Starting phenix.real_space_refine on Sat Jun 28 18:32:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cyt_46049/06_2025/9cyt_46049.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cyt_46049/06_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_46049/06_2025/9cyt_46049.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cyt_46049/06_2025/9cyt_46049.map" model { file = "/net/cci-nas-00/data/ceres_data/9cyt_46049/06_2025/9cyt_46049.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cyt_46049/06_2025/9cyt_46049.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 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): 1.47s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 21.32, per 1000 atoms: 0.63 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: 8.84 Conformation dependent library (CDL) restraints added in 4.6 seconds 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: 4.47 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: 16.37 Time building geometry restraints manager: 10.40 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: 3.890 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: 0.050 Extract box with map and model: 1.450 Check model and map are aligned: 0.260 Set scattering table: 0.330 Process input model: 81.780 Find NCS groups from input model: 1.210 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:3.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.700 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (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 TRP 0.016 0.001 TRP I 133 HIS 0.008 0.001 HIS I 304 PHE 0.032 0.002 PHE F 401 TYR 0.039 0.002 TYR I 354 ARG 0.005 0.000 ARG H 598 Details of bonding type rmsd hydrogen bonds : bond 0.16084 ( 1405) hydrogen bonds : angle 5.65221 ( 3804) covalent geometry : bond 0.00428 (34779) covalent geometry : angle 0.63185 (47401) *********************** 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 : 4.128 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: 0.4454 time to fit residues: 223.4114 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 : 3.856 ------------------------------------------------------------------------------- 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 367 optimal weight: 6.9990 chunk 329 optimal weight: 5.9990 chunk 182 optimal weight: 20.0000 chunk 112 optimal weight: 6.9990 chunk 222 optimal weight: 40.0000 chunk 176 optimal weight: 10.0000 chunk 340 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 chunk 207 optimal weight: 30.0000 chunk 253 optimal weight: 8.9990 chunk 395 optimal weight: 9.9990 overall best weight: 5.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 223 HIS J1202 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.099774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.089838 restraints weight = 72956.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 68)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.087930 restraints weight = 135483.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.087893 restraints weight = 101932.586| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.0686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 34779 Z= 0.147 Angle : 0.564 7.901 47401 Z= 0.296 Chirality : 0.044 0.168 5391 Planarity : 0.005 0.057 6143 Dihedral : 4.548 44.313 4726 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.61 % Allowed : 5.27 % Favored : 94.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.12), residues: 4368 helix: 1.44 (0.14), residues: 1464 sheet: -0.09 (0.22), residues: 569 loop : -1.04 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 133 HIS 0.007 0.001 HIS B 358 PHE 0.025 0.002 PHE F 401 TYR 0.024 0.002 TYR J 25 ARG 0.005 0.000 ARG L 239 Details of bonding type rmsd hydrogen bonds : bond 0.05754 ( 1405) hydrogen bonds : angle 4.77100 ( 3804) covalent geometry : bond 0.00342 (34779) covalent geometry : angle 0.56371 (47401) *********************** 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 295 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 272 time to evaluate : 3.818 Fit side-chains REVERT: J 71 GLN cc_start: 0.7352 (mp10) cc_final: 0.7137 (mp10) REVERT: J 162 ASP cc_start: 0.7417 (p0) cc_final: 0.7041 (t0) REVERT: J 241 MET cc_start: 0.7881 (ttt) cc_final: 0.7522 (ttt) REVERT: J 525 ASP cc_start: 0.6878 (m-30) cc_final: 0.6614 (m-30) REVERT: I 173 MET cc_start: 0.5101 (mtm) cc_final: 0.4900 (mtm) REVERT: I 256 HIS cc_start: 0.4564 (p-80) cc_final: 0.4256 (p-80) REVERT: D 7 ILE cc_start: 0.4676 (OUTLIER) cc_final: 0.3794 (tp) REVERT: G 166 TYR cc_start: 0.7834 (m-80) cc_final: 0.7628 (m-80) REVERT: G 357 MET cc_start: 0.4766 (ppp) cc_final: 0.4173 (tmm) REVERT: H 69 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7411 (mtpp) REVERT: L 171 ASN cc_start: 0.6615 (m-40) cc_final: 0.6388 (m110) REVERT: L 190 HIS cc_start: 0.5972 (m-70) cc_final: 0.5622 (m170) outliers start: 23 outliers final: 14 residues processed: 284 average time/residue: 0.4558 time to fit residues: 214.2712 Evaluate side-chains 273 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 257 time to evaluate : 3.783 ------------------------------------------------------------------------------- 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 423 THR Chi-restraints excluded: chain B residue 617 VAL 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 51 VAL 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 185 optimal weight: 10.0000 chunk 34 optimal weight: 20.0000 chunk 83 optimal weight: 8.9990 chunk 149 optimal weight: 20.0000 chunk 296 optimal weight: 20.0000 chunk 354 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 422 optimal weight: 40.0000 chunk 204 optimal weight: 9.9990 chunk 28 optimal weight: 9.9990 chunk 232 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: J 64 GLN J1202 GLN B 202 ASN ** B 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.097799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.087866 restraints weight = 73856.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.085665 restraints weight = 136536.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.085666 restraints weight = 101124.278| |-----------------------------------------------------------------------------| r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 34779 Z= 0.214 Angle : 0.634 8.763 47401 Z= 0.331 Chirality : 0.047 0.186 5391 Planarity : 0.006 0.061 6143 Dihedral : 4.794 42.095 4723 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.04 % Allowed : 9.15 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.12), residues: 4368 helix: 1.26 (0.14), residues: 1444 sheet: -0.21 (0.22), residues: 571 loop : -1.20 (0.12), residues: 2353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 188 HIS 0.013 0.001 HIS G 251 PHE 0.038 0.002 PHE F 401 TYR 0.023 0.002 TYR J 25 ARG 0.004 0.001 ARG H 598 Details of bonding type rmsd hydrogen bonds : bond 0.06822 ( 1405) hydrogen bonds : angle 4.86984 ( 3804) covalent geometry : bond 0.00528 (34779) covalent geometry : angle 0.63351 (47401) *********************** 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 299 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 260 time to evaluate : 4.297 Fit side-chains REVERT: J 241 MET cc_start: 0.7909 (ttt) cc_final: 0.7586 (ttt) REVERT: J 385 GLN cc_start: 0.6938 (tt0) cc_final: 0.6636 (mm110) REVERT: J 525 ASP cc_start: 0.6892 (m-30) cc_final: 0.6645 (m-30) REVERT: J 1154 MET cc_start: 0.6914 (tpt) cc_final: 0.6673 (tpt) REVERT: I 52 MET cc_start: 0.7847 (mmm) cc_final: 0.7561 (mmm) REVERT: I 256 HIS cc_start: 0.4559 (p-80) cc_final: 0.4278 (p-80) REVERT: I 300 GLU cc_start: 0.6529 (OUTLIER) cc_final: 0.6074 (mp0) REVERT: D 7 ILE cc_start: 0.4689 (OUTLIER) cc_final: 0.3805 (tp) REVERT: G 357 MET cc_start: 0.4890 (ppp) cc_final: 0.4185 (tmm) REVERT: H 69 LYS cc_start: 0.7885 (OUTLIER) cc_final: 0.7474 (mtpp) REVERT: L 110 MET cc_start: 0.5199 (tpt) cc_final: 0.4873 (tpt) REVERT: L 190 HIS cc_start: 0.6031 (m-70) cc_final: 0.5578 (m170) outliers start: 39 outliers final: 23 residues processed: 288 average time/residue: 0.4534 time to fit residues: 217.6024 Evaluate side-chains 274 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 3.694 ------------------------------------------------------------------------------- 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 579 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 359 LEU Chi-restraints excluded: chain F residue 620 ASP 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 24 optimal weight: 0.7980 chunk 373 optimal weight: 40.0000 chunk 294 optimal weight: 7.9990 chunk 278 optimal weight: 30.0000 chunk 336 optimal weight: 9.9990 chunk 230 optimal weight: 40.0000 chunk 132 optimal weight: 7.9990 chunk 424 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 4 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 overall best weight: 5.7588 ------------------------------------------------------------------------------- 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** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.098677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.088410 restraints weight = 73293.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.087428 restraints weight = 125593.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.087723 restraints weight = 116603.443| |-----------------------------------------------------------------------------| r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.1000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34779 Z= 0.148 Angle : 0.552 8.222 47401 Z= 0.289 Chirality : 0.044 0.177 5391 Planarity : 0.005 0.059 6143 Dihedral : 4.546 41.962 4723 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.25 % Allowed : 10.78 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.12), residues: 4368 helix: 1.44 (0.14), residues: 1450 sheet: -0.09 (0.22), residues: 567 loop : -1.15 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 95 HIS 0.010 0.001 HIS G 251 PHE 0.022 0.002 PHE F 401 TYR 0.027 0.001 TYR I 354 ARG 0.003 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.05645 ( 1405) hydrogen bonds : angle 4.66171 ( 3804) covalent geometry : bond 0.00347 (34779) covalent geometry : angle 0.55217 (47401) *********************** 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 308 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 261 time to evaluate : 4.063 Fit side-chains REVERT: J 241 MET cc_start: 0.7989 (ttt) cc_final: 0.7664 (ttt) REVERT: J 456 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7277 (pt) REVERT: J 525 ASP cc_start: 0.6810 (m-30) cc_final: 0.6549 (m-30) REVERT: J 1154 MET cc_start: 0.6979 (tpt) cc_final: 0.6722 (tpt) REVERT: I 52 MET cc_start: 0.7863 (mmm) cc_final: 0.7529 (mmm) REVERT: I 245 PRO cc_start: 0.6383 (Cg_exo) cc_final: 0.5861 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4554 (p-80) cc_final: 0.4310 (p-80) REVERT: D 7 ILE cc_start: 0.4903 (OUTLIER) cc_final: 0.3971 (tp) REVERT: G 166 TYR cc_start: 0.7760 (m-80) cc_final: 0.7535 (m-80) REVERT: G 252 PHE cc_start: 0.4944 (t80) cc_final: 0.4650 (t80) REVERT: G 254 LEU cc_start: 0.6875 (OUTLIER) cc_final: 0.6358 (pp) REVERT: G 357 MET cc_start: 0.4857 (ppp) cc_final: 0.4071 (ptm) REVERT: E 40 MET cc_start: 0.7775 (mmm) cc_final: 0.7502 (mmt) REVERT: H 69 LYS cc_start: 0.7837 (OUTLIER) cc_final: 0.7490 (mtpp) REVERT: L 110 MET cc_start: 0.5302 (tpt) cc_final: 0.4858 (tpt) REVERT: L 171 ASN cc_start: 0.6826 (m-40) cc_final: 0.6586 (m110) outliers start: 47 outliers final: 20 residues processed: 298 average time/residue: 0.4646 time to fit residues: 229.9249 Evaluate side-chains 278 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 254 time to evaluate : 3.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 239 THR 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 B residue 423 THR Chi-restraints excluded: chain B residue 493 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 121 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 359 LEU Chi-restraints excluded: chain F residue 620 ASP 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 346 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 326 optimal weight: 7.9990 chunk 360 optimal weight: 3.9990 chunk 280 optimal weight: 30.0000 chunk 105 optimal weight: 20.0000 chunk 172 optimal weight: 20.0000 chunk 207 optimal weight: 30.0000 chunk 99 optimal weight: 8.9990 chunk 165 optimal weight: 5.9990 chunk 36 optimal weight: 20.0000 chunk 109 optimal weight: 5.9990 chunk 302 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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 251 HIS ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.098894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.088773 restraints weight = 73420.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.087097 restraints weight = 132267.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.086676 restraints weight = 98208.707| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1098 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= 0.159 Angle : 0.559 8.462 47401 Z= 0.292 Chirality : 0.044 0.178 5391 Planarity : 0.005 0.057 6143 Dihedral : 4.543 41.455 4723 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 1.62 % Allowed : 11.68 % Favored : 86.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.12), residues: 4368 helix: 1.50 (0.14), residues: 1438 sheet: -0.07 (0.22), residues: 568 loop : -1.17 (0.12), residues: 2362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 95 HIS 0.005 0.001 HIS G 94 PHE 0.022 0.002 PHE F 401 TYR 0.020 0.001 TYR I 354 ARG 0.004 0.000 ARG J1152 Details of bonding type rmsd hydrogen bonds : bond 0.05733 ( 1405) hydrogen bonds : angle 4.62858 ( 3804) covalent geometry : bond 0.00383 (34779) covalent geometry : angle 0.55924 (47401) *********************** 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 324 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 263 time to evaluate : 3.793 Fit side-chains REVERT: J 241 MET cc_start: 0.7963 (ttt) cc_final: 0.7645 (ttt) REVERT: J 456 LEU cc_start: 0.7704 (OUTLIER) cc_final: 0.7279 (pt) REVERT: J 525 ASP cc_start: 0.6873 (m-30) cc_final: 0.6597 (m-30) REVERT: I 121 VAL cc_start: 0.5285 (OUTLIER) cc_final: 0.4975 (p) REVERT: I 173 MET cc_start: 0.4802 (OUTLIER) cc_final: 0.4557 (ttm) REVERT: I 245 PRO cc_start: 0.6440 (Cg_exo) cc_final: 0.5945 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4518 (p-80) cc_final: 0.4250 (p-80) REVERT: D 7 ILE cc_start: 0.4950 (OUTLIER) cc_final: 0.4008 (tp) REVERT: G 254 LEU cc_start: 0.6946 (OUTLIER) cc_final: 0.6508 (pp) REVERT: G 357 MET cc_start: 0.5136 (ppp) cc_final: 0.4385 (ptm) REVERT: H 69 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.7546 (mtpp) REVERT: H 330 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6609 (mt-10) REVERT: L 110 MET cc_start: 0.5112 (tpt) cc_final: 0.4619 (tpt) REVERT: L 357 MET cc_start: 0.4681 (OUTLIER) cc_final: 0.4478 (ttm) outliers start: 61 outliers final: 43 residues processed: 311 average time/residue: 0.4284 time to fit residues: 224.2649 Evaluate side-chains 303 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 253 time to evaluate : 4.011 ------------------------------------------------------------------------------- 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 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 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 365 THR 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 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 121 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 300 GLU Chi-restraints excluded: chain I residue 304 HIS 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 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 251 HIS 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 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 Chi-restraints excluded: chain L residue 357 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 220 optimal weight: 50.0000 chunk 109 optimal weight: 10.0000 chunk 322 optimal weight: 20.0000 chunk 432 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 chunk 55 optimal weight: 4.9990 chunk 341 optimal weight: 20.0000 chunk 312 optimal weight: 40.0000 chunk 108 optimal weight: 30.0000 chunk 270 optimal weight: 9.9990 chunk 98 optimal weight: 5.9990 overall best weight: 7.9992 ------------------------------------------------------------------------------- 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 205 GLN G 251 HIS ** H 196 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.098107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.087884 restraints weight = 73599.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.086643 restraints weight = 134211.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.087161 restraints weight = 130364.999| |-----------------------------------------------------------------------------| r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 34779 Z= 0.186 Angle : 0.588 8.580 47401 Z= 0.307 Chirality : 0.045 0.184 5391 Planarity : 0.006 0.059 6143 Dihedral : 4.653 40.990 4723 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.02 % Allowed : 12.53 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.12), residues: 4368 helix: 1.38 (0.14), residues: 1444 sheet: -0.15 (0.21), residues: 581 loop : -1.22 (0.12), residues: 2343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 95 HIS 0.005 0.001 HIS I 9 PHE 0.024 0.002 PHE F 401 TYR 0.026 0.002 TYR I 354 ARG 0.003 0.000 ARG L 90 Details of bonding type rmsd hydrogen bonds : bond 0.06125 ( 1405) hydrogen bonds : angle 4.69796 ( 3804) covalent geometry : bond 0.00455 (34779) covalent geometry : angle 0.58842 (47401) *********************** 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 333 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 257 time to evaluate : 4.166 Fit side-chains REVERT: J 241 MET cc_start: 0.8024 (ttt) cc_final: 0.7703 (ttt) REVERT: J 422 LEU cc_start: 0.8874 (OUTLIER) cc_final: 0.8606 (pp) REVERT: J 456 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7277 (pt) REVERT: J 525 ASP cc_start: 0.6857 (m-30) cc_final: 0.6586 (m-30) REVERT: I 52 MET cc_start: 0.7749 (mmm) cc_final: 0.7510 (mmm) REVERT: I 109 MET cc_start: 0.6378 (tpt) cc_final: 0.6174 (tpt) REVERT: I 173 MET cc_start: 0.4706 (OUTLIER) cc_final: 0.4474 (ttm) REVERT: I 245 PRO cc_start: 0.6380 (Cg_exo) cc_final: 0.5883 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4517 (p-80) cc_final: 0.4248 (p-80) REVERT: D 7 ILE cc_start: 0.4826 (OUTLIER) cc_final: 0.3850 (tp) REVERT: G 254 LEU cc_start: 0.6922 (OUTLIER) cc_final: 0.6413 (pp) REVERT: G 357 MET cc_start: 0.4783 (ppp) cc_final: 0.4116 (ptm) REVERT: H 69 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7520 (mtpp) REVERT: H 330 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6362 (mt-10) REVERT: L 106 MET cc_start: 0.7255 (tpp) cc_final: 0.6598 (mmp) REVERT: L 110 MET cc_start: 0.5262 (tpt) cc_final: 0.4876 (tpt) outliers start: 76 outliers final: 56 residues processed: 317 average time/residue: 0.4535 time to fit residues: 242.3985 Evaluate side-chains 314 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 252 time to evaluate : 4.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 71 GLN 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 793 VAL 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 1076 VAL 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 328 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 365 THR 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 55 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 121 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 230 HIS Chi-restraints excluded: chain I residue 304 HIS Chi-restraints excluded: chain I residue 328 MET 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 141 MET 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 302 VAL Chi-restraints excluded: chain G residue 320 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 137 ASP 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 435 random chunks: chunk 258 optimal weight: 0.1980 chunk 398 optimal weight: 10.0000 chunk 351 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 87 optimal weight: 0.0040 chunk 388 optimal weight: 20.0000 chunk 150 optimal weight: 9.9990 chunk 151 optimal weight: 8.9990 chunk 391 optimal weight: 10.0000 chunk 346 optimal weight: 30.0000 chunk 271 optimal weight: 6.9990 overall best weight: 4.0398 ------------------------------------------------------------------------------- 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 86 GLN L 111 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.089351 restraints weight = 73191.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.088232 restraints weight = 123577.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.088579 restraints weight = 110678.772| |-----------------------------------------------------------------------------| r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 34779 Z= 0.120 Angle : 0.513 8.069 47401 Z= 0.267 Chirality : 0.043 0.168 5391 Planarity : 0.005 0.055 6143 Dihedral : 4.292 40.494 4723 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 1.49 % Allowed : 13.54 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.13), residues: 4368 helix: 1.62 (0.14), residues: 1459 sheet: 0.01 (0.22), residues: 574 loop : -1.08 (0.12), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 95 HIS 0.004 0.001 HIS G 94 PHE 0.015 0.001 PHE L 19 TYR 0.012 0.001 TYR L 354 ARG 0.003 0.000 ARG L 239 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 1405) hydrogen bonds : angle 4.44997 ( 3804) covalent geometry : bond 0.00279 (34779) covalent geometry : angle 0.51295 (47401) *********************** 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 325 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 269 time to evaluate : 3.863 Fit side-chains REVERT: J 241 MET cc_start: 0.8039 (ttt) cc_final: 0.7721 (ttt) REVERT: J 422 LEU cc_start: 0.8806 (OUTLIER) cc_final: 0.8586 (pp) REVERT: J 525 ASP cc_start: 0.6782 (m-30) cc_final: 0.6508 (m-30) REVERT: B 617 VAL cc_start: 0.8222 (OUTLIER) cc_final: 0.7981 (t) REVERT: I 245 PRO cc_start: 0.6371 (Cg_exo) cc_final: 0.5881 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4537 (p-80) cc_final: 0.4292 (p-80) REVERT: D 7 ILE cc_start: 0.4821 (OUTLIER) cc_final: 0.3850 (tp) REVERT: D 40 MET cc_start: 0.7783 (mmt) cc_final: 0.7468 (mmt) REVERT: F 71 ILE cc_start: 0.7956 (mp) cc_final: 0.7747 (mm) REVERT: G 105 GLN cc_start: 0.6114 (pt0) cc_final: 0.4821 (tp40) REVERT: G 166 TYR cc_start: 0.7703 (m-80) cc_final: 0.7367 (m-80) REVERT: G 254 LEU cc_start: 0.6981 (OUTLIER) cc_final: 0.6523 (pp) REVERT: G 357 MET cc_start: 0.4790 (ppp) cc_final: 0.4130 (ptm) REVERT: E 40 MET cc_start: 0.7863 (mmm) cc_final: 0.7602 (mmt) REVERT: L 106 MET cc_start: 0.7253 (tpp) cc_final: 0.6940 (tpp) outliers start: 56 outliers final: 40 residues processed: 311 average time/residue: 0.4435 time to fit residues: 230.3563 Evaluate side-chains 298 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 254 time to evaluate : 3.996 ------------------------------------------------------------------------------- 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 497 ILE Chi-restraints excluded: chain J residue 972 THR Chi-restraints excluded: chain J residue 980 THR Chi-restraints excluded: chain J residue 1076 VAL 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 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 55 LEU 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 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 96 ILE 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 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 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 109 MET Chi-restraints excluded: chain L residue 137 ASP Chi-restraints excluded: chain L residue 192 PHE 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 38 optimal weight: 7.9990 chunk 79 optimal weight: 0.0470 chunk 211 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 309 optimal weight: 30.0000 chunk 123 optimal weight: 20.0000 chunk 346 optimal weight: 20.0000 chunk 122 optimal weight: 1.9990 chunk 67 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 overall best weight: 4.1684 ------------------------------------------------------------------------------- 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 = 0.3279 r_free = 0.3279 target = 0.100088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.089711 restraints weight = 73150.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.088554 restraints weight = 132335.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.089226 restraints weight = 127576.459| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 34779 Z= 0.122 Angle : 0.515 8.263 47401 Z= 0.267 Chirality : 0.043 0.171 5391 Planarity : 0.005 0.059 6143 Dihedral : 4.239 40.570 4723 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.70 % Allowed : 13.73 % Favored : 84.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.13), residues: 4368 helix: 1.69 (0.14), residues: 1453 sheet: 0.06 (0.22), residues: 574 loop : -1.04 (0.12), residues: 2341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 95 HIS 0.004 0.001 HIS G 94 PHE 0.016 0.001 PHE B 586 TYR 0.015 0.001 TYR J 350 ARG 0.006 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.04858 ( 1405) hydrogen bonds : angle 4.40566 ( 3804) covalent geometry : bond 0.00284 (34779) covalent geometry : angle 0.51516 (47401) *********************** 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 325 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 261 time to evaluate : 4.240 Fit side-chains revert: symmetry clash REVERT: J 241 MET cc_start: 0.8044 (ttt) cc_final: 0.7708 (ttt) REVERT: J 422 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8613 (pp) REVERT: J 456 LEU cc_start: 0.7682 (OUTLIER) cc_final: 0.7294 (pt) REVERT: J 525 ASP cc_start: 0.6841 (m-30) cc_final: 0.6577 (m-30) REVERT: B 341 MET cc_start: 0.3903 (tmm) cc_final: 0.3661 (tmm) REVERT: B 617 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7964 (t) REVERT: I 245 PRO cc_start: 0.6437 (Cg_exo) cc_final: 0.5996 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4479 (p-80) cc_final: 0.4238 (p-80) REVERT: I 328 MET cc_start: 0.6328 (tpp) cc_final: 0.6118 (tpp) REVERT: D 7 ILE cc_start: 0.5058 (OUTLIER) cc_final: 0.4069 (tp) REVERT: F 71 ILE cc_start: 0.7939 (mp) cc_final: 0.7708 (mm) REVERT: G 105 GLN cc_start: 0.6140 (pt0) cc_final: 0.4848 (tp40) REVERT: G 166 TYR cc_start: 0.7704 (m-80) cc_final: 0.7435 (m-80) REVERT: G 254 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6460 (pp) REVERT: G 357 MET cc_start: 0.4692 (ppp) cc_final: 0.4233 (ptm) REVERT: E 40 MET cc_start: 0.7827 (mmm) cc_final: 0.7555 (mmt) REVERT: L 106 MET cc_start: 0.7173 (tpp) cc_final: 0.6802 (tpp) outliers start: 64 outliers final: 49 residues processed: 314 average time/residue: 0.4471 time to fit residues: 238.7035 Evaluate side-chains 309 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 255 time to evaluate : 3.858 ------------------------------------------------------------------------------- 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 980 THR Chi-restraints excluded: chain J residue 1076 VAL 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 115 GLU 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 55 LEU 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 96 ILE 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 460 THR 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 320 MET Chi-restraints excluded: chain G residue 364 LEU 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 129 VAL Chi-restraints excluded: chain L residue 137 ASP Chi-restraints excluded: chain L residue 192 PHE 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 71 optimal weight: 9.9990 chunk 350 optimal weight: 10.0000 chunk 83 optimal weight: 9.9990 chunk 398 optimal weight: 9.9990 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 7.9990 chunk 424 optimal weight: 30.0000 chunk 203 optimal weight: 20.0000 chunk 127 optimal weight: 6.9990 chunk 229 optimal weight: 7.9990 chunk 201 optimal weight: 3.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 = 0.3254 r_free = 0.3254 target = 0.098827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.088212 restraints weight = 73698.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.087052 restraints weight = 115265.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.087420 restraints weight = 115621.723| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.1298 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= 0.168 Angle : 0.568 8.562 47401 Z= 0.295 Chirality : 0.044 0.183 5391 Planarity : 0.005 0.059 6143 Dihedral : 4.464 40.876 4723 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.94 % Allowed : 13.78 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.13), residues: 4368 helix: 1.56 (0.14), residues: 1440 sheet: -0.07 (0.22), residues: 581 loop : -1.15 (0.12), residues: 2347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 95 HIS 0.005 0.001 HIS I 9 PHE 0.020 0.002 PHE F 401 TYR 0.017 0.002 TYR B 321 ARG 0.004 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.05718 ( 1405) hydrogen bonds : angle 4.54840 ( 3804) covalent geometry : bond 0.00408 (34779) covalent geometry : angle 0.56783 (47401) *********************** 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 329 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 256 time to evaluate : 4.202 Fit side-chains revert: symmetry clash REVERT: J 241 MET cc_start: 0.8010 (ttt) cc_final: 0.7690 (ttt) REVERT: J 385 GLN cc_start: 0.6906 (tt0) cc_final: 0.6637 (mm110) REVERT: J 422 LEU cc_start: 0.8853 (OUTLIER) cc_final: 0.8611 (pp) REVERT: J 456 LEU cc_start: 0.7675 (OUTLIER) cc_final: 0.7258 (pt) REVERT: J 525 ASP cc_start: 0.6816 (m-30) cc_final: 0.6589 (m-30) REVERT: B 341 MET cc_start: 0.3993 (tmm) cc_final: 0.3748 (tmm) REVERT: I 245 PRO cc_start: 0.6500 (Cg_exo) cc_final: 0.6062 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4387 (p-80) cc_final: 0.4089 (p-80) REVERT: I 283 TYR cc_start: 0.7003 (OUTLIER) cc_final: 0.6510 (m-80) REVERT: D 7 ILE cc_start: 0.4842 (OUTLIER) cc_final: 0.3863 (tp) REVERT: F 71 ILE cc_start: 0.8004 (mp) cc_final: 0.7772 (mm) REVERT: F 502 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: G 105 GLN cc_start: 0.6150 (pt0) cc_final: 0.4855 (tp40) REVERT: G 254 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6494 (pp) REVERT: G 357 MET cc_start: 0.4769 (ppp) cc_final: 0.4424 (ptm) REVERT: E 40 MET cc_start: 0.7861 (mmm) cc_final: 0.7552 (mmt) REVERT: L 106 MET cc_start: 0.7242 (tpp) cc_final: 0.6622 (mmp) outliers start: 73 outliers final: 56 residues processed: 316 average time/residue: 0.4482 time to fit residues: 240.6828 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 : 4.175 ------------------------------------------------------------------------------- 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 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 793 VAL 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 1076 VAL 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 115 GLU Chi-restraints excluded: chain B residue 197 THR Chi-restraints excluded: chain B residue 328 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 55 LEU 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 283 TYR 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 96 ILE Chi-restraints excluded: chain F residue 343 THR Chi-restraints excluded: chain F residue 359 LEU Chi-restraints excluded: chain F residue 460 THR Chi-restraints excluded: chain F residue 502 GLU 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 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 566 VAL Chi-restraints excluded: chain H residue 679 CYS Chi-restraints excluded: chain L residue 23 VAL Chi-restraints excluded: chain L residue 129 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 115 optimal weight: 20.0000 chunk 393 optimal weight: 8.9990 chunk 408 optimal weight: 20.0000 chunk 418 optimal weight: 30.0000 chunk 72 optimal weight: 9.9990 chunk 398 optimal weight: 0.9990 chunk 273 optimal weight: 5.9990 chunk 107 optimal weight: 0.0050 chunk 314 optimal weight: 6.9990 chunk 324 optimal weight: 6.9990 chunk 90 optimal weight: 10.0000 overall best weight: 4.2002 ------------------------------------------------------------------------------- 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 = 0.3270 r_free = 0.3270 target = 0.099279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.088805 restraints weight = 73068.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.087728 restraints weight = 129275.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.088255 restraints weight = 122986.790| |-----------------------------------------------------------------------------| r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 34779 Z= 0.123 Angle : 0.520 8.189 47401 Z= 0.270 Chirality : 0.043 0.169 5391 Planarity : 0.005 0.055 6143 Dihedral : 4.270 40.417 4723 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.54 % Allowed : 14.13 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.13), residues: 4368 helix: 1.70 (0.14), residues: 1445 sheet: 0.09 (0.22), residues: 572 loop : -1.07 (0.12), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 95 HIS 0.005 0.001 HIS G 70 PHE 0.018 0.001 PHE B 586 TYR 0.013 0.001 TYR L 354 ARG 0.004 0.000 ARG J 349 Details of bonding type rmsd hydrogen bonds : bond 0.04900 ( 1405) hydrogen bonds : angle 4.43125 ( 3804) covalent geometry : bond 0.00286 (34779) covalent geometry : angle 0.51985 (47401) ********************** 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 316 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 258 time to evaluate : 3.894 Fit side-chains revert: symmetry clash REVERT: J 241 MET cc_start: 0.8028 (ttt) cc_final: 0.7708 (ttt) REVERT: J 422 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8577 (pp) REVERT: J 456 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7283 (pt) REVERT: J 525 ASP cc_start: 0.6800 (m-30) cc_final: 0.6565 (m-30) REVERT: B 341 MET cc_start: 0.4169 (tmm) cc_final: 0.3942 (tmm) REVERT: B 617 VAL cc_start: 0.8200 (OUTLIER) cc_final: 0.7965 (t) REVERT: I 120 ARG cc_start: 0.5031 (mtm180) cc_final: 0.4475 (ptt90) REVERT: I 245 PRO cc_start: 0.6481 (Cg_exo) cc_final: 0.6073 (Cg_endo) REVERT: I 256 HIS cc_start: 0.4476 (p-80) cc_final: 0.4224 (p-80) REVERT: D 7 ILE cc_start: 0.5071 (OUTLIER) cc_final: 0.4104 (tp) REVERT: F 71 ILE cc_start: 0.7963 (mp) cc_final: 0.7747 (mm) REVERT: G 105 GLN cc_start: 0.6077 (pt0) cc_final: 0.4879 (tp40) REVERT: G 166 TYR cc_start: 0.7863 (m-80) cc_final: 0.7538 (m-80) REVERT: G 254 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6497 (pp) REVERT: G 357 MET cc_start: 0.4762 (ppp) cc_final: 0.4424 (ptm) REVERT: E 40 MET cc_start: 0.7853 (mmm) cc_final: 0.7585 (mmt) REVERT: L 106 MET cc_start: 0.7228 (tpp) cc_final: 0.6924 (tpp) outliers start: 58 outliers final: 50 residues processed: 306 average time/residue: 0.4840 time to fit residues: 250.0643 Evaluate side-chains 310 residues out of total 3758 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 255 time to evaluate : 3.846 ------------------------------------------------------------------------------- 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 793 VAL 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 1076 VAL 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 328 ILE Chi-restraints excluded: chain B residue 337 ILE Chi-restraints excluded: chain B residue 365 THR 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 55 LEU 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 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 96 ILE 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 460 THR 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 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 129 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 ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 51.1176 > 50: distance: 134 - 138: 3.248 distance: 138 - 139: 5.333 distance: 139 - 142: 9.343 distance: 140 - 141: 8.459 distance: 140 - 143: 7.495 distance: 143 - 211: 8.281 distance: 144 - 147: 7.592 distance: 145 - 146: 7.995 distance: 145 - 150: 10.597 distance: 146 - 208: 5.087 distance: 147 - 148: 5.777 distance: 147 - 149: 4.736 distance: 150 - 151: 7.812 distance: 151 - 152: 4.696 distance: 151 - 154: 9.246 distance: 152 - 153: 6.535 distance: 152 - 157: 6.315 distance: 154 - 155: 7.853 distance: 154 - 156: 19.156 distance: 157 - 158: 8.184 distance: 158 - 159: 6.003 distance: 158 - 161: 4.658 distance: 159 - 160: 6.882 distance: 159 - 164: 12.885 distance: 161 - 162: 6.945 distance: 162 - 163: 7.553 distance: 164 - 165: 8.024 distance: 165 - 166: 7.365 distance: 165 - 168: 7.322 distance: 166 - 167: 11.691 distance: 166 - 172: 8.252 distance: 168 - 169: 13.103 distance: 168 - 170: 9.455 distance: 169 - 171: 10.430 distance: 172 - 173: 5.047 distance: 173 - 174: 22.418 distance: 173 - 176: 20.432 distance: 174 - 175: 17.689 distance: 174 - 180: 13.435 distance: 176 - 177: 20.091 distance: 177 - 178: 5.443 distance: 177 - 179: 25.251 distance: 180 - 181: 18.423 distance: 181 - 182: 6.057 distance: 182 - 183: 31.182 distance: 182 - 184: 8.511 distance: 184 - 185: 14.432 distance: 185 - 186: 29.608 distance: 185 - 188: 10.112 distance: 186 - 187: 15.974 distance: 186 - 193: 38.561 distance: 188 - 189: 31.693 distance: 189 - 190: 34.733 distance: 190 - 191: 26.474 distance: 191 - 192: 24.582 distance: 193 - 194: 6.464 distance: 194 - 195: 7.388 distance: 194 - 197: 20.835 distance: 195 - 196: 10.614 distance: 195 - 201: 14.440 distance: 197 - 198: 7.045 distance: 198 - 199: 10.510 distance: 199 - 200: 8.734 distance: 201 - 202: 20.471 distance: 201 - 207: 24.085 distance: 202 - 203: 4.920 distance: 202 - 205: 18.186 distance: 203 - 204: 26.511 distance: 203 - 208: 29.033 distance: 205 - 206: 9.888 distance: 206 - 207: 13.642