" O VAL I 107 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ALA I 109 " --> pdb=" O THR I 130 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LEU I 156 " --> pdb=" O VAL I 190 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N GLY I 192 " --> pdb=" O LEU I 156 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N ILE I 158 " --> pdb=" O GLY I 192 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 3 through 8 removed outlier: 4.179A pdb=" N VAL J 3 " --> pdb=" O HIS J 40 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ALA J 42 " --> pdb=" O VAL J 3 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N LEU J 5 " --> pdb=" O ALA J 42 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N ASN J 44 " --> pdb=" O LEU J 5 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N VAL J 7 " --> pdb=" O ASN J 44 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N THR J 46 " --> pdb=" O VAL J 7 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N ILE J 41 " --> pdb=" O TYR J 81 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ARG J 83 " --> pdb=" O ILE J 41 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE J 43 " --> pdb=" O ARG J 83 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N THR J 85 " --> pdb=" O ILE J 43 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N PHE J 45 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N ILE J 87 " --> pdb=" O PHE J 45 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N VAL J 47 " --> pdb=" O ILE J 87 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N ILE J 106 " --> pdb=" O LEU J 80 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N SER J 82 " --> pdb=" O ILE J 106 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N ALA J 108 " --> pdb=" O SER J 82 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ILE J 84 " --> pdb=" O ALA J 108 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N VAL J 107 " --> pdb=" O LEU J 128 " (cutoff:3.500A) removed outlier: 8.226A pdb=" N THR J 130 " --> pdb=" O VAL J 107 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N ALA J 109 " --> pdb=" O THR J 130 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU J 156 " --> pdb=" O VAL J 190 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N GLY J 192 " --> pdb=" O LEU J 156 " (cutoff:3.500A) removed outlier: 6.152A pdb=" N ILE J 158 " --> pdb=" O GLY J 192 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 92 through 95 removed outlier: 3.729A pdb=" N SER K 94 " --> pdb=" O ASN K 105 " (cutoff:3.500A) 916 hydrogen bonds defined for protein. 2673 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 174 hydrogen bond angles 0 basepair planarities 43 basepair parallelities 131 stacking parallelities Total time for adding SS restraints: 4.78 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 7450 1.34 - 1.46: 6731 1.46 - 1.58: 13692 1.58 - 1.70: 675 1.70 - 1.81: 162 Bond restraints: 28710 Sorted by residual: bond pdb=" C ASN B 199 " pdb=" N PRO B 200 " ideal model delta sigma weight residual 1.337 1.360 -0.024 9.80e-03 1.04e+04 5.75e+00 bond pdb=" CA ILE C 58 " pdb=" CB ILE C 58 " ideal model delta sigma weight residual 1.553 1.542 0.011 7.40e-03 1.83e+04 2.17e+00 bond pdb=" N LEU L 62 " pdb=" CA LEU L 62 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.87e+00 bond pdb=" CA ASP B 640 " pdb=" CB ASP B 640 " ideal model delta sigma weight residual 1.527 1.548 -0.020 1.61e-02 3.86e+03 1.61e+00 bond pdb=" CA ASN E 59 " pdb=" C ASN E 59 " ideal model delta sigma weight residual 1.525 1.513 0.012 1.02e-02 9.61e+03 1.49e+00 ... (remaining 28705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 38652 1.77 - 3.54: 1451 3.54 - 5.32: 237 5.32 - 7.09: 19 7.09 - 8.86: 1 Bond angle restraints: 40360 Sorted by residual: angle pdb=" N PHE C 27 " pdb=" CA PHE C 27 " pdb=" C PHE C 27 " ideal model delta sigma weight residual 112.93 107.15 5.78 1.33e+00 5.65e-01 1.89e+01 angle pdb=" N HIS K 22 " pdb=" CA HIS K 22 " pdb=" C HIS K 22 " ideal model delta sigma weight residual 111.96 117.97 -6.01 1.41e+00 5.03e-01 1.82e+01 angle pdb=" C LYS K 100 " pdb=" N CYS K 101 " pdb=" CA CYS K 101 " ideal model delta sigma weight residual 121.64 128.58 -6.94 1.70e+00 3.46e-01 1.67e+01 angle pdb=" C3' U A 299 " pdb=" O3' U A 299 " pdb=" P A A 300 " ideal model delta sigma weight residual 119.70 124.25 -4.55 1.20e+00 6.94e-01 1.44e+01 angle pdb=" N ILE B 641 " pdb=" CA ILE B 641 " pdb=" C ILE B 641 " ideal model delta sigma weight residual 111.67 108.08 3.59 9.50e-01 1.11e+00 1.43e+01 ... (remaining 40355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 15988 35.38 - 70.76: 714 70.76 - 106.14: 52 106.14 - 141.51: 3 141.51 - 176.89: 13 Dihedral angle restraints: 16770 sinusoidal: 9382 harmonic: 7388 Sorted by residual: dihedral pdb=" C4' A A 256 " pdb=" C3' A A 256 " pdb=" C2' A A 256 " pdb=" C1' A A 256 " ideal model delta sinusoidal sigma weight residual 36.35 -36.82 73.17 1 3.10e+00 1.04e-01 7.10e+02 dihedral pdb=" C4' G A 83 " pdb=" C3' G A 83 " pdb=" C2' G A 83 " pdb=" C1' G A 83 " ideal model delta sinusoidal sigma weight residual 36.34 -36.39 72.74 1 3.10e+00 1.04e-01 7.03e+02 dihedral pdb=" C4' G A 219 " pdb=" C3' G A 219 " pdb=" C2' G A 219 " pdb=" C1' G A 219 " ideal model delta sinusoidal sigma weight residual 36.35 -36.24 72.59 1 3.10e+00 1.04e-01 7.00e+02 ... (remaining 16767 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 4034 0.064 - 0.127: 343 0.127 - 0.191: 24 0.191 - 0.255: 360 0.255 - 0.319: 71 Chirality restraints: 4832 Sorted by residual: chirality pdb=" P A A 16 " pdb=" OP1 A A 16 " pdb=" OP2 A A 16 " pdb=" O5' A A 16 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" P U A 67 " pdb=" OP1 U A 67 " pdb=" OP2 U A 67 " pdb=" O5' U A 67 " both_signs ideal model delta sigma weight residual True 2.17 -2.49 -0.32 2.00e-01 2.50e+01 2.52e+00 chirality pdb=" P A A 300 " pdb=" OP1 A A 300 " pdb=" OP2 A A 300 " pdb=" O5' A A 300 " both_signs ideal model delta sigma weight residual True 2.17 -2.48 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 4829 not shown) Planarity restraints: 3869 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 614 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C PHE B 614 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE B 614 " 0.012 2.00e-02 2.50e+03 pdb=" N TYR B 615 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 301 " -0.024 2.00e-02 2.50e+03 1.10e-02 3.32e+00 pdb=" N9 A A 301 " 0.026 2.00e-02 2.50e+03 pdb=" C8 A A 301 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A A 301 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 301 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A A 301 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A A 301 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A A 301 " -0.002 2.00e-02 2.50e+03 pdb=" C2 A A 301 " 0.004 2.00e-02 2.50e+03 pdb=" N3 A A 301 " 0.002 2.00e-02 2.50e+03 pdb=" C4 A A 301 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A 14 " -0.023 2.00e-02 2.50e+03 1.07e-02 3.12e+00 pdb=" N9 A A 14 " 0.025 2.00e-02 2.50e+03 pdb=" C8 A A 14 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A A 14 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A A 14 " 0.003 2.00e-02 2.50e+03 pdb=" C6 A A 14 " -0.005 2.00e-02 2.50e+03 pdb=" N6 A A 14 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A A 14 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A A 14 " 0.002 2.00e-02 2.50e+03 pdb=" N3 A A 14 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A A 14 " 0.002 2.00e-02 2.50e+03 ... (remaining 3866 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 1153 2.71 - 3.25: 25404 3.25 - 3.80: 44095 3.80 - 4.35: 57500 4.35 - 4.90: 88238 Nonbonded interactions: 216390 Sorted by model distance: nonbonded pdb=" O2' A A 25 " pdb=" OP2 A A 26 " model vdw 2.157 3.040 nonbonded pdb=" OP1 G A 87 " pdb="MG MG R 101 " model vdw 2.171 2.170 nonbonded pdb=" OP2 A A 86 " pdb="MG MG A 401 " model vdw 2.172 2.170 nonbonded pdb=" OP1 A A 86 " pdb="MG MG A 402 " model vdw 2.178 2.170 nonbonded pdb=" O2' A A 37 " pdb=" O VAL G 35 " model vdw 2.182 3.040 ... (remaining 216385 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=0.40 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.170 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 26.430 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.552 28712 Z= 0.188 Angle : 0.750 8.861 40360 Z= 0.394 Chirality : 0.081 0.319 4832 Planarity : 0.003 0.041 3869 Dihedral : 17.331 176.894 11970 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.88 % Favored : 94.00 % Rotamer: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.84 (0.15), residues: 2485 helix: -1.09 (0.14), residues: 1039 sheet: -0.64 (0.26), residues: 374 loop : -3.18 (0.16), residues: 1072 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 148 TYR 0.013 0.001 TYR D 136 PHE 0.015 0.001 PHE C 153 TRP 0.022 0.001 TRP C 34 HIS 0.008 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (28710) covalent geometry : angle 0.74981 / 0.39 (40360) hydrogen bonds : bond 0.17609 / 9.01 ( 992) hydrogen bonds : angle 6.61126 / 2.59 ( 2847) metal coordination : bond 0.44924 / 22.46 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 613 time to evaluate : 0.949 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 114 MET cc_start: 0.8199 (tpp) cc_final: 0.7838 (tmt) REVERT: C 129 MET cc_start: 0.6784 (tpt) cc_final: 0.6014 (mtm) REVERT: C 176 PRO cc_start: 0.7017 (Cg_endo) cc_final: 0.6786 (Cg_exo) REVERT: F 102 TYR cc_start: 0.7376 (t80) cc_final: 0.6989 (t80) REVERT: H 95 LEU cc_start: 0.7006 (mt) cc_final: 0.6684 (tt) REVERT: K 28 ASN cc_start: 0.8376 (t0) cc_final: 0.7691 (m110) REVERT: K 114 LEU cc_start: 0.8415 (mt) cc_final: 0.8081 (mm) REVERT: L 75 GLN cc_start: 0.7916 (tt0) cc_final: 0.7601 (tt0) outliers start: 1 outliers final: 0 residues processed: 613 average time/residue: 0.6590 time to fit residues: 466.5276 Evaluate side-chains 278 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 197 optimal weight: 1.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.0470 chunk 244 optimal weight: 0.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 overall best weight: 1.2086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 90 GLN B 180 HIS B 201 ASN B 323 ASN B 362 GLN B 371 HIS B 377 GLN B 570 HIS B 595 GLN B 642 HIS B 803 ASN C 32 HIS C 59 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 158 GLN D 126 HIS D 190 ASN F 52 ASN F 76 GLN F 87 HIS F 89 GLN G 28 GLN G 56 HIS G 85 GLN H 27 HIS I 172 GLN I 235 ASN J 102 GLN K 41 HIS ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 22 ASN L 25 ASN L 58 GLN L 90 ASN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.133793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.102333 restraints weight = 57247.173| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.50 r_work: 0.3618 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 28712 Z= 0.224 Angle : 1.055 18.937 40360 Z= 0.453 Chirality : 0.081 1.390 4832 Planarity : 0.005 0.066 3869 Dihedral : 16.412 174.864 6802 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.64 % Favored : 93.28 % Rotamer: Outliers : 4.40 % Allowed : 16.25 % Favored : 79.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.59 (0.16), residues: 2485 helix: 0.21 (0.16), residues: 1056 sheet: -0.09 (0.26), residues: 379 loop : -2.84 (0.16), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 44 TYR 0.019 0.002 TYR B 258 PHE 0.022 0.002 PHE I 45 TRP 0.055 0.003 TRP H 118 HIS 0.012 0.002 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.22 (28710) covalent geometry : angle 1.05526 / 0.45 (40360) hydrogen bonds : bond 0.05418 / 2.81 ( 992) hydrogen bonds : angle 4.65064 / 1.84 ( 2847) metal coordination : bond 0.00470 / 0.23 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 324 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.8557 (mmm) cc_final: 0.8289 (mmm) REVERT: B 191 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.7590 (mpp) REVERT: B 358 VAL cc_start: 0.7802 (t) cc_final: 0.7583 (t) REVERT: B 455 HIS cc_start: 0.7118 (OUTLIER) cc_final: 0.6908 (m170) REVERT: B 540 ASP cc_start: 0.7703 (m-30) cc_final: 0.7486 (m-30) REVERT: B 684 MET cc_start: 0.7358 (tpp) cc_final: 0.6969 (mmt) REVERT: B 808 HIS cc_start: 0.7628 (OUTLIER) cc_final: 0.7372 (p90) REVERT: B 857 ILE cc_start: 0.8770 (OUTLIER) cc_final: 0.8512 (mp) REVERT: C 33 MET cc_start: 0.7123 (tmm) cc_final: 0.6715 (tmm) REVERT: C 129 MET cc_start: 0.7328 (tpt) cc_final: 0.6186 (mtt) REVERT: D 28 ARG cc_start: 0.7632 (OUTLIER) cc_final: 0.7195 (mmm160) REVERT: D 104 LEU cc_start: 0.8227 (tt) cc_final: 0.7792 (mm) REVERT: D 143 TYR cc_start: 0.7489 (m-80) cc_final: 0.6937 (m-80) REVERT: D 208 PHE cc_start: 0.7632 (OUTLIER) cc_final: 0.7139 (t80) REVERT: E 24 GLU cc_start: 0.8561 (mm-30) cc_final: 0.8076 (mm-30) REVERT: E 59 ASN cc_start: 0.8449 (m-40) cc_final: 0.8144 (t0) REVERT: F 119 ASP cc_start: 0.7829 (t0) cc_final: 0.7469 (m-30) REVERT: F 149 ASP cc_start: 0.8237 (m-30) cc_final: 0.7937 (p0) REVERT: G 127 LYS cc_start: 0.7438 (mmmt) cc_final: 0.7110 (tmtt) REVERT: H 9 TRP cc_start: 0.7958 (OUTLIER) cc_final: 0.7716 (p90) REVERT: H 36 GLN cc_start: 0.7974 (tm-30) cc_final: 0.7761 (tm-30) REVERT: H 102 GLU cc_start: 0.8029 (mp0) cc_final: 0.7044 (mp0) REVERT: I 78 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7824 (pp) REVERT: I 132 GLN cc_start: 0.8194 (mm110) cc_final: 0.7893 (tt0) REVERT: I 141 LEU cc_start: 0.7813 (OUTLIER) cc_final: 0.7261 (mm) REVERT: J 228 LEU cc_start: 0.8423 (mp) cc_final: 0.8214 (mp) REVERT: J 239 ARG cc_start: 0.7216 (ttp80) cc_final: 0.6850 (ttp80) REVERT: K 95 MET cc_start: 0.6578 (OUTLIER) cc_final: 0.5787 (pmm) REVERT: K 114 LEU cc_start: 0.8607 (mt) cc_final: 0.8347 (mm) REVERT: L 75 GLN cc_start: 0.8328 (tt0) cc_final: 0.7916 (tt0) REVERT: L 117 MET cc_start: 0.7808 (tpp) cc_final: 0.7502 (mmt) outliers start: 101 outliers final: 27 residues processed: 392 average time/residue: 0.6371 time to fit residues: 292.0012 Evaluate side-chains 304 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 267 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 415 CYS Chi-restraints excluded: chain B residue 455 HIS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 807 ASP Chi-restraints excluded: chain B residue 808 HIS Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 16 CYS Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 139 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 88 LYS Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 5 LEU Chi-restraints excluded: chain I residue 46 THR Chi-restraints excluded: chain I residue 78 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 87 ILE Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 189 ILE Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain L residue 112 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 216 optimal weight: 0.8980 chunk 277 optimal weight: 0.8980 chunk 222 optimal weight: 0.0370 chunk 266 optimal weight: 8.9990 chunk 263 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 247 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 67 optimal weight: 0.5980 chunk 13 optimal weight: 5.9990 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 234 GLN B 727 ASN C 107 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 197 GLN F 45 GLN F 76 GLN F 111 GLN G 56 HIS H 27 HIS J 102 GLN ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.132936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.101285 restraints weight = 57157.396| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.49 r_work: 0.3597 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3600 r_free = 0.3600 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (8 function evaluations) r_final: 0.3600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 28712 Z= 0.154 Angle : 0.832 11.251 40360 Z= 0.368 Chirality : 0.067 0.749 4832 Planarity : 0.004 0.063 3869 Dihedral : 16.282 175.513 6802 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.19 % Favored : 94.77 % Rotamer: Outliers : 4.01 % Allowed : 17.99 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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 (0.16), residues: 2485 helix: 0.79 (0.16), residues: 1053 sheet: 0.32 (0.26), residues: 391 loop : -2.72 (0.17), residues: 1041 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 43 TYR 0.011 0.001 TYR K 18 PHE 0.023 0.001 PHE D 139 TRP 0.015 0.001 TRP C 44 HIS 0.006 0.001 HIS K 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 (28710) covalent geometry : angle 0.83204 / 0.37 (40360) hydrogen bonds : bond 0.04174 / 2.16 ( 992) hydrogen bonds : angle 4.32535 / 1.72 ( 2847) metal coordination : bond 0.00098 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 301 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.8556 (mmm) cc_final: 0.8287 (mmm) REVERT: B 191 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7527 (mpp) REVERT: B 208 ARG cc_start: 0.7420 (tpp-160) cc_final: 0.7036 (tmm160) REVERT: B 509 THR cc_start: 0.8512 (m) cc_final: 0.8081 (m) REVERT: B 684 MET cc_start: 0.7446 (tpp) cc_final: 0.6988 (mmt) REVERT: B 808 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.7319 (p90) REVERT: B 853 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8410 (mmt-90) REVERT: B 857 ILE cc_start: 0.8791 (OUTLIER) cc_final: 0.8560 (mp) REVERT: C 33 MET cc_start: 0.7015 (tmm) cc_final: 0.6815 (tmm) REVERT: C 129 MET cc_start: 0.7429 (tpt) cc_final: 0.6642 (tpp) REVERT: D 3 ARG cc_start: 0.7907 (mmm160) cc_final: 0.7473 (mmm160) REVERT: D 28 ARG cc_start: 0.7639 (OUTLIER) cc_final: 0.7387 (mmm160) REVERT: D 135 GLN cc_start: 0.7587 (mm110) cc_final: 0.7249 (mm-40) REVERT: D 142 MET cc_start: 0.7967 (pmm) cc_final: 0.6814 (ptt) REVERT: D 143 TYR cc_start: 0.7601 (m-80) cc_final: 0.7072 (m-80) REVERT: E 24 GLU cc_start: 0.8469 (mm-30) cc_final: 0.8132 (mm-30) REVERT: E 59 ASN cc_start: 0.8358 (m-40) cc_final: 0.8148 (t0) REVERT: E 98 MET cc_start: 0.7888 (ttp) cc_final: 0.7423 (ttm) REVERT: F 76 GLN cc_start: 0.5773 (mt0) cc_final: 0.5134 (tt0) REVERT: F 119 ASP cc_start: 0.7821 (t0) cc_final: 0.7425 (m-30) REVERT: F 149 ASP cc_start: 0.8217 (m-30) cc_final: 0.8013 (p0) REVERT: G 127 LYS cc_start: 0.7454 (mmmt) cc_final: 0.7180 (tmtt) REVERT: H 9 TRP cc_start: 0.7821 (OUTLIER) cc_final: 0.7510 (p90) REVERT: H 10 GLN cc_start: 0.7455 (OUTLIER) cc_final: 0.7246 (tt0) REVERT: H 36 GLN cc_start: 0.7969 (tm-30) cc_final: 0.7716 (tm-30) REVERT: I 132 GLN cc_start: 0.8284 (mm110) cc_final: 0.8043 (tt0) REVERT: I 225 MET cc_start: 0.6402 (tmm) cc_final: 0.6134 (tpp) REVERT: J 51 GLU cc_start: 0.7273 (pm20) cc_final: 0.6913 (pm20) REVERT: J 196 MET cc_start: 0.6839 (ppp) cc_final: 0.5662 (mtp) REVERT: J 223 LYS cc_start: 0.6561 (mttt) cc_final: 0.6156 (ttpt) REVERT: J 268 ASP cc_start: 0.8213 (m-30) cc_final: 0.7884 (m-30) REVERT: K 28 ASN cc_start: 0.8418 (t0) cc_final: 0.7671 (m-40) REVERT: K 95 MET cc_start: 0.6731 (OUTLIER) cc_final: 0.5872 (pmm) REVERT: L 71 HIS cc_start: 0.7391 (t-90) cc_final: 0.7167 (t-90) REVERT: L 75 GLN cc_start: 0.8393 (tt0) cc_final: 0.8047 (tt0) REVERT: L 117 MET cc_start: 0.7631 (tpp) cc_final: 0.7367 (mmt) REVERT: L 123 ASN cc_start: 0.8523 (m-40) cc_final: 0.8086 (m-40) outliers start: 92 outliers final: 28 residues processed: 361 average time/residue: 0.6442 time to fit residues: 273.3888 Evaluate side-chains 296 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 260 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 808 HIS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 16 CYS Chi-restraints excluded: chain D residue 18 GLU Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 10 GLN Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain L residue 112 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 213 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 187 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 116 optimal weight: 6.9990 chunk 124 optimal weight: 4.9990 chunk 97 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 209 optimal weight: 0.6980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 612 ASN B 850 GLN C 59 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN F 45 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.124784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.091797 restraints weight = 56473.591| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 2.47 r_work: 0.3422 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3422 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3422 r_free = 0.3422 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.5713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 28712 Z= 0.214 Angle : 0.939 14.530 40360 Z= 0.416 Chirality : 0.074 1.011 4832 Planarity : 0.005 0.066 3869 Dihedral : 16.442 176.544 6802 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.80 % Favored : 93.08 % Rotamer: Outliers : 4.79 % Allowed : 18.90 % Favored : 76.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.91 (0.16), residues: 2485 helix: 0.83 (0.16), residues: 1048 sheet: 0.54 (0.26), residues: 379 loop : -2.64 (0.16), residues: 1058 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG L 56 TYR 0.017 0.002 TYR D 150 PHE 0.021 0.002 PHE I 45 TRP 0.025 0.002 TRP H 118 HIS 0.010 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.21 (28710) covalent geometry : angle 0.93913 / 0.42 (40360) hydrogen bonds : bond 0.05621 / 2.92 ( 992) hydrogen bonds : angle 4.53854 / 1.80 ( 2847) metal coordination : bond 0.00189 / 0.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 284 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 MET cc_start: 0.8612 (OUTLIER) cc_final: 0.7893 (mpp) REVERT: B 684 MET cc_start: 0.7407 (tpp) cc_final: 0.7128 (mmt) REVERT: B 857 ILE cc_start: 0.8913 (OUTLIER) cc_final: 0.8650 (mp) REVERT: C 129 MET cc_start: 0.7485 (tpt) cc_final: 0.6389 (tpp) REVERT: D 28 ARG cc_start: 0.7711 (OUTLIER) cc_final: 0.7489 (mmm-85) REVERT: D 104 LEU cc_start: 0.8313 (tt) cc_final: 0.7912 (mm) REVERT: D 142 MET cc_start: 0.7852 (pmm) cc_final: 0.6887 (ptt) REVERT: D 143 TYR cc_start: 0.7647 (m-80) cc_final: 0.7120 (m-80) REVERT: D 158 THR cc_start: 0.8359 (OUTLIER) cc_final: 0.8142 (p) REVERT: D 272 ASP cc_start: 0.7413 (t70) cc_final: 0.6968 (p0) REVERT: E 24 GLU cc_start: 0.8734 (mm-30) cc_final: 0.8362 (mm-30) REVERT: E 79 ASN cc_start: 0.8507 (p0) cc_final: 0.8306 (p0) REVERT: F 119 ASP cc_start: 0.7854 (t0) cc_final: 0.7327 (m-30) REVERT: F 125 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7592 (ptp-170) REVERT: F 149 ASP cc_start: 0.8386 (m-30) cc_final: 0.8052 (p0) REVERT: G 24 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8432 (mm) REVERT: G 100 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8289 (mm) REVERT: H 9 TRP cc_start: 0.7965 (OUTLIER) cc_final: 0.7101 (p90) REVERT: H 10 GLN cc_start: 0.7556 (OUTLIER) cc_final: 0.7247 (tt0) REVERT: H 36 GLN cc_start: 0.7932 (tm-30) cc_final: 0.7645 (tm-30) REVERT: H 66 TYR cc_start: 0.7541 (OUTLIER) cc_final: 0.7285 (m-80) REVERT: J 5 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8220 (mt) REVERT: J 196 MET cc_start: 0.7428 (ppp) cc_final: 0.6470 (mtm) REVERT: J 225 MET cc_start: 0.6368 (tpp) cc_final: 0.5717 (tpp) REVERT: J 268 ASP cc_start: 0.8440 (m-30) cc_final: 0.7917 (OUTLIER) REVERT: J 276 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7871 (tttp) REVERT: K 16 GLN cc_start: 0.8398 (tp40) cc_final: 0.8092 (tp-100) REVERT: K 95 MET cc_start: 0.6868 (OUTLIER) cc_final: 0.6008 (pmm) REVERT: L 63 LYS cc_start: 0.7437 (mppt) cc_final: 0.7213 (mmmm) REVERT: L 121 GLU cc_start: 0.6913 (pp20) cc_final: 0.6574 (pm20) outliers start: 110 outliers final: 36 residues processed: 370 average time/residue: 0.6833 time to fit residues: 293.0823 Evaluate side-chains 292 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 244 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 28 ARG Chi-restraints excluded: chain D residue 158 THR Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 56 HIS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 10 GLN Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain H residue 69 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 65 ILE Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 276 LYS Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 101 CYS Chi-restraints excluded: chain L residue 112 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 66 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 248 optimal weight: 0.4980 chunk 128 optimal weight: 0.4980 chunk 113 optimal weight: 10.0000 chunk 63 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN H 27 HIS J 34 HIS K 28 ASN ** K 71 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 = 0.4144 r_free = 0.4144 target = 0.126976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.094318 restraints weight = 56305.282| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.49 r_work: 0.3476 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.5882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 28712 Z= 0.147 Angle : 0.826 11.630 40360 Z= 0.365 Chirality : 0.065 0.813 4832 Planarity : 0.004 0.062 3869 Dihedral : 16.294 177.826 6802 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.43 % Favored : 94.53 % Rotamer: Outliers : 4.31 % Allowed : 21.34 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -0.62 (0.17), residues: 2485 helix: 1.10 (0.16), residues: 1053 sheet: 0.67 (0.26), residues: 378 loop : -2.54 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 76 TYR 0.016 0.001 TYR K 36 PHE 0.027 0.001 PHE K 60 TRP 0.025 0.001 TRP H 118 HIS 0.006 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.15 (28710) covalent geometry : angle 0.82603 / 0.36 (40360) hydrogen bonds : bond 0.04378 / 2.25 ( 992) hydrogen bonds : angle 4.28739 / 1.71 ( 2847) metal coordination : bond 0.00101 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 272 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 389 LEU cc_start: 0.8982 (OUTLIER) cc_final: 0.8642 (mt) REVERT: B 539 ASP cc_start: 0.8560 (m-30) cc_final: 0.8253 (p0) REVERT: B 626 ARG cc_start: 0.8391 (mmt90) cc_final: 0.8111 (mmm160) REVERT: B 684 MET cc_start: 0.7479 (tpp) cc_final: 0.7201 (mmt) REVERT: B 857 ILE cc_start: 0.8902 (OUTLIER) cc_final: 0.8638 (mp) REVERT: C 117 MET cc_start: 0.7500 (mpt) cc_final: 0.7297 (mpm) REVERT: C 129 MET cc_start: 0.7320 (tpt) cc_final: 0.6318 (tpp) REVERT: D 30 GLN cc_start: 0.8596 (mt0) cc_final: 0.8295 (mp10) REVERT: D 143 TYR cc_start: 0.7546 (m-80) cc_final: 0.7092 (m-80) REVERT: D 272 ASP cc_start: 0.7465 (t70) cc_final: 0.6996 (p0) REVERT: E 24 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8445 (mm-30) REVERT: E 98 MET cc_start: 0.7851 (ttp) cc_final: 0.7382 (ttm) REVERT: F 68 MET cc_start: 0.4510 (pmt) cc_final: 0.4148 (pmm) REVERT: F 119 ASP cc_start: 0.7763 (t0) cc_final: 0.7276 (m-30) REVERT: F 149 ASP cc_start: 0.8382 (m-30) cc_final: 0.8127 (p0) REVERT: G 16 THR cc_start: 0.6927 (OUTLIER) cc_final: 0.6531 (p) REVERT: G 100 LEU cc_start: 0.8432 (OUTLIER) cc_final: 0.8137 (mm) REVERT: H 9 TRP cc_start: 0.7796 (OUTLIER) cc_final: 0.7120 (p90) REVERT: H 36 GLN cc_start: 0.7957 (tm-30) cc_final: 0.7703 (tm-30) REVERT: I 141 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7928 (mm) REVERT: J 196 MET cc_start: 0.7263 (ppp) cc_final: 0.6340 (mtm) REVERT: J 225 MET cc_start: 0.5945 (tpp) cc_final: 0.5542 (mmt) REVERT: J 268 ASP cc_start: 0.8465 (m-30) cc_final: 0.7979 (OUTLIER) REVERT: K 11 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7919 (mm-30) REVERT: K 15 ARG cc_start: 0.7627 (mtm110) cc_final: 0.7408 (mtm110) REVERT: K 16 GLN cc_start: 0.8284 (tp40) cc_final: 0.7986 (tp40) REVERT: K 28 ASN cc_start: 0.8331 (t0) cc_final: 0.7716 (m-40) REVERT: K 95 MET cc_start: 0.6716 (OUTLIER) cc_final: 0.5972 (pmm) REVERT: K 114 LEU cc_start: 0.8760 (mt) cc_final: 0.8516 (mm) REVERT: L 63 LYS cc_start: 0.7635 (mppt) cc_final: 0.7349 (mmmm) outliers start: 99 outliers final: 41 residues processed: 347 average time/residue: 0.6568 time to fit residues: 267.2177 Evaluate side-chains 291 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 243 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 108 ASP Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 56 HIS Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 15 SER Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 101 CYS Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 112 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 39 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 222 optimal weight: 3.9990 chunk 184 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 57 optimal weight: 0.2980 chunk 126 optimal weight: 5.9990 chunk 177 optimal weight: 0.7980 chunk 174 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 392 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN F 111 GLN G 28 GLN H 27 HIS J 6 ASN ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.125711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.092824 restraints weight = 56459.439| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 2.48 r_work: 0.3445 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.6156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28712 Z= 0.159 Angle : 0.843 12.485 40360 Z= 0.372 Chirality : 0.065 0.831 4832 Planarity : 0.004 0.058 3869 Dihedral : 16.241 178.521 6802 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.44 % Favored : 93.52 % Rotamer: Outliers : 4.05 % Allowed : 21.65 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.54 (0.17), residues: 2485 helix: 1.14 (0.16), residues: 1060 sheet: 0.74 (0.26), residues: 375 loop : -2.50 (0.17), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 76 TYR 0.023 0.001 TYR J 160 PHE 0.013 0.001 PHE C 153 TRP 0.040 0.002 TRP H 118 HIS 0.007 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (28710) covalent geometry : angle 0.84342 / 0.37 (40360) hydrogen bonds : bond 0.04577 / 2.36 ( 992) hydrogen bonds : angle 4.32413 / 1.72 ( 2847) metal coordination : bond 0.00128 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 251 time to evaluate : 0.945 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 VAL cc_start: 0.8142 (OUTLIER) cc_final: 0.7922 (t) REVERT: B 191 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7943 (mpp) REVERT: B 389 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8664 (mt) REVERT: B 539 ASP cc_start: 0.8571 (m-30) cc_final: 0.8296 (p0) REVERT: B 629 MET cc_start: 0.8152 (OUTLIER) cc_final: 0.7923 (ttt) REVERT: B 684 MET cc_start: 0.7499 (tpp) cc_final: 0.7217 (mmt) REVERT: B 857 ILE cc_start: 0.8889 (OUTLIER) cc_final: 0.8611 (mp) REVERT: C 129 MET cc_start: 0.7192 (tpt) cc_final: 0.6330 (tpp) REVERT: C 140 MET cc_start: 0.1248 (pmm) cc_final: -0.0559 (mtm) REVERT: D 104 LEU cc_start: 0.8223 (tt) cc_final: 0.7793 (mm) REVERT: D 143 TYR cc_start: 0.7576 (m-80) cc_final: 0.7139 (m-80) REVERT: D 272 ASP cc_start: 0.7451 (t70) cc_final: 0.7001 (p0) REVERT: D 278 GLN cc_start: 0.6298 (mt0) cc_final: 0.6010 (mt0) REVERT: E 24 GLU cc_start: 0.8795 (mm-30) cc_final: 0.8375 (mm-30) REVERT: F 68 MET cc_start: 0.4411 (pmt) cc_final: 0.4138 (pmm) REVERT: F 119 ASP cc_start: 0.7749 (t0) cc_final: 0.7294 (m-30) REVERT: F 149 ASP cc_start: 0.8388 (m-30) cc_final: 0.8186 (p0) REVERT: G 16 THR cc_start: 0.6998 (OUTLIER) cc_final: 0.6626 (p) REVERT: G 100 LEU cc_start: 0.8509 (OUTLIER) cc_final: 0.8215 (mm) REVERT: H 9 TRP cc_start: 0.7767 (OUTLIER) cc_final: 0.6959 (p90) REVERT: H 36 GLN cc_start: 0.7875 (tm-30) cc_final: 0.7668 (tm-30) REVERT: I 227 ASP cc_start: 0.7424 (OUTLIER) cc_final: 0.7018 (m-30) REVERT: J 5 LEU cc_start: 0.8514 (OUTLIER) cc_final: 0.8193 (mt) REVERT: J 196 MET cc_start: 0.7358 (ppp) cc_final: 0.6278 (mtm) REVERT: J 268 ASP cc_start: 0.8442 (m-30) cc_final: 0.8011 (p0) REVERT: K 28 ASN cc_start: 0.8359 (t0) cc_final: 0.7807 (m-40) REVERT: K 95 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.5995 (pmm) REVERT: K 114 LEU cc_start: 0.8737 (mt) cc_final: 0.8463 (mm) REVERT: L 63 LYS cc_start: 0.7768 (mppt) cc_final: 0.7410 (mmmm) REVERT: L 121 GLU cc_start: 0.6938 (pp20) cc_final: 0.6662 (pp20) outliers start: 93 outliers final: 45 residues processed: 319 average time/residue: 0.6552 time to fit residues: 245.3987 Evaluate side-chains 293 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 237 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 110 LYS Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 612 ASN Chi-restraints excluded: chain B residue 629 MET Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 56 HIS Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 100 LEU Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 101 CYS Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 112 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 260 optimal weight: 3.9990 chunk 153 optimal weight: 0.6980 chunk 167 optimal weight: 6.9990 chunk 249 optimal weight: 0.7980 chunk 234 optimal weight: 3.9990 chunk 157 optimal weight: 0.8980 chunk 165 optimal weight: 0.8980 chunk 257 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 139 optimal weight: 0.9980 chunk 278 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 30 GLN F 111 GLN H 27 HIS ** K 71 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.125840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.093061 restraints weight = 56633.253| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.48 r_work: 0.3452 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.67 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.6356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 28712 Z= 0.152 Angle : 0.829 11.997 40360 Z= 0.368 Chirality : 0.064 0.797 4832 Planarity : 0.004 0.056 3869 Dihedral : 16.219 179.336 6802 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.00 % Favored : 93.96 % Rotamer: Outliers : 3.48 % Allowed : 22.65 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.44 (0.17), residues: 2485 helix: 1.22 (0.16), residues: 1067 sheet: 0.78 (0.26), residues: 380 loop : -2.46 (0.17), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 239 TYR 0.019 0.001 TYR K 36 PHE 0.011 0.001 PHE C 153 TRP 0.042 0.002 TRP H 118 HIS 0.008 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.15 (28710) covalent geometry : angle 0.82855 / 0.37 (40360) hydrogen bonds : bond 0.04469 / 2.29 ( 992) hydrogen bonds : angle 4.29047 / 1.71 ( 2847) metal coordination : bond 0.00110 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 253 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 VAL cc_start: 0.8138 (OUTLIER) cc_final: 0.7931 (t) REVERT: B 191 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.7932 (mpp) REVERT: B 389 LEU cc_start: 0.8974 (OUTLIER) cc_final: 0.8667 (mt) REVERT: B 539 ASP cc_start: 0.8566 (m-30) cc_final: 0.8321 (p0) REVERT: B 684 MET cc_start: 0.7679 (tpp) cc_final: 0.7277 (mmt) REVERT: B 857 ILE cc_start: 0.8885 (OUTLIER) cc_final: 0.8606 (mp) REVERT: C 33 MET cc_start: 0.6776 (tmm) cc_final: 0.6306 (tmm) REVERT: C 129 MET cc_start: 0.7172 (tpt) cc_final: 0.6315 (tpp) REVERT: C 140 MET cc_start: 0.1541 (pmm) cc_final: -0.0447 (mtm) REVERT: D 30 GLN cc_start: 0.8608 (OUTLIER) cc_final: 0.8316 (mp10) REVERT: D 104 LEU cc_start: 0.8223 (tt) cc_final: 0.7784 (mm) REVERT: D 142 MET cc_start: 0.7798 (pmm) cc_final: 0.7210 (tpp) REVERT: D 143 TYR cc_start: 0.7483 (m-80) cc_final: 0.7047 (m-80) REVERT: D 272 ASP cc_start: 0.7512 (t70) cc_final: 0.7016 (p0) REVERT: D 278 GLN cc_start: 0.6346 (mt0) cc_final: 0.6127 (mt0) REVERT: E 24 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8508 (mm-30) REVERT: E 98 MET cc_start: 0.7917 (ttp) cc_final: 0.7432 (ttm) REVERT: F 68 MET cc_start: 0.4434 (pmt) cc_final: 0.4196 (pmm) REVERT: F 119 ASP cc_start: 0.7731 (t0) cc_final: 0.7294 (m-30) REVERT: G 16 THR cc_start: 0.6950 (OUTLIER) cc_final: 0.6591 (p) REVERT: H 9 TRP cc_start: 0.7706 (OUTLIER) cc_final: 0.7028 (p90) REVERT: H 36 GLN cc_start: 0.7863 (tm-30) cc_final: 0.7647 (tm-30) REVERT: I 35 MET cc_start: 0.8622 (tmt) cc_final: 0.7925 (tmt) REVERT: I 75 ARG cc_start: 0.8618 (tpp80) cc_final: 0.8172 (ttp-170) REVERT: J 5 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8162 (mt) REVERT: J 196 MET cc_start: 0.7352 (ppp) cc_final: 0.6294 (mtm) REVERT: J 239 ARG cc_start: 0.7317 (ttp80) cc_final: 0.6995 (tmm-80) REVERT: J 268 ASP cc_start: 0.8357 (m-30) cc_final: 0.7993 (p0) REVERT: K 11 GLU cc_start: 0.8111 (OUTLIER) cc_final: 0.7890 (mm-30) REVERT: K 16 GLN cc_start: 0.8253 (tp40) cc_final: 0.8043 (tp-100) REVERT: K 28 ASN cc_start: 0.8364 (t0) cc_final: 0.7778 (m-40) REVERT: K 95 MET cc_start: 0.6938 (OUTLIER) cc_final: 0.5998 (pmm) REVERT: L 63 LYS cc_start: 0.7679 (mppt) cc_final: 0.7331 (mmmm) REVERT: L 121 GLU cc_start: 0.6934 (pp20) cc_final: 0.6650 (pp20) outliers start: 80 outliers final: 45 residues processed: 310 average time/residue: 0.6549 time to fit residues: 237.2128 Evaluate side-chains 294 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 239 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 56 HIS Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 124 LEU Chi-restraints excluded: chain J residue 125 ASP Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 101 CYS Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 112 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 237 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 174 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 153 optimal weight: 0.6980 chunk 171 optimal weight: 0.8980 chunk 127 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 234 optimal weight: 2.9990 chunk 137 optimal weight: 0.7980 chunk 50 optimal weight: 0.2980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 135 GLN F 111 GLN G 28 GLN H 27 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.126057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.093422 restraints weight = 56504.210| |-----------------------------------------------------------------------------| r_work (start): 0.3590 rms_B_bonded: 2.48 r_work: 0.3453 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3456 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.63 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3456 r_free = 0.3456 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3456 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28712 Z= 0.144 Angle : 0.826 11.985 40360 Z= 0.367 Chirality : 0.063 0.783 4832 Planarity : 0.004 0.076 3869 Dihedral : 16.196 179.254 6802 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.24 % Favored : 93.72 % Rotamer: Outliers : 3.40 % Allowed : 23.30 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.39 (0.17), residues: 2485 helix: 1.23 (0.16), residues: 1068 sheet: 0.76 (0.26), residues: 383 loop : -2.39 (0.17), residues: 1034 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG D 76 TYR 0.024 0.001 TYR K 36 PHE 0.009 0.001 PHE C 153 TRP 0.060 0.002 TRP H 118 HIS 0.008 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (28710) covalent geometry : angle 0.82595 / 0.37 (40360) hydrogen bonds : bond 0.04385 / 2.25 ( 992) hydrogen bonds : angle 4.27217 / 1.70 ( 2847) metal coordination : bond 0.00114 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 248 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.7926 (mpp) REVERT: B 389 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8688 (mt) REVERT: B 461 LYS cc_start: 0.8802 (mppt) cc_final: 0.8243 (mtmt) REVERT: B 466 GLN cc_start: 0.7697 (pp30) cc_final: 0.7349 (tm-30) REVERT: B 539 ASP cc_start: 0.8534 (m-30) cc_final: 0.8326 (p0) REVERT: B 684 MET cc_start: 0.7692 (tpp) cc_final: 0.7410 (mmt) REVERT: B 857 ILE cc_start: 0.8874 (OUTLIER) cc_final: 0.8591 (mp) REVERT: C 33 MET cc_start: 0.6790 (tmm) cc_final: 0.6245 (tmm) REVERT: C 129 MET cc_start: 0.7144 (tpt) cc_final: 0.6371 (tpp) REVERT: C 140 MET cc_start: 0.2414 (pmm) cc_final: -0.0094 (mtm) REVERT: C 175 ARG cc_start: 0.7475 (tmm-80) cc_final: 0.6863 (tpp-160) REVERT: D 9 LYS cc_start: 0.8500 (mmmm) cc_final: 0.8198 (mptt) REVERT: D 104 LEU cc_start: 0.8235 (tt) cc_final: 0.7805 (mm) REVERT: D 142 MET cc_start: 0.7774 (pmm) cc_final: 0.7160 (tpp) REVERT: D 143 TYR cc_start: 0.7532 (m-80) cc_final: 0.7090 (m-80) REVERT: D 272 ASP cc_start: 0.7509 (t70) cc_final: 0.7008 (p0) REVERT: D 278 GLN cc_start: 0.6298 (mt0) cc_final: 0.6083 (mt0) REVERT: E 24 GLU cc_start: 0.8888 (mm-30) cc_final: 0.8539 (mm-30) REVERT: E 98 MET cc_start: 0.7927 (ttp) cc_final: 0.7444 (ttm) REVERT: F 68 MET cc_start: 0.4510 (pmt) cc_final: 0.4291 (pmm) REVERT: F 119 ASP cc_start: 0.7714 (t0) cc_final: 0.7288 (m-30) REVERT: G 16 THR cc_start: 0.6993 (OUTLIER) cc_final: 0.6544 (p) REVERT: H 9 TRP cc_start: 0.7683 (OUTLIER) cc_final: 0.6986 (p90) REVERT: H 36 GLN cc_start: 0.7861 (tm-30) cc_final: 0.7586 (tm-30) REVERT: H 66 TYR cc_start: 0.7325 (OUTLIER) cc_final: 0.7092 (m-80) REVERT: I 75 ARG cc_start: 0.8564 (tpp80) cc_final: 0.8097 (ttp-170) REVERT: J 5 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8147 (mt) REVERT: J 196 MET cc_start: 0.7385 (ppp) cc_final: 0.6321 (mtm) REVERT: J 239 ARG cc_start: 0.7267 (ttp80) cc_final: 0.6940 (tmm-80) REVERT: J 268 ASP cc_start: 0.8390 (m-30) cc_final: 0.7928 (p0) REVERT: K 11 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.7837 (mm-30) REVERT: K 28 ASN cc_start: 0.8277 (t0) cc_final: 0.7730 (m-40) REVERT: K 95 MET cc_start: 0.6907 (OUTLIER) cc_final: 0.5954 (pmm) REVERT: L 63 LYS cc_start: 0.7605 (mppt) cc_final: 0.7184 (mmmm) REVERT: L 121 GLU cc_start: 0.7043 (pp20) cc_final: 0.6733 (pp20) outliers start: 78 outliers final: 51 residues processed: 306 average time/residue: 0.6362 time to fit residues: 228.6552 Evaluate side-chains 295 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 235 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain F residue 111 GLN Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 56 HIS Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 66 TYR Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 101 CYS Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 112 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 119 optimal weight: 5.9990 chunk 83 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 132 optimal weight: 0.9980 chunk 257 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 200 optimal weight: 0.7980 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.124236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.091170 restraints weight = 56699.162| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 2.51 r_work: 0.3410 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3413 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.55 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3413 r_free = 0.3413 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3413 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 28712 Z= 0.173 Angle : 0.869 12.804 40360 Z= 0.387 Chirality : 0.066 0.848 4832 Planarity : 0.004 0.065 3869 Dihedral : 16.238 179.604 6802 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.56 % Favored : 93.40 % Rotamer: Outliers : 3.57 % Allowed : 23.13 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.44 (0.17), residues: 2485 helix: 1.20 (0.16), residues: 1063 sheet: 0.77 (0.27), residues: 369 loop : -2.38 (0.17), residues: 1053 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG K 15 TYR 0.022 0.002 TYR K 36 PHE 0.028 0.001 PHE K 60 TRP 0.049 0.002 TRP H 118 HIS 0.010 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (28710) covalent geometry : angle 0.86920 / 0.39 (40360) hydrogen bonds : bond 0.04844 / 2.49 ( 992) hydrogen bonds : angle 4.32618 / 1.73 ( 2847) metal coordination : bond 0.00212 / 0.11 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 250 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 MET cc_start: 0.8744 (OUTLIER) cc_final: 0.7994 (mpp) REVERT: B 389 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8723 (mt) REVERT: B 466 GLN cc_start: 0.7787 (pp30) cc_final: 0.7231 (tm130) REVERT: B 684 MET cc_start: 0.7654 (tpp) cc_final: 0.7329 (mmt) REVERT: B 857 ILE cc_start: 0.8910 (OUTLIER) cc_final: 0.8620 (mp) REVERT: C 33 MET cc_start: 0.6824 (tmm) cc_final: 0.6344 (tmm) REVERT: C 129 MET cc_start: 0.7033 (tpt) cc_final: 0.6690 (tpp) REVERT: C 140 MET cc_start: 0.2354 (pmm) cc_final: -0.0020 (mtm) REVERT: C 175 ARG cc_start: 0.7472 (tmm-80) cc_final: 0.6978 (tpp-160) REVERT: D 30 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8396 (mp10) REVERT: D 104 LEU cc_start: 0.8193 (OUTLIER) cc_final: 0.7761 (mm) REVERT: D 142 MET cc_start: 0.7763 (pmm) cc_final: 0.7214 (tpp) REVERT: D 143 TYR cc_start: 0.7592 (m-80) cc_final: 0.7132 (m-80) REVERT: D 272 ASP cc_start: 0.7510 (t70) cc_final: 0.6901 (p0) REVERT: D 278 GLN cc_start: 0.6767 (mt0) cc_final: 0.6558 (mt0) REVERT: E 24 GLU cc_start: 0.8857 (mm-30) cc_final: 0.8576 (mm-30) REVERT: E 98 MET cc_start: 0.7939 (ttp) cc_final: 0.7448 (ttm) REVERT: E 127 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7742 (mp0) REVERT: F 68 MET cc_start: 0.4486 (pmt) cc_final: 0.4267 (pmm) REVERT: F 102 TYR cc_start: 0.7390 (t80) cc_final: 0.7172 (t80) REVERT: F 119 ASP cc_start: 0.7728 (t0) cc_final: 0.7296 (m-30) REVERT: F 131 GLU cc_start: 0.8292 (pt0) cc_final: 0.7846 (pp20) REVERT: G 16 THR cc_start: 0.7031 (OUTLIER) cc_final: 0.6609 (p) REVERT: H 9 TRP cc_start: 0.7746 (OUTLIER) cc_final: 0.6727 (p90) REVERT: H 36 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7646 (tm-30) REVERT: I 75 ARG cc_start: 0.8550 (tpp80) cc_final: 0.8133 (ttp-170) REVERT: I 227 ASP cc_start: 0.7577 (OUTLIER) cc_final: 0.7227 (m-30) REVERT: J 196 MET cc_start: 0.7429 (ppp) cc_final: 0.6402 (mtm) REVERT: J 239 ARG cc_start: 0.7226 (ttp80) cc_final: 0.6905 (tmm-80) REVERT: J 268 ASP cc_start: 0.8433 (m-30) cc_final: 0.7972 (p0) REVERT: J 276 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7977 (tptp) REVERT: K 11 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7820 (mm-30) REVERT: K 28 ASN cc_start: 0.8264 (t0) cc_final: 0.7699 (m-40) REVERT: K 95 MET cc_start: 0.7003 (OUTLIER) cc_final: 0.5985 (pmm) REVERT: L 30 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7961 (ttp-110) REVERT: L 63 LYS cc_start: 0.7760 (mppt) cc_final: 0.7327 (mmmm) REVERT: L 75 GLN cc_start: 0.8721 (tt0) cc_final: 0.8197 (tt0) REVERT: L 121 GLU cc_start: 0.7132 (pp20) cc_final: 0.6817 (pp20) REVERT: L 126 GLU cc_start: 0.7281 (tm-30) cc_final: 0.6958 (pm20) REVERT: L 128 ILE cc_start: 0.8672 (tt) cc_final: 0.8360 (pp) outliers start: 82 outliers final: 47 residues processed: 308 average time/residue: 0.6712 time to fit residues: 242.3679 Evaluate side-chains 300 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 240 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 111 LEU Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 168 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 22 VAL Chi-restraints excluded: chain E residue 127 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 276 LYS Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain K residue 101 CYS Chi-restraints excluded: chain K residue 112 SER Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 30 ARG Chi-restraints excluded: chain L residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 34 optimal weight: 4.9990 chunk 23 optimal weight: 5.9990 chunk 242 optimal weight: 0.8980 chunk 217 optimal weight: 0.3980 chunk 176 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 231 optimal weight: 0.0060 chunk 67 optimal weight: 0.9980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 135 GLN E 139 ASN H 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.126241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.093625 restraints weight = 56872.249| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 2.50 r_work: 0.3458 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.6740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 28712 Z= 0.139 Angle : 0.829 13.478 40360 Z= 0.371 Chirality : 0.062 0.760 4832 Planarity : 0.004 0.057 3869 Dihedral : 16.194 179.939 6802 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.16 % Favored : 93.80 % Rotamer: Outliers : 2.70 % Allowed : 24.00 % Favored : 73.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.34 (0.17), residues: 2485 helix: 1.26 (0.16), residues: 1066 sheet: 0.67 (0.26), residues: 388 loop : -2.30 (0.18), residues: 1031 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 15 TYR 0.022 0.001 TYR J 160 PHE 0.012 0.001 PHE D 29 TRP 0.036 0.001 TRP H 118 HIS 0.010 0.001 HIS B 371 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (28710) covalent geometry : angle 0.82922 / 0.37 (40360) hydrogen bonds : bond 0.04271 / 2.19 ( 992) hydrogen bonds : angle 4.25636 / 1.70 ( 2847) metal coordination : bond 0.00148 / 0.07 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4970 Ramachandran restraints generated. 2485 Oldfield, 0 Emsley, 2485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 243 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.7929 (mpp) REVERT: B 389 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8703 (mt) REVERT: B 466 GLN cc_start: 0.7767 (pp30) cc_final: 0.7164 (tm130) REVERT: B 684 MET cc_start: 0.7625 (tpp) cc_final: 0.7173 (mmt) REVERT: B 857 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8629 (mp) REVERT: C 33 MET cc_start: 0.6731 (tmm) cc_final: 0.6169 (tmm) REVERT: C 114 MET cc_start: 0.8091 (tpp) cc_final: 0.7375 (tmt) REVERT: C 117 MET cc_start: 0.7272 (mpm) cc_final: 0.6916 (mpt) REVERT: C 129 MET cc_start: 0.6776 (tpt) cc_final: 0.6084 (tpp) REVERT: C 140 MET cc_start: 0.2495 (pmm) cc_final: 0.0086 (mtm) REVERT: C 175 ARG cc_start: 0.7649 (tmm-80) cc_final: 0.7204 (tpp-160) REVERT: D 30 GLN cc_start: 0.8635 (mt0) cc_final: 0.8273 (mp10) REVERT: D 104 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7777 (mm) REVERT: D 142 MET cc_start: 0.7755 (pmm) cc_final: 0.7162 (tpp) REVERT: D 143 TYR cc_start: 0.7583 (m-80) cc_final: 0.7134 (m-80) REVERT: D 272 ASP cc_start: 0.7451 (t70) cc_final: 0.6892 (p0) REVERT: E 24 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8520 (mm-30) REVERT: E 98 MET cc_start: 0.7899 (ttp) cc_final: 0.7409 (ttm) REVERT: F 68 MET cc_start: 0.4425 (pmt) cc_final: 0.4213 (pmm) REVERT: F 102 TYR cc_start: 0.7506 (t80) cc_final: 0.7119 (t80) REVERT: F 119 ASP cc_start: 0.7708 (t0) cc_final: 0.7296 (m-30) REVERT: F 125 ARG cc_start: 0.8445 (OUTLIER) cc_final: 0.7982 (ptp-170) REVERT: F 131 GLU cc_start: 0.8285 (pt0) cc_final: 0.7847 (pp20) REVERT: G 16 THR cc_start: 0.6894 (OUTLIER) cc_final: 0.6430 (p) REVERT: H 9 TRP cc_start: 0.7623 (OUTLIER) cc_final: 0.6508 (p90) REVERT: H 36 GLN cc_start: 0.7901 (tm-30) cc_final: 0.7624 (tm-30) REVERT: I 75 ARG cc_start: 0.8542 (tpp80) cc_final: 0.8135 (ttp-170) REVERT: J 196 MET cc_start: 0.7384 (ppp) cc_final: 0.6348 (mtm) REVERT: J 239 ARG cc_start: 0.7407 (ttp80) cc_final: 0.7100 (tmm-80) REVERT: K 11 GLU cc_start: 0.8069 (OUTLIER) cc_final: 0.7865 (mm-30) REVERT: K 28 ASN cc_start: 0.8272 (t0) cc_final: 0.7709 (m-40) REVERT: K 95 MET cc_start: 0.6874 (OUTLIER) cc_final: 0.5919 (pmm) REVERT: L 63 LYS cc_start: 0.7715 (mppt) cc_final: 0.7318 (mmmm) REVERT: L 75 GLN cc_start: 0.8700 (tt0) cc_final: 0.8212 (tt0) REVERT: L 121 GLU cc_start: 0.7130 (pp20) cc_final: 0.6856 (pp20) outliers start: 62 outliers final: 41 residues processed: 287 average time/residue: 0.6527 time to fit residues: 219.7426 Evaluate side-chains 279 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 191 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 371 HIS Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 430 MET Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 857 ILE Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 93 VAL Chi-restraints excluded: chain C residue 118 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain F residue 125 ARG Chi-restraints excluded: chain F residue 156 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 98 GLU Chi-restraints excluded: chain G residue 132 SER Chi-restraints excluded: chain H residue 9 TRP Chi-restraints excluded: chain H residue 23 VAL Chi-restraints excluded: chain H residue 75 ASP Chi-restraints excluded: chain H residue 124 GLU Chi-restraints excluded: chain I residue 49 HIS Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 125 ASP Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 155 LYS Chi-restraints excluded: chain J residue 156 LEU Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 95 MET Chi-restraints excluded: chain L residue 6 ASN Chi-restraints excluded: chain L residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 1 optimal weight: 2.9990 chunk 211 optimal weight: 4.9990 chunk 271 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 124 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 272 optimal weight: 0.5980 chunk 219 optimal weight: 0.0270 overall best weight: 0.7038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN D 30 GLN G 28 GLN I 143 HIS J 6 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.125882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.093283 restraints weight = 56466.273| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 2.49 r_work: 0.3451 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3454 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.54 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3454 r_free = 0.3454 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (10 function evaluations) r_final: 0.3454 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.6815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 28712 Z= 0.145 Angle : 0.835 12.891 40360 Z= 0.374 Chirality : 0.063 0.760 4832 Planarity : 0.004 0.053 3869 Dihedral : 16.152 179.915 6802 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.36 % Favored : 93.60 % Rotamer: Outliers : 2.61 % Allowed : 24.39 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.30 (0.17), residues: 2485 helix: 1.26 (0.16), residues: 1062 sheet: 0.86 (0.27), residues: 381 loop : -2.28 (0.18), residues: 1042 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG K 15 TYR 0.019 0.001 TYR G 41 PHE 0.009 0.001 PHE I 45 TRP 0.064 0.002 TRP H 118 HIS 0.010 0.001 HIS K 41 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (28710) covalent geometry : angle 0.83481 / 0.37 (40360) hydrogen bonds : bond 0.04357 / 2.23 ( 992) hydrogen bonds : angle 4.27244 / 1.71 ( 2847) metal coordination : bond 0.00110 / 0.06 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13030.32 seconds wall clock time: 221 minutes 56.71 seconds (13316.71 seconds total)