Starting phenix.real_space_refine on Tue Aug 26 04:31:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyt_46049/08_2025/9cyt_46049.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyt_46049/08_2025/9cyt_46049.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cyt_46049/08_2025/9cyt_46049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyt_46049/08_2025/9cyt_46049.map" model { file = "/net/cci-nas-00/data/ceres_data/9cyt_46049/08_2025/9cyt_46049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyt_46049/08_2025/9cyt_46049.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 187 5.16 5 C 21559 2.51 5 N 5750 2.21 5 O 6495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33991 Number of models: 1 Model: "" Number of chains: 10 Chain: "J" Number of atoms: 10148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1288, 10148 Classifications: {'peptide': 1288} Modifications used: {'COO': 1} Link IDs: {'PCIS': 3, 'PTRANS': 73, 'TRANS': 1211} Chain: "A" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 290 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "B" Number of atoms: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4816 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "I" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2882 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "D" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 290 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "F" Number of atoms: 4816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 633, 4816 Classifications: {'peptide': 633} Link IDs: {'PTRANS': 45, 'TRANS': 587} Chain: "G" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2882 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 345} Chain: "E" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 290 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 3, 'TRANS': 38} Chain: "H" Number of atoms: 4695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4695 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 44, 'TRANS': 570} Chain breaks: 1 Chain: "L" Number of atoms: 2882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 2882 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 345} Time building chain proxies: 7.00, per 1000 atoms: 0.21 Number of scatterers: 33991 At special positions: 0 Unit cell: (196.9, 165, 169.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 187 16.00 O 6495 8.00 N 5750 7.00 C 21559 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.25 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8248 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 53 sheets defined 38.7% alpha, 12.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'J' and resid 26 through 36 Processing helix chain 'J' and resid 69 through 74 removed outlier: 4.106A pdb=" N TYR J 73 " --> pdb=" O ASP J 69 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N GLY J 74 " --> pdb=" O THR J 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 69 through 74' Processing helix chain 'J' and resid 78 through 101 removed outlier: 3.626A pdb=" N VAL J 92 " --> pdb=" O GLU J 88 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ILE J 100 " --> pdb=" O GLU J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 112 through 126 Processing helix chain 'J' and resid 132 through 136 Processing helix chain 'J' and resid 141 through 148 removed outlier: 3.947A pdb=" N LEU J 146 " --> pdb=" O MET J 142 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N GLY J 148 " --> pdb=" O GLY J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 154 removed outlier: 3.710A pdb=" N LEU J 153 " --> pdb=" O GLY J 150 " (cutoff:3.500A) Processing helix chain 'J' and resid 203 through 213 removed outlier: 3.592A pdb=" N LEU J 207 " --> pdb=" O THR J 203 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR J 213 " --> pdb=" O ARG J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 251 through 269 Processing helix chain 'J' and resid 296 through 310 removed outlier: 3.787A pdb=" N ARG J 300 " --> pdb=" O SER J 296 " (cutoff:3.500A) Processing helix chain 'J' and resid 323 through 335 Processing helix chain 'J' and resid 360 through 365 Processing helix chain 'J' and resid 406 through 418 Processing helix chain 'J' and resid 462 through 475 Processing helix chain 'J' and resid 480 through 494 Processing helix chain 'J' and resid 529 through 536 Processing helix chain 'J' and resid 587 through 605 Processing helix chain 'J' and resid 620 through 631 Processing helix chain 'J' and resid 632 through 635 removed outlier: 3.626A pdb=" N ILE J 635 " --> pdb=" O LEU J 632 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 632 through 635' Processing helix chain 'J' and resid 667 through 689 removed outlier: 3.780A pdb=" N TYR J 681 " --> pdb=" O HIS J 677 " (cutoff:3.500A) Processing helix chain 'J' and resid 715 through 719 removed outlier: 3.708A pdb=" N MET J 719 " --> pdb=" O PHE J 716 " (cutoff:3.500A) Processing helix chain 'J' and resid 720 through 734 removed outlier: 3.503A pdb=" N ARG J 724 " --> pdb=" O THR J 720 " (cutoff:3.500A) Processing helix chain 'J' and resid 759 through 768 removed outlier: 3.584A pdb=" N ARG J 768 " --> pdb=" O ARG J 764 " (cutoff:3.500A) Processing helix chain 'J' and resid 777 through 783 removed outlier: 3.786A pdb=" N GLN J 783 " --> pdb=" O SER J 779 " (cutoff:3.500A) Processing helix chain 'J' and resid 802 through 819 Processing helix chain 'J' and resid 834 through 839 Processing helix chain 'J' and resid 891 through 899 Processing helix chain 'J' and resid 902 through 916 removed outlier: 4.180A pdb=" N LYS J 916 " --> pdb=" O LYS J 912 " (cutoff:3.500A) Processing helix chain 'J' and resid 962 through 974 removed outlier: 3.547A pdb=" N LEU J 966 " --> pdb=" O ASP J 962 " (cutoff:3.500A) Processing helix chain 'J' and resid 988 through 998 removed outlier: 3.519A pdb=" N THR J 991 " --> pdb=" O LEU J 988 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N LEU J 995 " --> pdb=" O ARG J 992 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N LEU J 996 " --> pdb=" O LEU J 993 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER J 998 " --> pdb=" O LEU J 995 " (cutoff:3.500A) Processing helix chain 'J' and resid 1002 through 1014 Processing helix chain 'J' and resid 1188 through 1194 removed outlier: 3.651A pdb=" N LEU J1194 " --> pdb=" O ASP J1191 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.576A pdb=" N ASN A 42 " --> pdb=" O PRO A 38 " (cutoff:3.500A) Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 104 through 120 removed outlier: 3.533A pdb=" N LEU B 118 " --> pdb=" O ALA B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 128 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 151 through 157 removed outlier: 4.007A pdb=" N ASN B 157 " --> pdb=" O ARG B 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 184 Processing helix chain 'B' and resid 185 through 199 removed outlier: 4.611A pdb=" N LEU B 199 " --> pdb=" O ALA B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 223 removed outlier: 3.546A pdb=" N VAL B 215 " --> pdb=" O PRO B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 232 through 244 Processing helix chain 'B' and resid 263 through 271 Processing helix chain 'B' and resid 278 through 297 removed outlier: 3.659A pdb=" N LYS B 282 " --> pdb=" O PRO B 278 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU B 297 " --> pdb=" O VAL B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 299 through 303 removed outlier: 3.600A pdb=" N SER B 303 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 409 through 413 removed outlier: 3.598A pdb=" N TRP B 413 " --> pdb=" O PHE B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 518 Processing helix chain 'B' and resid 523 through 528 Processing helix chain 'B' and resid 534 through 554 removed outlier: 3.674A pdb=" N CYS B 538 " --> pdb=" O ASP B 534 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS B 545 " --> pdb=" O ASP B 541 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE B 546 " --> pdb=" O ARG B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 578 removed outlier: 3.714A pdb=" N GLN B 569 " --> pdb=" O SER B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 588 through 606 Processing helix chain 'B' and resid 620 through 637 removed outlier: 3.644A pdb=" N TRP B 624 " --> pdb=" O ASP B 620 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N LYS B 632 " --> pdb=" O ALA B 628 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N THR B 633 " --> pdb=" O GLN B 629 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N THR B 637 " --> pdb=" O THR B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 643 through 672 Processing helix chain 'I' and resid 7 through 19 removed outlier: 3.506A pdb=" N VAL I 11 " --> pdb=" O ASN I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 78 through 81 Processing helix chain 'I' and resid 82 through 113 removed outlier: 3.678A pdb=" N GLN I 86 " --> pdb=" O TYR I 82 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N SER I 101 " --> pdb=" O ARG I 97 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE I 102 " --> pdb=" O GLY I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 114 through 124 removed outlier: 3.692A pdb=" N LEU I 118 " --> pdb=" O SER I 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 178 Processing helix chain 'I' and resid 188 through 193 removed outlier: 3.990A pdb=" N PHE I 192 " --> pdb=" O PRO I 188 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN I 193 " --> pdb=" O SER I 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 188 through 193' Processing helix chain 'I' and resid 225 through 230 removed outlier: 3.503A pdb=" N GLU I 229 " --> pdb=" O TYR I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 235 through 242 Processing helix chain 'I' and resid 244 through 250 removed outlier: 4.125A pdb=" N ASP I 248 " --> pdb=" O THR I 244 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 293 Processing helix chain 'I' and resid 295 through 306 Processing helix chain 'I' and resid 307 through 316 Processing helix chain 'I' and resid 318 through 335 removed outlier: 3.925A pdb=" N GLY I 322 " --> pdb=" O GLY I 318 " (cutoff:3.500A) Proline residue: I 332 - end of helix Processing helix chain 'I' and resid 338 through 342 Processing helix chain 'D' and resid 37 through 42 removed outlier: 3.767A pdb=" N ASN D 42 " --> pdb=" O PRO D 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 71 through 79 removed outlier: 6.250A pdb=" N ILE F 76 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ILE F 77 " --> pdb=" O THR F 74 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N THR F 79 " --> pdb=" O ILE F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 120 removed outlier: 3.588A pdb=" N LEU F 118 " --> pdb=" O ALA F 114 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE F 120 " --> pdb=" O MET F 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 129 Processing helix chain 'F' and resid 136 through 141 removed outlier: 3.669A pdb=" N LEU F 141 " --> pdb=" O SER F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 151 through 157 removed outlier: 4.007A pdb=" N ASN F 157 " --> pdb=" O ARG F 153 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 185 removed outlier: 3.698A pdb=" N LEU F 185 " --> pdb=" O ALA F 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 185 through 198 Processing helix chain 'F' and resid 211 through 223 Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.852A pdb=" N ARG F 231 " --> pdb=" O SER F 227 " (cutoff:3.500A) Processing helix chain 'F' and resid 232 through 244 removed outlier: 3.536A pdb=" N ALA F 236 " --> pdb=" O TYR F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 271 removed outlier: 3.585A pdb=" N ALA F 269 " --> pdb=" O VAL F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 278 through 296 removed outlier: 3.671A pdb=" N ALA F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 302 Processing helix chain 'F' and resid 309 through 313 Processing helix chain 'F' and resid 409 through 413 Processing helix chain 'F' and resid 415 through 420 removed outlier: 3.616A pdb=" N GLY F 420 " --> pdb=" O SER F 417 " (cutoff:3.500A) Processing helix chain 'F' and resid 453 through 457 Processing helix chain 'F' and resid 514 through 519 removed outlier: 3.755A pdb=" N LEU F 518 " --> pdb=" O VAL F 514 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ILE F 519 " --> pdb=" O PRO F 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 514 through 519' Processing helix chain 'F' and resid 523 through 529 removed outlier: 3.896A pdb=" N ALA F 529 " --> pdb=" O GLU F 525 " (cutoff:3.500A) Processing helix chain 'F' and resid 534 through 553 removed outlier: 3.567A pdb=" N CYS F 538 " --> pdb=" O ASP F 534 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS F 545 " --> pdb=" O ASP F 541 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ILE F 546 " --> pdb=" O ARG F 542 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP F 553 " --> pdb=" O ALA F 549 " (cutoff:3.500A) Processing helix chain 'F' and resid 565 through 576 removed outlier: 3.873A pdb=" N GLN F 569 " --> pdb=" O SER F 565 " (cutoff:3.500A) Processing helix chain 'F' and resid 588 through 606 removed outlier: 3.525A pdb=" N LEU F 592 " --> pdb=" O PRO F 588 " (cutoff:3.500A) Processing helix chain 'F' and resid 607 through 612 Processing helix chain 'F' and resid 620 through 637 removed outlier: 4.388A pdb=" N LYS F 632 " --> pdb=" O ALA F 628 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N THR F 633 " --> pdb=" O GLN F 629 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N THR F 637 " --> pdb=" O THR F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 643 through 671 Processing helix chain 'G' and resid 7 through 21 Processing helix chain 'G' and resid 82 through 111 Processing helix chain 'G' and resid 114 through 125 Processing helix chain 'G' and resid 132 through 136 removed outlier: 3.799A pdb=" N VAL G 136 " --> pdb=" O TRP G 133 " (cutoff:3.500A) Processing helix chain 'G' and resid 158 through 178 Processing helix chain 'G' and resid 187 through 191 Processing helix chain 'G' and resid 225 through 231 Processing helix chain 'G' and resid 235 through 242 Processing helix chain 'G' and resid 244 through 248 Processing helix chain 'G' and resid 274 through 278 Processing helix chain 'G' and resid 287 through 293 removed outlier: 3.511A pdb=" N LYS G 293 " --> pdb=" O THR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 306 Processing helix chain 'G' and resid 307 through 315 Processing helix chain 'G' and resid 318 through 330 Processing helix chain 'G' and resid 330 through 335 removed outlier: 3.724A pdb=" N VAL G 334 " --> pdb=" O GLN G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 337 through 342 removed outlier: 3.669A pdb=" N MET G 342 " --> pdb=" O ALA G 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 71 removed outlier: 3.653A pdb=" N ILE H 71 " --> pdb=" O SER H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 104 through 120 removed outlier: 3.812A pdb=" N ILE H 108 " --> pdb=" O THR H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 128 Processing helix chain 'H' and resid 136 through 140 Processing helix chain 'H' and resid 151 through 158 Processing helix chain 'H' and resid 167 through 185 Processing helix chain 'H' and resid 185 through 199 removed outlier: 4.683A pdb=" N LEU H 199 " --> pdb=" O ALA H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 223 removed outlier: 3.570A pdb=" N VAL H 215 " --> pdb=" O PRO H 211 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 244 Processing helix chain 'H' and resid 265 through 270 Processing helix chain 'H' and resid 278 through 297 removed outlier: 3.517A pdb=" N LYS H 282 " --> pdb=" O PRO H 278 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 302 removed outlier: 3.668A pdb=" N ILE H 301 " --> pdb=" O GLU H 297 " (cutoff:3.500A) Processing helix chain 'H' and resid 309 through 313 Processing helix chain 'H' and resid 409 through 413 Processing helix chain 'H' and resid 415 through 419 Processing helix chain 'H' and resid 453 through 457 Processing helix chain 'H' and resid 514 through 519 removed outlier: 3.684A pdb=" N LEU H 518 " --> pdb=" O VAL H 514 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ILE H 519 " --> pdb=" O PRO H 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 514 through 519' Processing helix chain 'H' and resid 523 through 529 Processing helix chain 'H' and resid 534 through 553 removed outlier: 3.608A pdb=" N CYS H 538 " --> pdb=" O ASP H 534 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS H 545 " --> pdb=" O ASP H 541 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ILE H 546 " --> pdb=" O ARG H 542 " (cutoff:3.500A) Processing helix chain 'H' and resid 565 through 578 removed outlier: 3.676A pdb=" N GLN H 569 " --> pdb=" O SER H 565 " (cutoff:3.500A) Processing helix chain 'H' and resid 588 through 606 removed outlier: 3.646A pdb=" N LEU H 592 " --> pdb=" O PRO H 588 " (cutoff:3.500A) Processing helix chain 'H' and resid 607 through 610 removed outlier: 4.123A pdb=" N ILE H 610 " --> pdb=" O PRO H 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 607 through 610' Processing helix chain 'H' and resid 620 through 636 removed outlier: 4.001A pdb=" N TRP H 624 " --> pdb=" O ASP H 620 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LYS H 632 " --> pdb=" O ALA H 628 " (cutoff:3.500A) Processing helix chain 'H' and resid 643 through 671 Processing helix chain 'L' and resid 7 through 20 Processing helix chain 'L' and resid 78 through 81 removed outlier: 3.588A pdb=" N ASP L 81 " --> pdb=" O ARG L 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 81' Processing helix chain 'L' and resid 82 through 112 Processing helix chain 'L' and resid 114 through 125 Processing helix chain 'L' and resid 158 through 177 removed outlier: 3.718A pdb=" N SER L 177 " --> pdb=" O MET L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 193 removed outlier: 3.670A pdb=" N ALA L 191 " --> pdb=" O ASP L 187 " (cutoff:3.500A) Processing helix chain 'L' and resid 225 through 230 Processing helix chain 'L' and resid 235 through 243 Processing helix chain 'L' and resid 244 through 248 Processing helix chain 'L' and resid 251 through 255 removed outlier: 3.773A pdb=" N SER L 255 " --> pdb=" O PHE L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 274 through 278 Processing helix chain 'L' and resid 287 through 293 Processing helix chain 'L' and resid 295 through 306 removed outlier: 3.875A pdb=" N VAL L 299 " --> pdb=" O VAL L 295 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU L 300 " --> pdb=" O ARG L 296 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA L 301 " --> pdb=" O LYS L 297 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 316 Processing helix chain 'L' and resid 318 through 330 Processing helix chain 'L' and resid 330 through 335 Processing helix chain 'L' and resid 350 through 354 removed outlier: 3.820A pdb=" N ASN L 353 " --> pdb=" O GLY L 350 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N TYR L 354 " --> pdb=" O ASP L 351 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 350 through 354' Processing sheet with id=AA1, first strand: chain 'J' and resid 3 through 4 Processing sheet with id=AA2, first strand: chain 'J' and resid 12 through 13 Processing sheet with id=AA3, first strand: chain 'J' and resid 43 through 47 Processing sheet with id=AA4, first strand: chain 'J' and resid 158 through 159 Processing sheet with id=AA5, first strand: chain 'J' and resid 240 through 241 Processing sheet with id=AA6, first strand: chain 'J' and resid 351 through 354 removed outlier: 6.098A pdb=" N VAL J 351 " --> pdb=" O VAL J 370 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS J 372 " --> pdb=" O VAL J 351 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N ILE J 353 " --> pdb=" O LYS J 372 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'J' and resid 394 through 395 removed outlier: 3.709A pdb=" N GLY J 705 " --> pdb=" O ARG J 758 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 400 through 405 removed outlier: 5.341A pdb=" N ASP J 403 " --> pdb=" O LEU J 774 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 435 through 440 removed outlier: 4.085A pdb=" N LEU J 435 " --> pdb=" O PHE J 644 " (cutoff:3.500A) removed outlier: 7.570A pdb=" N GLN J 572 " --> pdb=" O GLY J 609 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS J 615 " --> pdb=" O SER J 576 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N ALA J 513 " --> pdb=" O TYR J 575 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 865 through 869 Processing sheet with id=AB2, first strand: chain 'J' and resid 941 through 943 Processing sheet with id=AB3, first strand: chain 'J' and resid 1029 through 1030 removed outlier: 3.694A pdb=" N GLN J1075 " --> pdb=" O VAL J1092 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 1061 through 1064 removed outlier: 3.692A pdb=" N PHE J1063 " --> pdb=" O CYS J1055 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY J1097 " --> pdb=" O VAL J1118 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL J1118 " --> pdb=" O GLY J1097 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N TYR J1099 " --> pdb=" O SER J1116 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER J1116 " --> pdb=" O TYR J1099 " (cutoff:3.500A) removed outlier: 5.197A pdb=" N MET J1101 " --> pdb=" O LEU J1114 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 1127 through 1129 removed outlier: 3.862A pdb=" N LEU J1181 " --> pdb=" O ILE J1145 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'J' and resid 1162 through 1165 Processing sheet with id=AB7, first strand: chain 'J' and resid 1228 through 1231 Processing sheet with id=AB8, first strand: chain 'J' and resid 1245 through 1250 removed outlier: 6.943A pdb=" N VAL J1240 " --> pdb=" O ILE J1247 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ILE J1249 " --> pdb=" O TRP J1238 " (cutoff:3.500A) removed outlier: 5.689A pdb=" N TRP J1238 " --> pdb=" O ILE J1249 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 19 through 20 Processing sheet with id=AC1, first strand: chain 'B' and resid 63 through 65 removed outlier: 8.421A pdb=" N ALA B 50 " --> pdb=" O ASP B 145 " (cutoff:3.500A) removed outlier: 13.039A pdb=" N ASP B 145 " --> pdb=" O ALA B 50 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N CYS B 146 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS B 161 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 148 " --> pdb=" O PHE B 159 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N PHE B 159 " --> pdb=" O VAL B 148 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 307 through 308 Processing sheet with id=AC3, first strand: chain 'B' and resid 319 through 322 Processing sheet with id=AC4, first strand: chain 'B' and resid 334 through 336 removed outlier: 7.574A pdb=" N ARG B 366 " --> pdb=" O ALA B 470 " (cutoff:3.500A) removed outlier: 5.641A pdb=" N ALA B 470 " --> pdb=" O ARG B 366 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LYS B 398 " --> pdb=" O ILE B 473 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ASN B 426 " --> pdb=" O PHE B 401 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 403 " --> pdb=" O VAL B 424 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N VAL B 424 " --> pdb=" O VAL B 403 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLN B 405 " --> pdb=" O ALA B 422 " (cutoff:3.500A) removed outlier: 5.407A pdb=" N ALA B 422 " --> pdb=" O GLN B 405 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 345 through 350 Processing sheet with id=AC6, first strand: chain 'B' and resid 432 through 434 Processing sheet with id=AC7, first strand: chain 'B' and resid 503 through 505 removed outlier: 4.571A pdb=" N VAL B 503 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 25 through 26 removed outlier: 6.302A pdb=" N CYS I 51 " --> pdb=" O VAL I 57 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL I 57 " --> pdb=" O CYS I 51 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 127 through 130 removed outlier: 6.829A pdb=" N ILE I 363 " --> pdb=" O LEU I 128 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 184 through 185 removed outlier: 3.582A pdb=" N MET I 185 " --> pdb=" O ALA I 260 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ALA I 260 " --> pdb=" O MET I 185 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'I' and resid 222 through 223 Processing sheet with id=AD3, first strand: chain 'D' and resid 19 through 20 Processing sheet with id=AD4, first strand: chain 'F' and resid 63 through 65 removed outlier: 3.676A pdb=" N TYR F 147 " --> pdb=" O TRP F 48 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ALA F 50 " --> pdb=" O ASP F 145 " (cutoff:3.500A) removed outlier: 13.306A pdb=" N ASP F 145 " --> pdb=" O ALA F 50 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N CYS F 146 " --> pdb=" O LYS F 161 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N LYS F 161 " --> pdb=" O CYS F 146 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'F' and resid 307 through 308 Processing sheet with id=AD6, first strand: chain 'F' and resid 319 through 321 Processing sheet with id=AD7, first strand: chain 'F' and resid 334 through 336 removed outlier: 7.532A pdb=" N ARG F 366 " --> pdb=" O ALA F 470 " (cutoff:3.500A) removed outlier: 5.458A pdb=" N ALA F 470 " --> pdb=" O ARG F 366 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS F 398 " --> pdb=" O ILE F 473 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N VAL F 399 " --> pdb=" O TYR F 427 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR F 427 " --> pdb=" O VAL F 399 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N PHE F 401 " --> pdb=" O VAL F 425 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'F' and resid 345 through 350 Processing sheet with id=AD9, first strand: chain 'F' and resid 432 through 434 Processing sheet with id=AE1, first strand: chain 'F' and resid 503 through 505 removed outlier: 4.519A pdb=" N VAL F 503 " --> pdb=" O VAL F 510 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'G' and resid 25 through 26 removed outlier: 6.661A pdb=" N VAL G 49 " --> pdb=" O VAL G 58 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'G' and resid 126 through 130 removed outlier: 5.664A pdb=" N SER G 127 " --> pdb=" O GLY G 365 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N GLY G 365 " --> pdb=" O SER G 127 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N VAL G 129 " --> pdb=" O ILE G 363 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'G' and resid 222 through 223 Processing sheet with id=AE5, first strand: chain 'G' and resid 270 through 272 Processing sheet with id=AE6, first strand: chain 'E' and resid 19 through 20 Processing sheet with id=AE7, first strand: chain 'H' and resid 63 through 65 removed outlier: 3.667A pdb=" N TYR H 147 " --> pdb=" O TRP H 48 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N ALA H 50 " --> pdb=" O ASP H 145 " (cutoff:3.500A) removed outlier: 13.299A pdb=" N ASP H 145 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N CYS H 146 " --> pdb=" O LYS H 161 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LYS H 161 " --> pdb=" O CYS H 146 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'H' and resid 307 through 308 Processing sheet with id=AE9, first strand: chain 'H' and resid 319 through 322 Processing sheet with id=AF1, first strand: chain 'H' and resid 334 through 336 removed outlier: 7.613A pdb=" N ARG H 366 " --> pdb=" O ALA H 470 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N ALA H 470 " --> pdb=" O ARG H 366 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N LYS H 398 " --> pdb=" O ILE H 473 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ASN H 426 " --> pdb=" O PHE H 401 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N VAL H 403 " --> pdb=" O VAL H 424 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N VAL H 424 " --> pdb=" O VAL H 403 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'H' and resid 345 through 350 Processing sheet with id=AF3, first strand: chain 'H' and resid 432 through 434 Processing sheet with id=AF4, first strand: chain 'H' and resid 503 through 505 removed outlier: 4.672A pdb=" N VAL H 503 " --> pdb=" O VAL H 510 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'L' and resid 25 through 26 Processing sheet with id=AF6, first strand: chain 'L' and resid 127 through 130 removed outlier: 7.007A pdb=" N ILE L 363 " --> pdb=" O LEU L 128 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'L' and resid 184 through 185 removed outlier: 3.731A pdb=" N ALA L 260 " --> pdb=" O MET L 185 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N ALA L 270 " --> pdb=" O THR L 261 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'L' and resid 221 through 222 1405 hydrogen bonds defined for protein. 3804 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.84 Time building geometry restraints manager: 3.05 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: 10979 1.34 - 1.46: 5385 1.46 - 1.58: 18084 1.58 - 1.70: 0 1.70 - 1.82: 331 Bond restraints: 34779 Sorted by residual: bond pdb=" N VAL D 8 " pdb=" CA VAL D 8 " ideal model delta sigma weight residual 1.455 1.495 -0.040 1.04e-02 9.25e+03 1.49e+01 bond pdb=" N VAL I 103 " pdb=" CA VAL I 103 " ideal model delta sigma weight residual 1.460 1.498 -0.039 1.21e-02 6.83e+03 1.03e+01 bond pdb=" N LEU F 361 " pdb=" CA LEU F 361 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.19e-02 7.06e+03 8.68e+00 bond pdb=" N LEU H 361 " pdb=" CA LEU H 361 " ideal model delta sigma weight residual 1.454 1.488 -0.034 1.19e-02 7.06e+03 8.33e+00 bond pdb=" N HIS F 358 " pdb=" CA HIS F 358 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.23e-02 6.61e+03 8.17e+00 ... (remaining 34774 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 46110 1.69 - 3.38: 1150 3.38 - 5.07: 117 5.07 - 6.75: 18 6.75 - 8.44: 6 Bond angle restraints: 47401 Sorted by residual: angle pdb=" CA ARG J 509 " pdb=" C ARG J 509 " pdb=" O ARG J 509 " ideal model delta sigma weight residual 121.65 117.34 4.31 1.17e+00 7.31e-01 1.36e+01 angle pdb=" N MET I 106 " pdb=" CA MET I 106 " pdb=" C MET I 106 " ideal model delta sigma weight residual 111.28 107.26 4.02 1.09e+00 8.42e-01 1.36e+01 angle pdb=" CA LEU F 359 " pdb=" C LEU F 359 " pdb=" O LEU F 359 " ideal model delta sigma weight residual 121.40 117.24 4.16 1.13e+00 7.83e-01 1.36e+01 angle pdb=" CA TRP F 357 " pdb=" C TRP F 357 " pdb=" O TRP F 357 " ideal model delta sigma weight residual 121.40 117.28 4.12 1.13e+00 7.83e-01 1.33e+01 angle pdb=" CA LEU B 359 " pdb=" C LEU B 359 " pdb=" O LEU B 359 " ideal model delta sigma weight residual 121.38 117.71 3.67 1.06e+00 8.90e-01 1.20e+01 ... (remaining 47396 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.95: 18968 17.95 - 35.91: 1652 35.91 - 53.86: 258 53.86 - 71.82: 68 71.82 - 89.77: 28 Dihedral angle restraints: 20974 sinusoidal: 8201 harmonic: 12773 Sorted by residual: dihedral pdb=" CA GLY L 359 " pdb=" C GLY L 359 " pdb=" N ASP L 360 " pdb=" CA ASP L 360 " ideal model delta harmonic sigma weight residual -180.00 -161.29 -18.71 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ASN L 353 " pdb=" C ASN L 353 " pdb=" N TYR L 354 " pdb=" CA TYR L 354 " ideal model delta harmonic sigma weight residual -180.00 -161.36 -18.64 0 5.00e+00 4.00e-02 1.39e+01 dihedral pdb=" CA PRO I 361 " pdb=" C PRO I 361 " pdb=" N MET I 362 " pdb=" CA MET I 362 " ideal model delta harmonic sigma weight residual -180.00 -161.58 -18.42 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 20971 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 4197 0.052 - 0.104: 973 0.104 - 0.156: 207 0.156 - 0.207: 9 0.207 - 0.259: 5 Chirality restraints: 5391 Sorted by residual: chirality pdb=" CA LEU F 359 " pdb=" N LEU F 359 " pdb=" C LEU F 359 " pdb=" CB LEU F 359 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA ILE D 7 " pdb=" N ILE D 7 " pdb=" C ILE D 7 " pdb=" CB ILE D 7 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE D 11 " pdb=" N ILE D 11 " pdb=" C ILE D 11 " pdb=" CB ILE D 11 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 5388 not shown) Planarity restraints: 6143 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY I 98 " 0.014 2.00e-02 2.50e+03 2.90e-02 8.41e+00 pdb=" C GLY I 98 " -0.050 2.00e-02 2.50e+03 pdb=" O GLY I 98 " 0.019 2.00e-02 2.50e+03 pdb=" N MET I 99 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP B 461 " 0.044 5.00e-02 4.00e+02 6.65e-02 7.07e+00 pdb=" N PRO B 462 " -0.115 5.00e-02 4.00e+02 pdb=" CA PRO B 462 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO B 462 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 354 " 0.011 2.00e-02 2.50e+03 1.62e-02 5.23e+00 pdb=" CG TYR I 354 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR I 354 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR I 354 " 0.016 2.00e-02 2.50e+03 pdb=" CE1 TYR I 354 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR I 354 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR I 354 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR I 354 " -0.004 2.00e-02 2.50e+03 ... (remaining 6140 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 639 2.69 - 3.24: 32563 3.24 - 3.79: 50381 3.79 - 4.35: 66747 4.35 - 4.90: 114395 Nonbonded interactions: 264725 Sorted by model distance: nonbonded pdb=" OG SER F 475 " pdb=" NH1 ARG L 22 " model vdw 2.137 3.120 nonbonded pdb=" O ARG L 120 " pdb=" OG1 THR L 123 " model vdw 2.156 3.040 nonbonded pdb=" OG SER L 101 " pdb=" OD1 ASP L 137 " model vdw 2.161 3.040 nonbonded pdb=" OH TYR B 321 " pdb=" O SER B 530 " model vdw 2.175 3.040 nonbonded pdb=" OD2 ASP J 280 " pdb=" OH TYR J 369 " model vdw 2.197 3.040 ... (remaining 264720 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 43 through 72 or resid 95 through 675)) selection = (chain 'F' and (resid 43 through 72 or resid 95 through 675)) selection = (chain 'H' and resid 43 through 675) } ncs_group { reference = chain 'G' selection = chain 'I' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 27.190 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 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 0.044 34779 Z= 0.202 Angle : 0.632 8.442 47401 Z= 0.350 Chirality : 0.046 0.259 5391 Planarity : 0.005 0.066 6143 Dihedral : 14.097 89.773 12726 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.21 % Allowed : 0.53 % Favored : 99.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.12), residues: 4368 helix: 1.41 (0.14), residues: 1408 sheet: -0.16 (0.22), residues: 564 loop : -1.07 (0.12), residues: 2396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 598 TYR 0.039 0.002 TYR I 354 PHE 0.032 0.002 PHE F 401 TRP 0.016 0.001 TRP I 133 HIS 0.008 0.001 HIS I 304 Details of bonding type rmsd covalent geometry : bond 0.00428 (34779) covalent geometry : angle 0.63185 (47401) hydrogen bonds : bond 0.16084 ( 1405) hydrogen bonds : angle 5.65221 ( 3804) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 296 time to evaluate : 1.018 Fit side-chains revert: symmetry clash REVERT: J 162 ASP cc_start: 0.7377 (p0) cc_final: 0.7169 (t0) REVERT: J 525 ASP cc_start: 0.6917 (m-30) cc_final: 0.6638 (m-30) REVERT: I 256 HIS cc_start: 0.4789 (p-80) cc_final: 0.4540 (p-80) REVERT: D 7 ILE cc_start: 0.4964 (OUTLIER) cc_final: 0.4199 (tp) REVERT: D 9 GLN cc_start: 0.3644 (OUTLIER) cc_final: 0.3271 (tt0) REVERT: G 357 MET cc_start: 0.4138 (ppp) cc_final: 0.3397 (tmm) REVERT: L 341 THR cc_start: 0.7221 (p) cc_final: 0.6874 (p) outliers start: 8 outliers final: 0 residues processed: 301 average time/residue: 0.1870 time to fit residues: 93.8085 Evaluate side-chains 249 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 247 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain D residue 9 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 432 optimal weight: 0.7980 chunk 197 optimal weight: 0.0170 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 10.0000 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 30.0000 chunk 401 optimal weight: 20.0000 chunk 424 optimal weight: 20.0000 overall best weight: 4.3626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 64 GLN J 223 HIS J1202 GLN A 42 ASN B 110 ASN B 358 HIS I 190 HIS ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 12 ASN F 202 ASN G 165 GLN G 251 HIS ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 7 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.100135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.090479 restraints weight = 73156.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 64)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.088173 restraints weight = 125797.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.087677 restraints weight = 88975.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.087549 restraints weight = 96469.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.087551 restraints weight = 95056.833| |-----------------------------------------------------------------------------| r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.0684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 34779 Z= 0.135 Angle : 0.548 7.842 47401 Z= 0.288 Chirality : 0.044 0.165 5391 Planarity : 0.005 0.056 6143 Dihedral : 4.471 44.532 4726 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.40 % Allowed : 5.22 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.01 (0.13), residues: 4368 helix: 1.52 (0.14), residues: 1462 sheet: -0.09 (0.22), residues: 572 loop : -1.00 (0.12), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 239 TYR 0.025 0.001 TYR L 225 PHE 0.021 0.001 PHE F 401 TRP 0.014 0.001 TRP I 133 HIS 0.007 0.001 HIS B 358 Details of bonding type rmsd covalent geometry : bond 0.00304 (34779) covalent geometry : angle 0.54792 (47401) hydrogen bonds : bond 0.05642 ( 1405) hydrogen bonds : angle 4.75412 ( 3804) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 274 time to evaluate : 1.371 Fit side-chains REVERT: J 162 ASP cc_start: 0.7328 (p0) cc_final: 0.7016 (t0) REVERT: J 241 MET cc_start: 0.7923 (ttt) cc_final: 0.7541 (ttt) REVERT: J 525 ASP cc_start: 0.6903 (m-30) cc_final: 0.6632 (m-30) REVERT: I 256 HIS cc_start: 0.4706 (p-80) cc_final: 0.4366 (p-80) REVERT: D 7 ILE cc_start: 0.4689 (OUTLIER) cc_final: 0.3815 (tp) REVERT: G 166 TYR cc_start: 0.7807 (m-80) cc_final: 0.7536 (m-80) REVERT: G 357 MET cc_start: 0.4820 (ppp) cc_final: 0.4200 (tmm) REVERT: H 69 LYS cc_start: 0.7768 (OUTLIER) cc_final: 0.7353 (mtpp) REVERT: L 190 HIS cc_start: 0.5930 (m-70) cc_final: 0.5573 (m170) outliers start: 15 outliers final: 8 residues processed: 281 average time/residue: 0.1835 time to fit residues: 85.8382 Evaluate side-chains 265 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 255 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 497 ILE Chi-restraints excluded: chain J residue 972 THR Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain F residue 657 ILE Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 282 MET Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 370 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 196 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 91 optimal weight: 5.9990 chunk 430 optimal weight: 6.9990 chunk 296 optimal weight: 20.0000 chunk 373 optimal weight: 30.0000 chunk 127 optimal weight: 20.0000 chunk 229 optimal weight: 7.9990 chunk 189 optimal weight: 30.0000 chunk 48 optimal weight: 6.9990 chunk 235 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1024 HIS J1202 GLN ** A 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 202 ASN I 105 GLN I 190 HIS ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 HIS ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.099238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.089171 restraints weight = 73705.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.087992 restraints weight = 137273.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.088539 restraints weight = 129210.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.088481 restraints weight = 86839.786| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.088502 restraints weight = 88532.843| |-----------------------------------------------------------------------------| r_work (final): 0.3075 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.0826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34779 Z= 0.164 Angle : 0.568 8.395 47401 Z= 0.296 Chirality : 0.045 0.176 5391 Planarity : 0.005 0.056 6143 Dihedral : 4.477 42.006 4723 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.96 % Allowed : 8.14 % Favored : 90.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.12), residues: 4368 helix: 1.43 (0.14), residues: 1470 sheet: -0.07 (0.22), residues: 568 loop : -1.06 (0.12), residues: 2330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 598 TYR 0.020 0.002 TYR J 25 PHE 0.029 0.002 PHE F 401 TRP 0.012 0.001 TRP G 95 HIS 0.013 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00395 (34779) covalent geometry : angle 0.56774 (47401) hydrogen bonds : bond 0.05905 ( 1405) hydrogen bonds : angle 4.68831 ( 3804) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 265 time to evaluate : 1.345 Fit side-chains REVERT: J 241 MET cc_start: 0.7944 (ttt) cc_final: 0.7591 (ttt) REVERT: J 525 ASP cc_start: 0.6862 (m-30) cc_final: 0.6588 (m-30) REVERT: I 52 MET cc_start: 0.7841 (mmm) cc_final: 0.7579 (mmm) REVERT: I 256 HIS cc_start: 0.4608 (p-80) cc_final: 0.4332 (p-80) REVERT: I 300 GLU cc_start: 0.6399 (OUTLIER) cc_final: 0.5899 (mp0) REVERT: D 7 ILE cc_start: 0.4823 (OUTLIER) cc_final: 0.3924 (tp) REVERT: G 105 GLN cc_start: 0.6122 (pt0) cc_final: 0.4852 (tp40) REVERT: G 357 MET cc_start: 0.4795 (ppp) cc_final: 0.4247 (tmm) REVERT: H 69 LYS cc_start: 0.7809 (OUTLIER) cc_final: 0.7435 (mtpp) REVERT: L 110 MET cc_start: 0.5296 (tpt) cc_final: 0.5049 (tpt) REVERT: L 171 ASN cc_start: 0.6752 (m-40) cc_final: 0.6515 (m110) REVERT: L 190 HIS cc_start: 0.6133 (m-70) cc_final: 0.5813 (m170) outliers start: 36 outliers final: 22 residues processed: 289 average time/residue: 0.1877 time to fit residues: 90.1857 Evaluate side-chains 280 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 497 ILE Chi-restraints excluded: chain J residue 972 THR Chi-restraints excluded: chain B residue 258 MET Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 328 MET Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 657 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 282 MET Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 679 CYS Chi-restraints excluded: chain L residue 346 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 417 optimal weight: 5.9990 chunk 163 optimal weight: 20.0000 chunk 179 optimal weight: 20.0000 chunk 176 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 285 optimal weight: 9.9990 chunk 368 optimal weight: 20.0000 chunk 159 optimal weight: 5.9990 chunk 366 optimal weight: 0.0000 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 30.0000 overall best weight: 6.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1202 GLN A 42 ASN I 190 HIS ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 132 ASN G 251 HIS ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.098822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.088724 restraints weight = 72920.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.087060 restraints weight = 133703.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.087236 restraints weight = 102790.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.087017 restraints weight = 87687.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.087110 restraints weight = 81688.993| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 34779 Z= 0.155 Angle : 0.555 8.319 47401 Z= 0.289 Chirality : 0.044 0.176 5391 Planarity : 0.005 0.059 6143 Dihedral : 4.461 42.246 4723 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.01 % Allowed : 10.32 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.06 (0.13), residues: 4368 helix: 1.49 (0.14), residues: 1457 sheet: -0.03 (0.22), residues: 568 loop : -1.07 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 239 TYR 0.021 0.001 TYR I 354 PHE 0.026 0.002 PHE F 401 TRP 0.013 0.001 TRP G 95 HIS 0.013 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00370 (34779) covalent geometry : angle 0.55483 (47401) hydrogen bonds : bond 0.05661 ( 1405) hydrogen bonds : angle 4.61873 ( 3804) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 258 time to evaluate : 1.302 Fit side-chains REVERT: J 241 MET cc_start: 0.7986 (ttt) cc_final: 0.7670 (ttt) REVERT: J 525 ASP cc_start: 0.6864 (m-30) cc_final: 0.6593 (m-30) REVERT: I 52 MET cc_start: 0.7919 (mmm) cc_final: 0.7576 (mmm) REVERT: I 173 MET cc_start: 0.4985 (OUTLIER) cc_final: 0.4775 (ttm) REVERT: I 245 PRO cc_start: 0.6474 (Cg_exo) cc_final: 0.5950 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4533 (p-80) cc_final: 0.4274 (p-80) REVERT: I 300 GLU cc_start: 0.6434 (OUTLIER) cc_final: 0.5976 (mp0) REVERT: D 7 ILE cc_start: 0.4836 (OUTLIER) cc_final: 0.3921 (tp) REVERT: G 166 TYR cc_start: 0.7753 (m-80) cc_final: 0.7536 (m-80) REVERT: G 254 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6389 (pp) REVERT: G 357 MET cc_start: 0.4864 (ppp) cc_final: 0.4096 (ptm) REVERT: H 69 LYS cc_start: 0.7824 (OUTLIER) cc_final: 0.7485 (mtpp) REVERT: L 110 MET cc_start: 0.5092 (tpt) cc_final: 0.4635 (tpt) REVERT: L 171 ASN cc_start: 0.6729 (m-40) cc_final: 0.6458 (m110) outliers start: 38 outliers final: 25 residues processed: 287 average time/residue: 0.1826 time to fit residues: 87.4772 Evaluate side-chains 281 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 251 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 497 ILE Chi-restraints excluded: chain J residue 972 THR Chi-restraints excluded: chain J residue 1155 THR Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 121 VAL Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 304 HIS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 657 ILE Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 282 MET Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 679 CYS Chi-restraints excluded: chain L residue 137 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 169 optimal weight: 0.0050 chunk 368 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 102 optimal weight: 5.9990 chunk 176 optimal weight: 6.9990 chunk 399 optimal weight: 20.0000 chunk 405 optimal weight: 0.9980 chunk 178 optimal weight: 10.0000 chunk 54 optimal weight: 0.0270 chunk 59 optimal weight: 8.9990 overall best weight: 2.8056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1202 GLN I 190 HIS ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN G 251 HIS ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 86 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.101117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.090889 restraints weight = 73114.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.089744 restraints weight = 133969.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.090292 restraints weight = 124866.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.090260 restraints weight = 85416.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.090311 restraints weight = 77423.559| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.1155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 34779 Z= 0.104 Angle : 0.490 8.017 47401 Z= 0.255 Chirality : 0.042 0.164 5391 Planarity : 0.005 0.052 6143 Dihedral : 4.127 41.690 4723 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.14 % Allowed : 10.94 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.21 (0.13), residues: 4368 helix: 1.74 (0.14), residues: 1468 sheet: 0.08 (0.21), residues: 587 loop : -0.92 (0.12), residues: 2313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 509 TYR 0.022 0.001 TYR I 354 PHE 0.016 0.001 PHE I 102 TRP 0.013 0.001 TRP G 95 HIS 0.020 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00230 (34779) covalent geometry : angle 0.48978 (47401) hydrogen bonds : bond 0.04472 ( 1405) hydrogen bonds : angle 4.37683 ( 3804) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 279 time to evaluate : 1.405 Fit side-chains REVERT: J 71 GLN cc_start: 0.7965 (mp10) cc_final: 0.7574 (mp10) REVERT: J 241 MET cc_start: 0.8009 (ttt) cc_final: 0.7767 (ttt) REVERT: J 525 ASP cc_start: 0.6791 (m-30) cc_final: 0.6526 (m-30) REVERT: I 52 MET cc_start: 0.7884 (mmm) cc_final: 0.7638 (mmm) REVERT: I 173 MET cc_start: 0.4785 (OUTLIER) cc_final: 0.4582 (ttm) REVERT: I 245 PRO cc_start: 0.6486 (Cg_exo) cc_final: 0.6035 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4531 (p-80) cc_final: 0.4303 (p-80) REVERT: D 7 ILE cc_start: 0.4925 (OUTLIER) cc_final: 0.3992 (tp) REVERT: G 105 GLN cc_start: 0.6060 (pt0) cc_final: 0.4768 (tp40) REVERT: G 254 LEU cc_start: 0.6926 (OUTLIER) cc_final: 0.6467 (pp) REVERT: G 357 MET cc_start: 0.4894 (ppp) cc_final: 0.4152 (ptm) REVERT: E 40 MET cc_start: 0.7647 (mmm) cc_final: 0.7389 (mmt) REVERT: L 52 MET cc_start: 0.8032 (mmm) cc_final: 0.7807 (mmt) REVERT: L 110 MET cc_start: 0.5307 (tpt) cc_final: 0.4845 (tpt) outliers start: 43 outliers final: 27 residues processed: 313 average time/residue: 0.1908 time to fit residues: 98.9348 Evaluate side-chains 285 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 497 ILE Chi-restraints excluded: chain J residue 1155 THR Chi-restraints excluded: chain J residue 1185 VAL Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 304 HIS Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 657 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 282 MET Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 679 CYS Chi-restraints excluded: chain L residue 137 ASP Chi-restraints excluded: chain L residue 192 PHE Chi-restraints excluded: chain L residue 346 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 110 optimal weight: 8.9990 chunk 319 optimal weight: 9.9990 chunk 281 optimal weight: 8.9990 chunk 167 optimal weight: 30.0000 chunk 148 optimal weight: 6.9990 chunk 37 optimal weight: 20.0000 chunk 185 optimal weight: 9.9990 chunk 259 optimal weight: 20.0000 chunk 303 optimal weight: 20.0000 chunk 289 optimal weight: 8.9990 chunk 233 optimal weight: 0.1980 overall best weight: 6.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1202 GLN I 190 HIS ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 251 HIS ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.088890 restraints weight = 73352.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.087622 restraints weight = 144051.119| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.088297 restraints weight = 132066.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.088059 restraints weight = 92681.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.088142 restraints weight = 87592.307| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 34779 Z= 0.166 Angle : 0.564 8.560 47401 Z= 0.293 Chirality : 0.044 0.183 5391 Planarity : 0.005 0.056 6143 Dihedral : 4.404 41.700 4723 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.57 % Allowed : 11.97 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.13), residues: 4368 helix: 1.63 (0.14), residues: 1449 sheet: -0.02 (0.22), residues: 581 loop : -1.02 (0.12), residues: 2338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 584 TYR 0.023 0.002 TYR I 354 PHE 0.025 0.002 PHE F 401 TRP 0.011 0.001 TRP H 188 HIS 0.012 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00403 (34779) covalent geometry : angle 0.56444 (47401) hydrogen bonds : bond 0.05710 ( 1405) hydrogen bonds : angle 4.54353 ( 3804) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 255 time to evaluate : 1.210 Fit side-chains REVERT: J 241 MET cc_start: 0.8004 (ttt) cc_final: 0.7684 (ttt) REVERT: J 422 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8608 (pp) REVERT: J 456 LEU cc_start: 0.7657 (OUTLIER) cc_final: 0.7237 (pt) REVERT: J 525 ASP cc_start: 0.6842 (m-30) cc_final: 0.6585 (m-30) REVERT: B 341 MET cc_start: 0.4087 (tmm) cc_final: 0.3829 (tmm) REVERT: B 577 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7830 (mp) REVERT: I 173 MET cc_start: 0.4835 (OUTLIER) cc_final: 0.4630 (ttm) REVERT: I 245 PRO cc_start: 0.6463 (Cg_exo) cc_final: 0.5951 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4611 (p-80) cc_final: 0.4351 (p-80) REVERT: I 328 MET cc_start: 0.5996 (tpp) cc_final: 0.5776 (tpp) REVERT: D 7 ILE cc_start: 0.4997 (OUTLIER) cc_final: 0.4042 (tp) REVERT: G 166 TYR cc_start: 0.7810 (m-80) cc_final: 0.7576 (m-80) REVERT: G 251 HIS cc_start: 0.4679 (OUTLIER) cc_final: 0.4408 (m-70) REVERT: G 254 LEU cc_start: 0.6954 (OUTLIER) cc_final: 0.6551 (pp) REVERT: G 357 MET cc_start: 0.5089 (ppp) cc_final: 0.4334 (ptm) REVERT: H 330 GLU cc_start: 0.6830 (mt-10) cc_final: 0.6227 (mp0) REVERT: L 52 MET cc_start: 0.8036 (mmm) cc_final: 0.7792 (mmt) REVERT: L 110 MET cc_start: 0.5295 (tpt) cc_final: 0.4817 (tpt) outliers start: 59 outliers final: 39 residues processed: 304 average time/residue: 0.1762 time to fit residues: 90.5243 Evaluate side-chains 295 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 249 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 497 ILE Chi-restraints excluded: chain J residue 972 THR Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1022 ASP Chi-restraints excluded: chain J residue 1155 THR Chi-restraints excluded: chain J residue 1185 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 173 MET Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 304 HIS Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 657 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 251 HIS Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 282 MET Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 679 CYS Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 137 ASP Chi-restraints excluded: chain L residue 192 PHE Chi-restraints excluded: chain L residue 346 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 412 optimal weight: 30.0000 chunk 160 optimal weight: 20.0000 chunk 319 optimal weight: 9.9990 chunk 83 optimal weight: 9.9990 chunk 266 optimal weight: 10.0000 chunk 235 optimal weight: 9.9990 chunk 184 optimal weight: 10.0000 chunk 103 optimal weight: 20.0000 chunk 361 optimal weight: 20.0000 chunk 337 optimal weight: 6.9990 chunk 262 optimal weight: 20.0000 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1202 GLN I 79 HIS I 190 HIS ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 171 GLN G 205 GLN G 251 HIS ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.097816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.087695 restraints weight = 73834.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.086542 restraints weight = 144375.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.087046 restraints weight = 132430.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.086969 restraints weight = 91287.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.087006 restraints weight = 93203.939| |-----------------------------------------------------------------------------| r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.1221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 34779 Z= 0.212 Angle : 0.618 8.727 47401 Z= 0.322 Chirality : 0.046 0.189 5391 Planarity : 0.006 0.060 6143 Dihedral : 4.720 41.387 4723 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 1.65 % Allowed : 12.75 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.12), residues: 4368 helix: 1.36 (0.14), residues: 1444 sheet: -0.13 (0.21), residues: 581 loop : -1.20 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 90 TYR 0.019 0.002 TYR B 321 PHE 0.028 0.002 PHE F 401 TRP 0.014 0.002 TRP H 188 HIS 0.015 0.001 HIS G 251 Details of bonding type rmsd covalent geometry : bond 0.00522 (34779) covalent geometry : angle 0.61798 (47401) hydrogen bonds : bond 0.06494 ( 1405) hydrogen bonds : angle 4.72433 ( 3804) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 251 time to evaluate : 1.218 Fit side-chains revert: symmetry clash REVERT: J 241 MET cc_start: 0.8012 (ttt) cc_final: 0.7718 (ttt) REVERT: J 422 LEU cc_start: 0.8758 (OUTLIER) cc_final: 0.8499 (pp) REVERT: J 456 LEU cc_start: 0.7751 (OUTLIER) cc_final: 0.7364 (pt) REVERT: J 525 ASP cc_start: 0.6904 (m-30) cc_final: 0.6630 (m-30) REVERT: I 52 MET cc_start: 0.7776 (mmm) cc_final: 0.7547 (mmm) REVERT: I 245 PRO cc_start: 0.6451 (Cg_exo) cc_final: 0.6008 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4404 (p-80) cc_final: 0.4092 (p-80) REVERT: D 7 ILE cc_start: 0.4797 (OUTLIER) cc_final: 0.3826 (tp) REVERT: D 40 MET cc_start: 0.7673 (mmt) cc_final: 0.7344 (mmt) REVERT: G 166 TYR cc_start: 0.7701 (m-80) cc_final: 0.7486 (m-80) REVERT: G 254 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6482 (pp) REVERT: G 357 MET cc_start: 0.4541 (ppp) cc_final: 0.4073 (ptm) REVERT: H 69 LYS cc_start: 0.7881 (OUTLIER) cc_final: 0.7550 (mtpp) REVERT: H 330 GLU cc_start: 0.6789 (mt-10) cc_final: 0.6252 (mt-10) REVERT: L 110 MET cc_start: 0.5477 (tpt) cc_final: 0.5069 (tpt) outliers start: 62 outliers final: 44 residues processed: 302 average time/residue: 0.1766 time to fit residues: 90.3340 Evaluate side-chains 294 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 245 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 239 THR Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 497 ILE Chi-restraints excluded: chain J residue 926 VAL Chi-restraints excluded: chain J residue 972 THR Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1155 THR Chi-restraints excluded: chain J residue 1185 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 554 ASP Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain I residue 55 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 227 GLU Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 657 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 282 MET Chi-restraints excluded: chain G residue 364 LEU Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain H residue 57 VAL Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 679 CYS Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 109 MET Chi-restraints excluded: chain L residue 192 PHE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 356 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 114 optimal weight: 10.0000 chunk 369 optimal weight: 0.0770 chunk 204 optimal weight: 5.9990 chunk 313 optimal weight: 6.9990 chunk 359 optimal weight: 7.9990 chunk 113 optimal weight: 0.9990 chunk 208 optimal weight: 4.9990 chunk 338 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 333 optimal weight: 40.0000 chunk 191 optimal weight: 1.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1202 GLN B 121 ASN I 39 GLN I 190 HIS ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 111 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100301 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 84)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.090271 restraints weight = 72706.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.088558 restraints weight = 123743.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.088300 restraints weight = 84194.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.088156 restraints weight = 92863.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.088084 restraints weight = 93311.334| |-----------------------------------------------------------------------------| r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7600 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 34779 Z= 0.108 Angle : 0.499 7.925 47401 Z= 0.259 Chirality : 0.042 0.164 5391 Planarity : 0.005 0.054 6143 Dihedral : 4.175 40.920 4723 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.25 % Allowed : 13.41 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.13), residues: 4368 helix: 1.71 (0.14), residues: 1458 sheet: 0.03 (0.21), residues: 592 loop : -0.97 (0.12), residues: 2318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 584 TYR 0.020 0.001 TYR I 354 PHE 0.015 0.001 PHE L 19 TRP 0.015 0.001 TRP G 95 HIS 0.004 0.001 HIS G 94 Details of bonding type rmsd covalent geometry : bond 0.00240 (34779) covalent geometry : angle 0.49891 (47401) hydrogen bonds : bond 0.04488 ( 1405) hydrogen bonds : angle 4.36913 ( 3804) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 260 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: J 241 MET cc_start: 0.8039 (ttt) cc_final: 0.7715 (ttt) REVERT: J 422 LEU cc_start: 0.8858 (OUTLIER) cc_final: 0.8621 (pp) REVERT: J 456 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7279 (pt) REVERT: J 525 ASP cc_start: 0.6784 (m-30) cc_final: 0.6529 (m-30) REVERT: B 341 MET cc_start: 0.3755 (tmm) cc_final: 0.3513 (tmm) REVERT: B 387 TYR cc_start: 0.8255 (m-80) cc_final: 0.8055 (m-80) REVERT: I 245 PRO cc_start: 0.6500 (Cg_exo) cc_final: 0.6052 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4584 (p-80) cc_final: 0.4311 (p-80) REVERT: D 7 ILE cc_start: 0.5004 (OUTLIER) cc_final: 0.4019 (tp) REVERT: D 40 MET cc_start: 0.7814 (mmt) cc_final: 0.7399 (mmt) REVERT: G 105 GLN cc_start: 0.5916 (pt0) cc_final: 0.4556 (tp40) REVERT: G 166 TYR cc_start: 0.7665 (m-80) cc_final: 0.7297 (m-80) REVERT: G 357 MET cc_start: 0.4703 (ppp) cc_final: 0.4228 (ptm) REVERT: E 40 MET cc_start: 0.7759 (mmm) cc_final: 0.7517 (mmt) REVERT: L 106 MET cc_start: 0.7440 (tpp) cc_final: 0.6768 (mmp) outliers start: 47 outliers final: 37 residues processed: 297 average time/residue: 0.1864 time to fit residues: 92.3309 Evaluate side-chains 292 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 252 time to evaluate : 1.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 497 ILE Chi-restraints excluded: chain J residue 972 THR Chi-restraints excluded: chain J residue 1155 THR Chi-restraints excluded: chain J residue 1185 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 577 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 304 HIS Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 657 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 282 MET Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 566 VAL Chi-restraints excluded: chain H residue 679 CYS Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 192 PHE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 356 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 190 optimal weight: 30.0000 chunk 45 optimal weight: 10.0000 chunk 113 optimal weight: 0.9990 chunk 368 optimal weight: 8.9990 chunk 124 optimal weight: 20.0000 chunk 109 optimal weight: 9.9990 chunk 249 optimal weight: 5.9990 chunk 279 optimal weight: 20.0000 chunk 39 optimal weight: 9.9990 chunk 420 optimal weight: 30.0000 chunk 293 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1202 GLN I 190 HIS ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 190 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.098762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.088943 restraints weight = 73091.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.087477 restraints weight = 109614.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.086607 restraints weight = 75368.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.086412 restraints weight = 87056.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.086380 restraints weight = 86668.237| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 34779 Z= 0.172 Angle : 0.575 8.681 47401 Z= 0.297 Chirality : 0.045 0.184 5391 Planarity : 0.005 0.057 6143 Dihedral : 4.467 41.570 4723 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.44 % Allowed : 13.25 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.13), residues: 4368 helix: 1.58 (0.14), residues: 1439 sheet: -0.03 (0.22), residues: 579 loop : -1.09 (0.12), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 349 TYR 0.017 0.002 TYR B 321 PHE 0.021 0.002 PHE F 401 TRP 0.012 0.001 TRP G 95 HIS 0.006 0.001 HIS I 9 Details of bonding type rmsd covalent geometry : bond 0.00418 (34779) covalent geometry : angle 0.57451 (47401) hydrogen bonds : bond 0.05793 ( 1405) hydrogen bonds : angle 4.54497 ( 3804) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 250 time to evaluate : 1.164 Fit side-chains revert: symmetry clash REVERT: J 241 MET cc_start: 0.7998 (ttt) cc_final: 0.7691 (ttt) REVERT: J 385 GLN cc_start: 0.6922 (tt0) cc_final: 0.6653 (mm110) REVERT: J 422 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8584 (pp) REVERT: J 456 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7270 (pt) REVERT: J 525 ASP cc_start: 0.6853 (m-30) cc_final: 0.6595 (m-30) REVERT: B 341 MET cc_start: 0.3957 (tmm) cc_final: 0.3689 (tmm) REVERT: I 245 PRO cc_start: 0.6506 (Cg_exo) cc_final: 0.6062 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4387 (p-80) cc_final: 0.4064 (p-80) REVERT: D 7 ILE cc_start: 0.4791 (OUTLIER) cc_final: 0.3822 (tp) REVERT: G 166 TYR cc_start: 0.7697 (m-80) cc_final: 0.7357 (m-80) REVERT: G 254 LEU cc_start: 0.7107 (OUTLIER) cc_final: 0.6740 (pp) REVERT: G 357 MET cc_start: 0.4735 (ppp) cc_final: 0.4405 (ptm) REVERT: L 106 MET cc_start: 0.7494 (tpp) cc_final: 0.6812 (mmp) outliers start: 54 outliers final: 42 residues processed: 294 average time/residue: 0.1787 time to fit residues: 89.2228 Evaluate side-chains 292 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 246 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 497 ILE Chi-restraints excluded: chain J residue 926 VAL Chi-restraints excluded: chain J residue 972 THR Chi-restraints excluded: chain J residue 1155 THR Chi-restraints excluded: chain J residue 1185 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 304 HIS Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain I residue 347 ILE Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 657 ILE Chi-restraints excluded: chain G residue 128 LEU Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 282 MET Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 566 VAL Chi-restraints excluded: chain H residue 679 CYS Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 192 PHE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 356 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 146 optimal weight: 5.9990 chunk 321 optimal weight: 2.9990 chunk 306 optimal weight: 7.9990 chunk 157 optimal weight: 6.9990 chunk 34 optimal weight: 20.0000 chunk 385 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 274 optimal weight: 50.0000 chunk 130 optimal weight: 0.0010 chunk 224 optimal weight: 9.9990 overall best weight: 4.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1202 GLN I 190 HIS ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.089369 restraints weight = 73450.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.087605 restraints weight = 137110.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.087393 restraints weight = 96645.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.087221 restraints weight = 93573.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.087295 restraints weight = 87570.394| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 34779 Z= 0.127 Angle : 0.524 8.454 47401 Z= 0.271 Chirality : 0.043 0.171 5391 Planarity : 0.005 0.059 6143 Dihedral : 4.284 40.916 4723 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.28 % Allowed : 13.41 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.10 (0.13), residues: 4368 helix: 1.67 (0.14), residues: 1453 sheet: 0.11 (0.22), residues: 572 loop : -1.02 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 584 TYR 0.014 0.001 TYR I 324 PHE 0.016 0.001 PHE F 401 TRP 0.014 0.001 TRP G 95 HIS 0.004 0.001 HIS G 94 Details of bonding type rmsd covalent geometry : bond 0.00298 (34779) covalent geometry : angle 0.52433 (47401) hydrogen bonds : bond 0.04983 ( 1405) hydrogen bonds : angle 4.42147 ( 3804) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8736 Ramachandran restraints generated. 4368 Oldfield, 0 Emsley, 4368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 252 time to evaluate : 1.351 Fit side-chains revert: symmetry clash REVERT: J 241 MET cc_start: 0.8030 (ttt) cc_final: 0.7704 (ttt) REVERT: J 422 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8596 (pp) REVERT: J 456 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7308 (pt) REVERT: J 525 ASP cc_start: 0.6815 (m-30) cc_final: 0.6559 (m-30) REVERT: B 341 MET cc_start: 0.4130 (tmm) cc_final: 0.3880 (tmm) REVERT: I 120 ARG cc_start: 0.4994 (mtm180) cc_final: 0.4388 (ptt90) REVERT: I 245 PRO cc_start: 0.6500 (Cg_exo) cc_final: 0.6065 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4516 (p-80) cc_final: 0.4255 (p-80) REVERT: D 7 ILE cc_start: 0.4814 (OUTLIER) cc_final: 0.3883 (tp) REVERT: G 105 GLN cc_start: 0.5901 (pt0) cc_final: 0.4523 (tp40) REVERT: G 166 TYR cc_start: 0.7693 (m-80) cc_final: 0.7370 (m-80) REVERT: G 254 LEU cc_start: 0.7039 (OUTLIER) cc_final: 0.6653 (pp) REVERT: G 357 MET cc_start: 0.4855 (ppp) cc_final: 0.4534 (ptm) REVERT: E 40 MET cc_start: 0.7841 (mmm) cc_final: 0.7569 (mmt) REVERT: L 106 MET cc_start: 0.7471 (tpp) cc_final: 0.6797 (mmp) outliers start: 48 outliers final: 43 residues processed: 291 average time/residue: 0.1801 time to fit residues: 88.8940 Evaluate side-chains 296 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 249 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 203 THR Chi-restraints excluded: chain J residue 422 LEU Chi-restraints excluded: chain J residue 456 LEU Chi-restraints excluded: chain J residue 497 ILE Chi-restraints excluded: chain J residue 972 THR Chi-restraints excluded: chain J residue 1155 THR Chi-restraints excluded: chain J residue 1185 VAL Chi-restraints excluded: chain B residue 96 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 423 THR Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain B residue 518 LEU Chi-restraints excluded: chain B residue 579 THR Chi-restraints excluded: chain B residue 617 VAL Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 150 THR Chi-restraints excluded: chain I residue 230 HIS Chi-restraints excluded: chain I residue 295 VAL Chi-restraints excluded: chain I residue 300 GLU Chi-restraints excluded: chain I residue 304 HIS Chi-restraints excluded: chain I residue 334 VAL Chi-restraints excluded: chain D residue 7 ILE Chi-restraints excluded: chain F residue 51 VAL Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 128 MET Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 620 ASP Chi-restraints excluded: chain F residue 657 ILE Chi-restraints excluded: chain G residue 155 VAL Chi-restraints excluded: chain G residue 185 MET Chi-restraints excluded: chain G residue 254 LEU Chi-restraints excluded: chain G residue 282 MET Chi-restraints excluded: chain G residue 302 VAL Chi-restraints excluded: chain G residue 320 MET Chi-restraints excluded: chain E residue 26 THR Chi-restraints excluded: chain H residue 69 LYS Chi-restraints excluded: chain H residue 370 LEU Chi-restraints excluded: chain H residue 566 VAL Chi-restraints excluded: chain H residue 679 CYS Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 192 PHE Chi-restraints excluded: chain L residue 346 THR Chi-restraints excluded: chain L residue 356 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 110 optimal weight: 20.0000 chunk 29 optimal weight: 2.9990 chunk 220 optimal weight: 40.0000 chunk 74 optimal weight: 4.9990 chunk 330 optimal weight: 9.9990 chunk 6 optimal weight: 9.9990 chunk 282 optimal weight: 20.0000 chunk 432 optimal weight: 6.9990 chunk 427 optimal weight: 7.9990 chunk 191 optimal weight: 4.9990 chunk 258 optimal weight: 0.5980 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J1202 GLN ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 190 HIS ** D 3 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.089623 restraints weight = 72808.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.088659 restraints weight = 128132.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.089225 restraints weight = 115413.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.089126 restraints weight = 83061.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.089178 restraints weight = 77041.108| |-----------------------------------------------------------------------------| r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.1381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34779 Z= 0.121 Angle : 0.515 8.473 47401 Z= 0.266 Chirality : 0.043 0.171 5391 Planarity : 0.005 0.055 6143 Dihedral : 4.198 41.157 4723 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.38 % Allowed : 13.49 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.13), residues: 4368 helix: 1.75 (0.14), residues: 1453 sheet: 0.12 (0.21), residues: 586 loop : -0.98 (0.12), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 247 TYR 0.013 0.001 TYR L 354 PHE 0.019 0.001 PHE B 586 TRP 0.013 0.001 TRP G 95 HIS 0.004 0.001 HIS G 94 Details of bonding type rmsd covalent geometry : bond 0.00282 (34779) covalent geometry : angle 0.51497 (47401) hydrogen bonds : bond 0.04785 ( 1405) hydrogen bonds : angle 4.37508 ( 3804) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4364.59 seconds wall clock time: 76 minutes 40.24 seconds (4600.24 seconds total)