Starting phenix.real_space_refine on Mon Jun 23 16:38:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7c7a_30297/06_2025/7c7a_30297.cif Found real_map, /net/cci-nas-00/data/ceres_data/7c7a_30297/06_2025/7c7a_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7c7a_30297/06_2025/7c7a_30297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7c7a_30297/06_2025/7c7a_30297.map" model { file = "/net/cci-nas-00/data/ceres_data/7c7a_30297/06_2025/7c7a_30297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7c7a_30297/06_2025/7c7a_30297.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'RNA': 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: {'RNA': 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: 15.80, per 1000 atoms: 0.57 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: 6.20 Conformation dependent library (CDL) restraints added in 2.7 seconds 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: 9.65 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: 10.24 Time building geometry restraints manager: 7.56 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=" O5' G A 80 " pdb=" C5' G A 80 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.86e+00 bond pdb=" O5' U A 77 " pdb=" C5' U A 77 " ideal model delta sigma weight residual 1.420 1.440 -0.020 1.50e-02 4.44e+03 1.85e+00 ... (remaining 28705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 39559 1.77 - 3.54: 693 3.54 - 5.32: 88 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=" 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 angle pdb=" N ARG D 269 " pdb=" CA ARG D 269 " pdb=" C ARG D 269 " ideal model delta sigma weight residual 114.75 110.05 4.70 1.26e+00 6.30e-01 1.39e+01 ... (remaining 40355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.38: 16902 35.38 - 70.76: 863 70.76 - 106.14: 84 106.14 - 141.51: 3 141.51 - 176.89: 14 Dihedral angle restraints: 17866 sinusoidal: 10478 harmonic: 7388 Sorted by residual: dihedral pdb=" C4' U A 143 " pdb=" C3' U A 143 " pdb=" C2' U A 143 " pdb=" C1' U A 143 " ideal model delta sinusoidal sigma weight residual -35.00 33.79 -68.79 1 8.00e+00 1.56e-02 9.57e+01 dihedral pdb=" CA HIS K 22 " pdb=" C HIS K 22 " pdb=" N VAL K 23 " pdb=" CA VAL K 23 " ideal model delta harmonic sigma weight residual -180.00 -131.15 -48.85 0 5.00e+00 4.00e-02 9.54e+01 dihedral pdb=" C5' U A 143 " pdb=" C4' U A 143 " pdb=" C3' U A 143 " pdb=" O3' U A 143 " ideal model delta sinusoidal sigma weight residual 147.00 82.73 64.27 1 8.00e+00 1.56e-02 8.49e+01 ... (remaining 17863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4413 0.060 - 0.120: 373 0.120 - 0.180: 42 0.180 - 0.240: 3 0.240 - 0.301: 1 Chirality restraints: 4832 Sorted by residual: chirality pdb=" C3' U A 143 " pdb=" C4' U A 143 " pdb=" O3' U A 143 " pdb=" C2' U A 143 " both_signs ideal model delta sigma weight residual False -2.74 -2.44 -0.30 2.00e-01 2.50e+01 2.26e+00 chirality pdb=" C2' U A 143 " pdb=" C3' U A 143 " pdb=" O2' U A 143 " pdb=" C1' U A 143 " both_signs ideal model delta sigma weight residual False -2.52 -2.75 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" C3' G A 79 " pdb=" C4' G A 79 " pdb=" O3' G A 79 " pdb=" C2' G A 79 " both_signs ideal model delta sigma weight residual False -2.48 -2.67 0.20 2.00e-01 2.50e+01 9.54e-01 ... (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: 4.950 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: 0.020 Extract box with map and model: 0.970 Check model and map are aligned: 0.200 Set scattering table: 0.220 Process input model: 69.840 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 90.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 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 : 0.004 0.552 28712 Z= 0.179 Angle : 0.582 8.861 40360 Z= 0.358 Chirality : 0.035 0.301 4832 Planarity : 0.003 0.041 3869 Dihedral : 18.472 176.894 13066 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.022 0.001 TRP C 34 HIS 0.008 0.001 HIS B 371 PHE 0.015 0.001 PHE C 153 TYR 0.013 0.001 TYR D 136 ARG 0.002 0.000 ARG C 148 Details of bonding type rmsd hydrogen bonds : bond 0.17609 ( 992) hydrogen bonds : angle 6.61126 ( 2847) metal coordination : bond 0.44924 ( 2) covalent geometry : bond 0.00217 (28710) covalent geometry : angle 0.58214 (40360) *********************** 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 : 2.736 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: 1.5486 time to fit residues: 1084.6164 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 : 2.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 238 optimal weight: 0.7980 chunk 213 optimal weight: 0.7980 chunk 118 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 144 optimal weight: 2.9990 chunk 114 optimal weight: 7.9990 chunk 221 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 134 optimal weight: 0.7980 chunk 164 optimal weight: 1.9990 chunk 256 optimal weight: 5.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 90 GLN B 180 HIS B 201 ASN B 323 ASN B 371 HIS B 377 GLN B 570 HIS B 595 GLN B 642 HIS B 803 ASN C 32 HIS C 48 GLN 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 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.131924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.099929 restraints weight = 57087.981| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 2.51 r_work: 0.3570 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3574 r_free = 0.3574 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3573 r_free = 0.3573 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28712 Z= 0.187 Angle : 0.698 8.573 40360 Z= 0.360 Chirality : 0.041 0.311 4832 Planarity : 0.005 0.081 3869 Dihedral : 19.707 168.034 7898 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.64 % Favored : 93.28 % Rotamer: Outliers : 4.40 % Allowed : 16.20 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.16), residues: 2485 helix: 0.19 (0.16), residues: 1055 sheet: -0.05 (0.26), residues: 376 loop : -2.87 (0.16), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.003 TRP H 118 HIS 0.012 0.002 HIS B 371 PHE 0.021 0.002 PHE I 45 TYR 0.019 0.002 TYR B 258 ARG 0.012 0.001 ARG H 44 Details of bonding type rmsd hydrogen bonds : bond 0.05270 ( 992) hydrogen bonds : angle 4.62784 ( 2847) metal coordination : bond 0.05632 ( 2) covalent geometry : bond 0.00412 (28710) covalent geometry : angle 0.69766 (40360) *********************** 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 428 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 327 time to evaluate : 2.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 MET cc_start: 0.8504 (mmm) cc_final: 0.8193 (mmm) REVERT: B 455 HIS cc_start: 0.7149 (OUTLIER) cc_final: 0.6904 (m170) REVERT: B 540 ASP cc_start: 0.7746 (m-30) cc_final: 0.7483 (m-30) REVERT: B 684 MET cc_start: 0.7398 (tpp) cc_final: 0.6829 (mmt) REVERT: B 857 ILE cc_start: 0.8849 (OUTLIER) cc_final: 0.8609 (mp) REVERT: C 33 MET cc_start: 0.7113 (tmm) cc_final: 0.6785 (tmm) REVERT: C 129 MET cc_start: 0.7348 (tpt) cc_final: 0.6191 (mtt) REVERT: D 3 ARG cc_start: 0.7980 (mmm160) cc_final: 0.7705 (mmm160) REVERT: D 28 ARG cc_start: 0.7640 (OUTLIER) cc_final: 0.7181 (mmm160) REVERT: D 104 LEU cc_start: 0.8203 (tt) cc_final: 0.7786 (mm) REVERT: D 143 TYR cc_start: 0.7617 (m-80) cc_final: 0.7058 (m-80) REVERT: E 24 GLU cc_start: 0.8637 (mm-30) cc_final: 0.8179 (mm-30) REVERT: E 59 ASN cc_start: 0.8479 (m-40) cc_final: 0.8201 (t0) REVERT: E 86 ILE cc_start: 0.8625 (mm) cc_final: 0.8352 (tt) REVERT: E 91 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.8004 (pt0) REVERT: E 131 MET cc_start: 0.8169 (mpm) cc_final: 0.7968 (mpt) REVERT: F 119 ASP cc_start: 0.7787 (t0) cc_final: 0.7453 (m-30) REVERT: F 149 ASP cc_start: 0.8248 (m-30) cc_final: 0.7975 (p0) REVERT: G 127 LYS cc_start: 0.7586 (mmmt) cc_final: 0.7302 (tmtt) REVERT: H 9 TRP cc_start: 0.8056 (OUTLIER) cc_final: 0.7707 (p90) REVERT: H 36 GLN cc_start: 0.7981 (tm-30) cc_final: 0.7743 (tm-30) REVERT: H 102 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7053 (mp0) REVERT: I 132 GLN cc_start: 0.8347 (mm110) cc_final: 0.8046 (tt0) REVERT: I 141 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7350 (mm) REVERT: I 172 GLN cc_start: 0.8599 (OUTLIER) cc_final: 0.8398 (mm-40) REVERT: J 223 LYS cc_start: 0.6694 (mttt) cc_final: 0.6274 (ttpp) REVERT: J 239 ARG cc_start: 0.7173 (ttp80) cc_final: 0.6779 (ttp80) REVERT: K 95 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.5847 (pmm) REVERT: K 114 LEU cc_start: 0.8625 (mt) cc_final: 0.8351 (mm) REVERT: L 75 GLN cc_start: 0.8320 (tt0) cc_final: 0.7850 (tt0) REVERT: L 117 MET cc_start: 0.7772 (tpp) cc_final: 0.7500 (mmt) outliers start: 101 outliers final: 26 residues processed: 398 average time/residue: 1.4740 time to fit residues: 677.1484 Evaluate side-chains 299 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 264 time to evaluate : 2.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 363 LYS Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 411 SER 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 857 ILE 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 139 PHE Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain E residue 91 GLU Chi-restraints excluded: chain F residue 120 ILE Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 56 HIS 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 102 GLU 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 80 LEU Chi-restraints excluded: chain I residue 141 LEU Chi-restraints excluded: chain I residue 172 GLN Chi-restraints excluded: chain J residue 5 LEU 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 188 optimal weight: 0.9980 chunk 211 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 chunk 261 optimal weight: 0.9980 chunk 242 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 253 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 234 GLN B 727 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 197 GLN F 45 GLN F 111 GLN G 56 HIS H 27 HIS I 172 GLN J 102 GLN J 240 ASN ** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.128394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.095669 restraints weight = 56749.460| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 2.53 r_work: 0.3490 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.4612 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= 0.147 Angle : 0.608 10.126 40360 Z= 0.312 Chirality : 0.038 0.263 4832 Planarity : 0.004 0.064 3869 Dihedral : 19.557 170.868 7898 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.35 % Favored : 94.61 % Rotamer: Outliers : 4.27 % Allowed : 17.68 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.03 (0.16), residues: 2485 helix: 0.79 (0.16), residues: 1046 sheet: 0.28 (0.26), residues: 387 loop : -2.70 (0.16), residues: 1052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP H 118 HIS 0.006 0.001 HIS G 56 PHE 0.020 0.001 PHE K 60 TYR 0.013 0.001 TYR K 18 ARG 0.008 0.001 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 992) hydrogen bonds : angle 4.37367 ( 2847) metal coordination : bond 0.00178 ( 2) covalent geometry : bond 0.00322 (28710) covalent geometry : angle 0.60816 (40360) *********************** 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 396 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 298 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 191 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.7638 (mpp) REVERT: B 401 VAL cc_start: 0.8470 (OUTLIER) cc_final: 0.8238 (p) REVERT: B 455 HIS cc_start: 0.7323 (OUTLIER) cc_final: 0.7115 (m170) REVERT: B 614 PHE cc_start: 0.6696 (t80) cc_final: 0.6495 (m-80) REVERT: B 684 MET cc_start: 0.7484 (tpp) cc_final: 0.7040 (mmt) REVERT: B 853 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8470 (mmt-90) REVERT: B 857 ILE cc_start: 0.8852 (OUTLIER) cc_final: 0.8609 (mp) REVERT: C 129 MET cc_start: 0.7377 (tpt) cc_final: 0.6328 (tpp) REVERT: D 3 ARG cc_start: 0.7846 (mmm160) cc_final: 0.7399 (mmm160) REVERT: D 28 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7436 (mmm160) REVERT: D 138 ASP cc_start: 0.7817 (t0) cc_final: 0.7586 (OUTLIER) REVERT: D 142 MET cc_start: 0.7911 (pmm) cc_final: 0.6963 (ptt) REVERT: D 143 TYR cc_start: 0.7716 (m-80) cc_final: 0.7241 (m-80) REVERT: D 272 ASP cc_start: 0.7363 (t70) cc_final: 0.6897 (p0) REVERT: E 24 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8102 (mm-30) REVERT: E 79 ASN cc_start: 0.8412 (p0) cc_final: 0.8176 (p0) REVERT: E 98 MET cc_start: 0.7919 (ttp) cc_final: 0.7404 (ttm) REVERT: F 119 ASP cc_start: 0.7853 (t0) cc_final: 0.7426 (m-30) REVERT: F 149 ASP cc_start: 0.8303 (m-30) cc_final: 0.8101 (p0) REVERT: G 127 LYS cc_start: 0.7454 (mmmt) cc_final: 0.7161 (tmtt) REVERT: H 9 TRP cc_start: 0.7911 (OUTLIER) cc_final: 0.7527 (p90) REVERT: H 36 GLN cc_start: 0.7968 (tm-30) cc_final: 0.7683 (tm-30) REVERT: I 132 GLN cc_start: 0.8276 (mm110) cc_final: 0.8060 (tt0) REVERT: J 189 ILE cc_start: 0.8198 (OUTLIER) cc_final: 0.7836 (mm) REVERT: J 196 MET cc_start: 0.7163 (ppp) cc_final: 0.6022 (mtm) REVERT: J 223 LYS cc_start: 0.6931 (mttt) cc_final: 0.6540 (ttpt) REVERT: J 225 MET cc_start: 0.6318 (tpp) cc_final: 0.5530 (tpp) REVERT: J 268 ASP cc_start: 0.8318 (m-30) cc_final: 0.7986 (m-30) REVERT: J 282 GLU cc_start: 0.8696 (mp0) cc_final: 0.8384 (pp20) REVERT: K 95 MET cc_start: 0.6734 (OUTLIER) cc_final: 0.5912 (pmm) REVERT: L 117 MET cc_start: 0.7631 (tpp) cc_final: 0.7382 (mmt) REVERT: L 123 ASN cc_start: 0.8594 (m-40) cc_final: 0.8129 (m-40) outliers start: 98 outliers final: 30 residues processed: 363 average time/residue: 1.4544 time to fit residues: 611.5946 Evaluate side-chains 298 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 260 time to evaluate : 2.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 401 VAL Chi-restraints excluded: chain B residue 455 HIS 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 853 ARG Chi-restraints excluded: chain B residue 857 ILE 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 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 G residue 24 LEU 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 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 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 J residue 214 LEU 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 28 optimal weight: 10.0000 chunk 156 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 242 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 258 optimal weight: 1.9990 chunk 124 optimal weight: 9.9990 chunk 118 optimal weight: 0.5980 chunk 197 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 201 ASN C 59 GLN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN F 45 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS J 34 HIS ** L 58 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.122229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.088665 restraints weight = 57104.423| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.53 r_work: 0.3357 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3360 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.57 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.61 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 28712 Z= 0.208 Angle : 0.679 10.221 40360 Z= 0.351 Chirality : 0.041 0.336 4832 Planarity : 0.005 0.061 3869 Dihedral : 19.671 170.697 7898 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.88 % Favored : 93.00 % Rotamer: Outliers : 5.53 % Allowed : 18.25 % Favored : 76.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.16), residues: 2485 helix: 0.78 (0.16), residues: 1050 sheet: 0.50 (0.26), residues: 381 loop : -2.63 (0.16), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP H 118 HIS 0.006 0.001 HIS K 41 PHE 0.020 0.002 PHE I 45 TYR 0.017 0.002 TYR D 150 ARG 0.008 0.001 ARG I 136 Details of bonding type rmsd hydrogen bonds : bond 0.05729 ( 992) hydrogen bonds : angle 4.54060 ( 2847) metal coordination : bond 0.00227 ( 2) covalent geometry : bond 0.00460 (28710) covalent geometry : angle 0.67929 (40360) *********************** 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 399 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 272 time to evaluate : 2.669 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 385 HIS cc_start: 0.7903 (t70) cc_final: 0.7699 (t70) REVERT: B 389 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8699 (mt) REVERT: B 455 HIS cc_start: 0.7681 (OUTLIER) cc_final: 0.7479 (m170) REVERT: B 539 ASP cc_start: 0.8614 (m-30) cc_final: 0.8332 (OUTLIER) REVERT: B 684 MET cc_start: 0.7454 (tpp) cc_final: 0.7073 (mmt) REVERT: B 857 ILE cc_start: 0.8925 (OUTLIER) cc_final: 0.8648 (mp) REVERT: C 114 MET cc_start: 0.7400 (tpt) cc_final: 0.6841 (tmt) REVERT: C 129 MET cc_start: 0.7476 (tpt) cc_final: 0.6607 (tpp) REVERT: D 7 PHE cc_start: 0.8650 (m-10) cc_final: 0.8446 (m-10) REVERT: D 28 ARG cc_start: 0.7805 (OUTLIER) cc_final: 0.7534 (mmm160) REVERT: D 143 TYR cc_start: 0.7680 (m-80) cc_final: 0.7226 (m-80) REVERT: D 158 THR cc_start: 0.8354 (OUTLIER) cc_final: 0.8145 (p) REVERT: D 272 ASP cc_start: 0.7446 (t70) cc_final: 0.6973 (p0) REVERT: E 24 GLU cc_start: 0.8742 (mm-30) cc_final: 0.8376 (mm-30) REVERT: F 119 ASP cc_start: 0.7864 (t0) cc_final: 0.7322 (m-30) REVERT: F 125 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7209 (ptp-170) REVERT: F 149 ASP cc_start: 0.8434 (m-30) cc_final: 0.8185 (p0) REVERT: G 16 THR cc_start: 0.7243 (OUTLIER) cc_final: 0.6865 (p) REVERT: G 97 ILE cc_start: 0.9190 (OUTLIER) cc_final: 0.8970 (mm) REVERT: G 100 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8309 (mm) REVERT: G 104 ILE cc_start: 0.9139 (mt) cc_final: 0.8929 (pt) REVERT: H 9 TRP cc_start: 0.7901 (OUTLIER) cc_final: 0.6917 (p90) REVERT: H 36 GLN cc_start: 0.7975 (tm-30) cc_final: 0.7747 (tm-30) REVERT: H 43 LYS cc_start: 0.7099 (tptp) cc_final: 0.6799 (tppp) REVERT: H 66 TYR cc_start: 0.7501 (OUTLIER) cc_final: 0.7198 (m-80) REVERT: I 227 ASP cc_start: 0.7631 (OUTLIER) cc_final: 0.7267 (m-30) REVERT: I 239 ARG cc_start: 0.7699 (OUTLIER) cc_final: 0.7433 (ttm110) REVERT: J 5 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8169 (mt) REVERT: J 51 GLU cc_start: 0.7326 (pm20) cc_final: 0.7032 (pm20) REVERT: J 144 LYS cc_start: 0.8308 (pptt) cc_final: 0.7603 (mmpt) REVERT: J 196 MET cc_start: 0.7445 (ppp) cc_final: 0.6460 (mtm) REVERT: J 223 LYS cc_start: 0.6992 (mttt) cc_final: 0.6449 (ttpp) REVERT: J 225 MET cc_start: 0.6217 (tpp) cc_final: 0.5904 (mmt) REVERT: J 268 ASP cc_start: 0.8549 (m-30) cc_final: 0.8021 (OUTLIER) REVERT: J 282 GLU cc_start: 0.8713 (mp0) cc_final: 0.8508 (pp20) REVERT: K 16 GLN cc_start: 0.8348 (tp40) cc_final: 0.8133 (tp-100) REVERT: K 95 MET cc_start: 0.6950 (OUTLIER) cc_final: 0.6112 (pmm) REVERT: L 121 GLU cc_start: 0.6923 (pp20) cc_final: 0.6303 (pm20) outliers start: 127 outliers final: 48 residues processed: 371 average time/residue: 1.4381 time to fit residues: 617.2202 Evaluate side-chains 297 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 236 time to evaluate : 2.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 SER 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 455 HIS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 594 LYS Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 706 VAL Chi-restraints excluded: chain B residue 727 ASN Chi-restraints excluded: chain B residue 828 THR 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 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 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 22 VAL Chi-restraints excluded: chain E residue 108 ASP 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 24 LEU Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 56 HIS Chi-restraints excluded: chain G residue 97 ILE 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 51 GLU 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 5 LEU Chi-restraints excluded: chain I residue 80 LEU Chi-restraints excluded: chain I residue 110 LEU Chi-restraints excluded: chain I residue 227 ASP Chi-restraints excluded: chain I residue 239 ARG Chi-restraints excluded: chain J residue 5 LEU Chi-restraints excluded: chain J residue 58 LYS 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 189 ILE Chi-restraints excluded: chain J residue 214 LEU Chi-restraints excluded: chain J residue 240 ASN Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 279 MET Chi-restraints excluded: chain K residue 67 VAL Chi-restraints excluded: chain K residue 95 MET 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 91 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 252 optimal weight: 0.7980 chunk 64 optimal weight: 0.0980 chunk 102 optimal weight: 0.5980 chunk 272 optimal weight: 0.5980 chunk 2 optimal weight: 3.9990 chunk 256 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 193 optimal weight: 0.6980 chunk 162 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 323 ASN ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 107 GLN ** C 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 135 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN H 27 HIS K 10 GLN K 28 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.124982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.091847 restraints weight = 56394.359| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.53 r_work: 0.3421 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3421 ------------------------------------------------------------------------------- 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 = 0.61 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 = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3422 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.5798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28712 Z= 0.120 Angle : 0.587 10.443 40360 Z= 0.302 Chirality : 0.037 0.267 4832 Planarity : 0.004 0.054 3869 Dihedral : 19.545 173.408 7898 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.39 % Favored : 94.57 % Rotamer: Outliers : 4.05 % Allowed : 20.95 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.17), residues: 2485 helix: 1.13 (0.16), residues: 1046 sheet: 0.61 (0.26), residues: 378 loop : -2.52 (0.17), residues: 1061 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP H 118 HIS 0.006 0.001 HIS K 41 PHE 0.026 0.001 PHE K 60 TYR 0.012 0.001 TYR G 41 ARG 0.008 0.000 ARG J 239 Details of bonding type rmsd hydrogen bonds : bond 0.04203 ( 992) hydrogen bonds : angle 4.28257 ( 2847) metal coordination : bond 0.00050 ( 2) covalent geometry : bond 0.00262 (28710) covalent geometry : angle 0.58741 (40360) *********************** 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 366 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 273 time to evaluate : 2.704 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 389 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8610 (mt) REVERT: B 455 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.7126 (m170) REVERT: B 539 ASP cc_start: 0.8612 (m-30) cc_final: 0.8322 (p0) REVERT: B 684 MET cc_start: 0.7664 (OUTLIER) cc_final: 0.7383 (mmt) REVERT: B 700 ILE cc_start: 0.7098 (mm) cc_final: 0.6807 (tp) REVERT: B 857 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8595 (mp) REVERT: C 129 MET cc_start: 0.7378 (tpt) cc_final: 0.6252 (tpp) REVERT: D 7 PHE cc_start: 0.8589 (m-10) cc_final: 0.8373 (m-10) REVERT: D 30 GLN cc_start: 0.8545 (OUTLIER) cc_final: 0.8284 (mp10) REVERT: D 143 TYR cc_start: 0.7458 (m-80) cc_final: 0.7094 (m-80) REVERT: D 175 MET cc_start: 0.5203 (OUTLIER) cc_final: 0.4766 (mtm) REVERT: D 272 ASP cc_start: 0.7465 (t70) cc_final: 0.6964 (p0) REVERT: E 24 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8415 (mm-30) REVERT: F 68 MET cc_start: 0.4853 (pmt) cc_final: 0.4571 (pmm) REVERT: F 119 ASP cc_start: 0.7771 (t0) cc_final: 0.7284 (m-30) REVERT: G 100 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8144 (mm) REVERT: H 9 TRP cc_start: 0.7881 (OUTLIER) cc_final: 0.7174 (p90) REVERT: H 36 GLN cc_start: 0.7934 (tm-30) cc_final: 0.7676 (tm-30) REVERT: J 125 ASP cc_start: 0.6802 (p0) cc_final: 0.6598 (OUTLIER) REVERT: J 196 MET cc_start: 0.7296 (ppp) cc_final: 0.6345 (mtm) REVERT: J 268 ASP cc_start: 0.8439 (m-30) cc_final: 0.7977 (OUTLIER) REVERT: K 11 GLU cc_start: 0.8124 (OUTLIER) cc_final: 0.7848 (mm-30) REVERT: K 16 GLN cc_start: 0.8211 (tp40) cc_final: 0.7948 (tp40) REVERT: K 28 ASN cc_start: 0.8327 (t0) cc_final: 0.7693 (m-40) REVERT: K 95 MET cc_start: 0.6809 (OUTLIER) cc_final: 0.6003 (pmm) REVERT: K 114 LEU cc_start: 0.8771 (mt) cc_final: 0.8536 (mm) outliers start: 93 outliers final: 34 residues processed: 343 average time/residue: 1.4198 time to fit residues: 567.2220 Evaluate side-chains 280 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 238 time to evaluate : 2.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 SER 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 455 HIS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 684 MET 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 118 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 16 CYS Chi-restraints excluded: chain D residue 30 GLN Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 175 MET 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 G residue 21 LEU Chi-restraints excluded: chain G residue 24 LEU 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 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 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 246 THR Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 279 MET Chi-restraints excluded: chain K residue 11 GLU Chi-restraints excluded: chain K residue 95 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 83 optimal weight: 0.9980 chunk 100 optimal weight: 0.0010 chunk 211 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 226 optimal weight: 0.5980 chunk 189 optimal weight: 0.9980 chunk 164 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 overall best weight: 0.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 48 GLN C 107 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN G 28 GLN H 27 HIS J 6 ASN K 19 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.124692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.091540 restraints weight = 56799.517| |-----------------------------------------------------------------------------| r_work (start): 0.3553 rms_B_bonded: 2.53 r_work: 0.3415 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3415 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3415 r_free = 0.3415 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3415 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.5957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 28712 Z= 0.125 Angle : 0.599 10.462 40360 Z= 0.304 Chirality : 0.037 0.275 4832 Planarity : 0.004 0.054 3869 Dihedral : 19.470 172.771 7898 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.96 % Favored : 94.00 % Rotamer: Outliers : 3.79 % Allowed : 22.17 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.17), residues: 2485 helix: 1.21 (0.16), residues: 1054 sheet: 0.72 (0.26), residues: 377 loop : -2.47 (0.17), residues: 1054 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP H 118 HIS 0.006 0.001 HIS K 41 PHE 0.016 0.001 PHE J 45 TYR 0.023 0.001 TYR J 160 ARG 0.009 0.000 ARG J 239 Details of bonding type rmsd hydrogen bonds : bond 0.04241 ( 992) hydrogen bonds : angle 4.26824 ( 2847) metal coordination : bond 0.00074 ( 2) covalent geometry : bond 0.00275 (28710) covalent geometry : angle 0.59907 (40360) *********************** 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 342 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 255 time to evaluate : 2.456 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: B 191 MET cc_start: 0.8615 (OUTLIER) cc_final: 0.7827 (mpp) REVERT: B 389 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8617 (mt) REVERT: B 455 HIS cc_start: 0.7370 (OUTLIER) cc_final: 0.7115 (m170) REVERT: B 539 ASP cc_start: 0.8593 (m-30) cc_final: 0.8322 (p0) REVERT: B 684 MET cc_start: 0.7667 (OUTLIER) cc_final: 0.7340 (mmt) REVERT: B 857 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8605 (mp) REVERT: C 140 MET cc_start: 0.1481 (pmm) cc_final: -0.0331 (mtm) REVERT: D 7 PHE cc_start: 0.8603 (m-10) cc_final: 0.8402 (m-10) REVERT: D 30 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8524 (mp10) REVERT: D 104 LEU cc_start: 0.8243 (OUTLIER) cc_final: 0.7821 (mm) REVERT: D 143 TYR cc_start: 0.7426 (m-80) cc_final: 0.7141 (m-80) REVERT: D 272 ASP cc_start: 0.7516 (t70) cc_final: 0.7008 (p0) REVERT: D 278 GLN cc_start: 0.6219 (mt0) cc_final: 0.5995 (mt0) REVERT: E 24 GLU cc_start: 0.8796 (mm-30) cc_final: 0.8342 (mm-30) REVERT: F 68 MET cc_start: 0.4779 (pmt) cc_final: 0.4539 (pmm) REVERT: F 119 ASP cc_start: 0.7738 (t0) cc_final: 0.7281 (m-30) REVERT: G 16 THR cc_start: 0.6881 (OUTLIER) cc_final: 0.6532 (p) REVERT: H 9 TRP cc_start: 0.7813 (OUTLIER) cc_final: 0.6817 (p90) REVERT: H 36 GLN cc_start: 0.7889 (tm-30) cc_final: 0.7664 (tm-30) REVERT: I 75 ARG cc_start: 0.8625 (tpp80) cc_final: 0.8146 (ttp-170) REVERT: J 5 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8093 (mt) REVERT: J 196 MET cc_start: 0.7309 (ppp) cc_final: 0.6364 (mtm) REVERT: J 268 ASP cc_start: 0.8394 (m-30) cc_final: 0.7990 (p0) REVERT: K 11 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7850 (mm-30) REVERT: K 16 GLN cc_start: 0.8176 (tp40) cc_final: 0.7878 (tp-100) REVERT: K 28 ASN cc_start: 0.8324 (t0) cc_final: 0.7744 (m-40) REVERT: K 95 MET cc_start: 0.6924 (OUTLIER) cc_final: 0.5988 (pmm) REVERT: L 121 GLU cc_start: 0.6832 (pp20) cc_final: 0.6549 (pp20) outliers start: 87 outliers final: 46 residues processed: 317 average time/residue: 1.3779 time to fit residues: 508.6602 Evaluate side-chains 300 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 242 time to evaluate : 2.682 ------------------------------------------------------------------------------- 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 223 ILE 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 455 HIS 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 684 MET 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 118 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 16 CYS 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 138 ASP Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 260 ARG 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 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 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 J residue 5 LEU Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 125 ASP 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 258 ASP Chi-restraints excluded: chain J residue 279 MET 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 112 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 265 optimal weight: 2.9990 chunk 278 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 270 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 151 optimal weight: 3.9990 chunk 239 optimal weight: 0.0370 chunk 240 optimal weight: 0.7980 chunk 209 optimal weight: 0.6980 chunk 21 optimal weight: 8.9990 chunk 168 optimal weight: 0.0060 overall best weight: 0.7076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 135 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 GLN H 27 HIS K 41 HIS L 111 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.124516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.091393 restraints weight = 56526.464| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.53 r_work: 0.3408 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3408 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3408 r_free = 0.3408 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3408 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.6067 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= 0.129 Angle : 0.603 13.179 40360 Z= 0.307 Chirality : 0.038 0.275 4832 Planarity : 0.004 0.053 3869 Dihedral : 19.433 172.689 7898 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.08 % Favored : 93.88 % Rotamer: Outliers : 3.75 % Allowed : 22.30 % Favored : 73.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.17), residues: 2485 helix: 1.24 (0.16), residues: 1061 sheet: 0.58 (0.25), residues: 398 loop : -2.45 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP H 118 HIS 0.006 0.001 HIS K 41 PHE 0.016 0.001 PHE J 45 TYR 0.014 0.001 TYR K 36 ARG 0.010 0.000 ARG H 116 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 992) hydrogen bonds : angle 4.26178 ( 2847) metal coordination : bond 0.00088 ( 2) covalent geometry : bond 0.00286 (28710) covalent geometry : angle 0.60257 (40360) *********************** 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 338 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 252 time to evaluate : 2.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 389 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8492 (mt) REVERT: B 455 HIS cc_start: 0.7335 (OUTLIER) cc_final: 0.7115 (m170) REVERT: B 461 LYS cc_start: 0.8717 (mppt) cc_final: 0.8183 (mtmt) REVERT: B 466 GLN cc_start: 0.7727 (pp30) cc_final: 0.7340 (tm-30) REVERT: B 539 ASP cc_start: 0.8583 (m-30) cc_final: 0.8305 (p0) REVERT: B 626 ARG cc_start: 0.8463 (mmt90) cc_final: 0.8213 (mmm160) REVERT: B 684 MET cc_start: 0.7724 (OUTLIER) cc_final: 0.7392 (mmt) REVERT: B 857 ILE cc_start: 0.8859 (OUTLIER) cc_final: 0.8578 (mp) REVERT: C 114 MET cc_start: 0.8087 (tpp) cc_final: 0.7512 (tmt) REVERT: C 129 MET cc_start: 0.5624 (tpp) cc_final: 0.5390 (tpp) REVERT: C 140 MET cc_start: 0.1210 (pmm) cc_final: -0.0664 (mtm) REVERT: D 7 PHE cc_start: 0.8666 (m-10) cc_final: 0.8442 (m-10) REVERT: D 104 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7821 (mm) REVERT: D 143 TYR cc_start: 0.7475 (m-80) cc_final: 0.7202 (m-80) REVERT: D 175 MET cc_start: 0.6140 (OUTLIER) cc_final: 0.5902 (mtm) REVERT: D 272 ASP cc_start: 0.7546 (t70) cc_final: 0.7026 (p0) REVERT: D 278 GLN cc_start: 0.6221 (mt0) cc_final: 0.5947 (mt0) REVERT: E 24 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8383 (mm-30) REVERT: E 127 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: F 68 MET cc_start: 0.4751 (pmt) cc_final: 0.4498 (pmm) REVERT: F 119 ASP cc_start: 0.7738 (t0) cc_final: 0.7294 (m-30) REVERT: F 131 GLU cc_start: 0.8242 (pt0) cc_final: 0.7814 (pp20) REVERT: G 16 THR cc_start: 0.6903 (OUTLIER) cc_final: 0.6560 (p) REVERT: G 68 MET cc_start: 0.8622 (ptt) cc_final: 0.8381 (ptt) REVERT: H 9 TRP cc_start: 0.7784 (OUTLIER) cc_final: 0.6259 (p90) REVERT: H 36 GLN cc_start: 0.7888 (tm-30) cc_final: 0.7659 (tm-30) REVERT: I 75 ARG cc_start: 0.8637 (tpp80) cc_final: 0.8155 (ttp-170) REVERT: I 227 ASP cc_start: 0.7471 (OUTLIER) cc_final: 0.7100 (m-30) REVERT: J 5 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8101 (mt) REVERT: J 196 MET cc_start: 0.7366 (ppp) cc_final: 0.6399 (mtm) REVERT: J 239 ARG cc_start: 0.7388 (ttp80) cc_final: 0.7051 (tmm-80) REVERT: J 268 ASP cc_start: 0.8385 (m-30) cc_final: 0.7892 (p0) REVERT: J 276 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7918 (tptp) REVERT: K 28 ASN cc_start: 0.8336 (t0) cc_final: 0.7770 (m-40) REVERT: K 95 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.5951 (pmm) REVERT: K 114 LEU cc_start: 0.8758 (mt) cc_final: 0.8477 (mm) REVERT: L 121 GLU cc_start: 0.6864 (pp20) cc_final: 0.6587 (pp20) outliers start: 86 outliers final: 48 residues processed: 315 average time/residue: 1.3548 time to fit residues: 502.1917 Evaluate side-chains 309 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 248 time to evaluate : 3.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 169 SER 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 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 455 HIS Chi-restraints excluded: chain B residue 462 LEU Chi-restraints excluded: chain B residue 560 LEU Chi-restraints excluded: chain B residue 621 LYS Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 684 MET 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 118 THR Chi-restraints excluded: chain C residue 149 VAL Chi-restraints excluded: chain D residue 16 CYS Chi-restraints excluded: chain D residue 103 CYS Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 138 ASP Chi-restraints excluded: chain D residue 175 MET Chi-restraints excluded: chain D residue 185 VAL Chi-restraints excluded: chain D residue 208 PHE Chi-restraints excluded: chain D residue 260 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 98 MET Chi-restraints excluded: chain E residue 127 GLU 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 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 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 240 ASN Chi-restraints excluded: chain J residue 246 THR Chi-restraints excluded: chain J residue 258 ASP Chi-restraints excluded: chain J residue 276 LYS Chi-restraints excluded: chain J residue 279 MET 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 112 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 282 random chunks: chunk 212 optimal weight: 1.9990 chunk 271 optimal weight: 0.0570 chunk 184 optimal weight: 0.7980 chunk 13 optimal weight: 8.9990 chunk 139 optimal weight: 0.5980 chunk 109 optimal weight: 0.0470 chunk 58 optimal weight: 0.0170 chunk 171 optimal weight: 1.9990 chunk 219 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 243 HIS ** C 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN ** F 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 27 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.126926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.094292 restraints weight = 57097.616| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.53 r_work: 0.3464 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.51 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.6103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 28712 Z= 0.106 Angle : 0.580 12.273 40360 Z= 0.293 Chirality : 0.036 0.244 4832 Planarity : 0.004 0.051 3869 Dihedral : 19.354 168.321 7898 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 2.74 % Allowed : 23.21 % Favored : 74.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2485 helix: 1.33 (0.16), residues: 1064 sheet: 0.67 (0.26), residues: 395 loop : -2.37 (0.17), residues: 1026 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.001 TRP H 118 HIS 0.004 0.001 HIS B 455 PHE 0.013 0.001 PHE J 45 TYR 0.021 0.001 TYR J 160 ARG 0.014 0.000 ARG K 15 Details of bonding type rmsd hydrogen bonds : bond 0.03651 ( 992) hydrogen bonds : angle 4.13213 ( 2847) metal coordination : bond 0.00053 ( 2) covalent geometry : bond 0.00234 (28710) covalent geometry : angle 0.57959 (40360) *********************** 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 336 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 273 time to evaluate : 2.790 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 MET cc_start: 0.8990 (tpp) cc_final: 0.8761 (mmt) REVERT: B 389 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8613 (mt) REVERT: B 461 LYS cc_start: 0.8704 (mppt) cc_final: 0.8160 (mtmt) REVERT: B 466 GLN cc_start: 0.7754 (pp30) cc_final: 0.7159 (tm130) REVERT: B 539 ASP cc_start: 0.8571 (m-30) cc_final: 0.8316 (p0) REVERT: B 626 ARG cc_start: 0.8393 (mmt90) cc_final: 0.8166 (mmm160) REVERT: B 684 MET cc_start: 0.7716 (OUTLIER) cc_final: 0.7354 (mmt) REVERT: C 114 MET cc_start: 0.8073 (tpp) cc_final: 0.7540 (tmt) REVERT: C 140 MET cc_start: 0.1810 (pmm) cc_final: -0.0070 (mtm) REVERT: D 7 PHE cc_start: 0.8655 (m-10) cc_final: 0.8428 (m-10) REVERT: D 9 LYS cc_start: 0.8399 (mmmm) cc_final: 0.8114 (mptt) REVERT: D 76 ARG cc_start: 0.7555 (ptt-90) cc_final: 0.7259 (ptt90) REVERT: D 272 ASP cc_start: 0.7483 (t70) cc_final: 0.6968 (p0) REVERT: D 278 GLN cc_start: 0.6161 (mt0) cc_final: 0.5953 (mt0) REVERT: E 24 GLU cc_start: 0.8867 (mm-30) cc_final: 0.8523 (mm-30) REVERT: F 68 MET cc_start: 0.4741 (pmt) cc_final: 0.4507 (pmm) REVERT: F 102 TYR cc_start: 0.7360 (t80) cc_final: 0.6776 (t80) REVERT: F 107 LYS cc_start: 0.8468 (mttt) cc_final: 0.8084 (mppt) REVERT: F 119 ASP cc_start: 0.7689 (t0) cc_final: 0.7290 (m-30) REVERT: F 131 GLU cc_start: 0.8237 (pt0) cc_final: 0.7842 (pp20) REVERT: F 149 ASP cc_start: 0.7582 (p0) cc_final: 0.7290 (p0) REVERT: G 16 THR cc_start: 0.6785 (OUTLIER) cc_final: 0.6283 (p) REVERT: G 68 MET cc_start: 0.8589 (ptt) cc_final: 0.8329 (ptt) REVERT: H 9 TRP cc_start: 0.7721 (OUTLIER) cc_final: 0.6127 (p90) REVERT: H 36 GLN cc_start: 0.7913 (tm-30) cc_final: 0.7670 (tm-30) REVERT: H 43 LYS cc_start: 0.6947 (tptp) cc_final: 0.6643 (tptt) REVERT: H 51 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8401 (mp0) REVERT: H 81 ILE cc_start: 0.8954 (mm) cc_final: 0.8716 (mt) REVERT: I 75 ARG cc_start: 0.8626 (tpp80) cc_final: 0.8244 (ttp-170) REVERT: J 5 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8090 (mt) REVERT: J 196 MET cc_start: 0.7339 (ppp) cc_final: 0.6332 (mtm) REVERT: J 239 ARG cc_start: 0.7448 (ttp80) cc_final: 0.7125 (tmm-80) REVERT: K 28 ASN cc_start: 0.8196 (t0) cc_final: 0.7673 (m-40) REVERT: K 95 MET cc_start: 0.6803 (OUTLIER) cc_final: 0.5910 (pmm) REVERT: K 114 LEU cc_start: 0.8762 (mt) cc_final: 0.8499 (mm) REVERT: L 121 GLU cc_start: 0.6895 (pp20) cc_final: 0.6645 (pp20) outliers start: 63 outliers final: 34 residues processed: 316 average time/residue: 1.6919 time to fit residues: 629.7555 Evaluate side-chains 286 residues out of total 2296 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 245 time to evaluate : 3.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 223 ILE Chi-restraints excluded: chain B residue 389 LEU Chi-restraints excluded: chain B residue 401 VAL Chi-restraints excluded: chain B residue 683 LEU Chi-restraints excluded: chain B residue 684 MET Chi-restraints excluded: chain B residue 770 LEU Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain C residue 28 THR 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 260 ARG Chi-restraints excluded: chain E residue 7 ARG Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 98 MET 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 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 51 GLU 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 K residue 95 MET Chi-restraints excluded: chain K residue 101 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 60.0871 > 50: distance: 40 - 61: 29.576 distance: 44 - 69: 12.333 distance: 47 - 53: 30.142 distance: 48 - 77: 3.701 distance: 53 - 54: 29.640 distance: 54 - 55: 40.212 distance: 54 - 57: 22.451 distance: 55 - 56: 17.957 distance: 55 - 61: 35.360 distance: 56 - 83: 32.073 distance: 57 - 58: 26.765 distance: 57 - 59: 29.114 distance: 58 - 60: 40.233 distance: 61 - 62: 34.741 distance: 62 - 63: 23.003 distance: 62 - 65: 26.252 distance: 63 - 64: 23.958 distance: 63 - 69: 30.137 distance: 64 - 93: 49.153 distance: 65 - 66: 16.611 distance: 66 - 67: 49.344 distance: 66 - 68: 39.645 distance: 69 - 70: 20.109 distance: 70 - 71: 45.753 distance: 70 - 73: 8.296 distance: 71 - 72: 26.993 distance: 71 - 77: 26.757 distance: 73 - 74: 28.093 distance: 74 - 75: 32.505 distance: 74 - 76: 37.933 distance: 77 - 78: 18.409 distance: 78 - 79: 15.579 distance: 78 - 81: 5.385 distance: 79 - 80: 41.830 distance: 79 - 83: 6.309 distance: 81 - 82: 12.033 distance: 83 - 84: 14.308 distance: 84 - 85: 13.105 distance: 84 - 87: 27.459 distance: 85 - 86: 29.712 distance: 85 - 93: 21.263 distance: 87 - 88: 35.709 distance: 88 - 89: 58.281 distance: 88 - 90: 44.954 distance: 89 - 91: 56.932 distance: 90 - 92: 46.037 distance: 91 - 92: 51.590 distance: 93 - 94: 15.289 distance: 94 - 95: 27.658 distance: 94 - 97: 38.050 distance: 95 - 96: 14.851 distance: 95 - 103: 8.931 distance: 97 - 98: 39.350 distance: 98 - 99: 49.533 distance: 98 - 100: 40.967 distance: 99 - 101: 52.225 distance: 100 - 102: 46.940 distance: 101 - 102: 50.703 distance: 103 - 104: 27.709 distance: 104 - 105: 17.121 distance: 104 - 107: 14.277 distance: 105 - 106: 21.197 distance: 105 - 114: 21.464 distance: 107 - 108: 10.939 distance: 108 - 109: 15.881 distance: 109 - 110: 16.567 distance: 110 - 111: 9.777 distance: 111 - 112: 15.473 distance: 111 - 113: 14.730 distance: 114 - 115: 28.170 distance: 115 - 116: 31.275 distance: 115 - 118: 11.972 distance: 116 - 117: 27.207 distance: 116 - 119: 18.412 distance: 119 - 120: 31.295 distance: 120 - 121: 29.461 distance: 120 - 123: 21.279 distance: 121 - 122: 36.821 distance: 121 - 125: 55.996 distance: 123 - 124: 40.713 distance: 125 - 126: 53.092 distance: 125 - 131: 30.242 distance: 126 - 127: 53.409 distance: 126 - 129: 41.951 distance: 127 - 128: 55.441 distance: 127 - 132: 34.755 distance: 129 - 130: 26.319 distance: 130 - 131: 40.959