Starting phenix.real_space_refine on Sat Mar 7 08:15:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7aqo_11871/03_2026/7aqo_11871.cif Found real_map, /net/cci-nas-00/data/ceres_data/7aqo_11871/03_2026/7aqo_11871.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7aqo_11871/03_2026/7aqo_11871.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7aqo_11871/03_2026/7aqo_11871.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7aqo_11871/03_2026/7aqo_11871.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7aqo_11871/03_2026/7aqo_11871.map" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.060 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 136 5.16 5 C 25983 2.51 5 N 6865 2.21 5 O 7277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 198 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 40261 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1079, 7785 Classifications: {'peptide': 1079} Incomplete info: {'truncation_to_alanine': 297} Link IDs: {'PTRANS': 31, 'TRANS': 1047} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 1009 Unresolved non-hydrogen angles: 1256 Unresolved non-hydrogen dihedrals: 806 Unresolved non-hydrogen chiralities: 67 Planarities with less than four sites: {'GLN:plan1': 14, 'GLU:plan': 50, 'ARG:plan': 15, 'ASN:plan1': 28, 'TRP:plan': 2, 'ASP:plan': 33, 'PHE:plan': 6, 'HIS:plan': 4, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 609 Chain: "B" Number of atoms: 4143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4143 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 167} Link IDs: {'PTRANS': 22, 'TRANS': 540} Chain breaks: 3 Unresolved non-hydrogen bonds: 560 Unresolved non-hydrogen angles: 680 Unresolved non-hydrogen dihedrals: 452 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ASN:plan1': 15, 'GLU:plan': 35, 'GLN:plan1': 5, 'HIS:plan': 1, 'ASP:plan': 24, 'ARG:plan': 10, 'PHE:plan': 2, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 358 Chain: "E" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 348, 2357 Classifications: {'peptide': 348} Incomplete info: {'truncation_to_alanine': 130} Link IDs: {'PTRANS': 8, 'TRANS': 339} Chain breaks: 1 Unresolved non-hydrogen bonds: 370 Unresolved non-hydrogen angles: 447 Unresolved non-hydrogen dihedrals: 300 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'ASN:plan1': 12, 'GLU:plan': 12, 'ASP:plan': 19, 'ARG:plan': 1, 'HIS:plan': 2, 'GLN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 171 Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2818 Classifications: {'peptide': 361} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 14, 'TRANS': 346} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'PHE:plan': 3, 'ASP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 54 Chain: "J" Number of atoms: 1588 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 230, 1583 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 10, 'GLN:plan1': 3, 'ASP:plan': 14, 'ASN:plan1': 3, 'HIS:plan': 2, 'TRP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 167 Conformer: "B" Number of residues, atoms: 230, 1583 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'PTRANS': 6, 'TRANS': 223} Chain breaks: 2 Unresolved non-hydrogen bonds: 308 Unresolved non-hydrogen angles: 379 Unresolved non-hydrogen dihedrals: 257 Unresolved non-hydrogen chiralities: 19 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 10, 'GLN:plan1': 3, 'ASP:plan': 14, 'ASN:plan1': 3, 'HIS:plan': 2, 'TRP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 167 bond proxies already assigned to first conformer: 1598 Chain: "I" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1452 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 109} Link IDs: {'PTRANS': 3, 'TRANS': 223} Chain breaks: 1 Unresolved non-hydrogen bonds: 391 Unresolved non-hydrogen angles: 488 Unresolved non-hydrogen dihedrals: 322 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ASP:plan': 10, 'GLU:plan': 19, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ARG:plan': 6, 'TRP:plan': 2, 'PHE:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 213 Chain: "C" Number of atoms: 1573 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1568 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 10, 'GLN:plan1': 3, 'ASP:plan': 13, 'ASN:plan1': 3, 'HIS:plan': 2, 'TRP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 164 Conformer: "B" Number of residues, atoms: 227, 1568 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 81} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 301 Unresolved non-hydrogen angles: 370 Unresolved non-hydrogen dihedrals: 252 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'ARG:plan': 6, 'GLU:plan': 10, 'GLN:plan1': 3, 'ASP:plan': 13, 'ASN:plan1': 3, 'HIS:plan': 2, 'TRP:plan': 2, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 164 bond proxies already assigned to first conformer: 1584 Chain: "D" Number of atoms: 1442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1442 Classifications: {'peptide': 225} Incomplete info: {'truncation_to_alanine': 107} Link IDs: {'PTRANS': 3, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 382 Unresolved non-hydrogen angles: 477 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 32 Planarities with less than four sites: {'ASP:plan': 9, 'GLU:plan': 19, 'ASN:plan1': 3, 'GLN:plan1': 3, 'ARG:plan': 5, 'TRP:plan': 2, 'PHE:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 205 Restraints were copied for chains: G, H, K, L Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ALEU J 47 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU J 47 " occ=0.50 residue: pdb=" N ALEU C 47 " occ=0.50 ... (8 atoms not shown) pdb=" CB BLEU C 47 " occ=0.50 Time building chain proxies: 14.73, per 1000 atoms: 0.37 Number of scatterers: 40261 At special positions: 0 Unit cell: (157.32, 222.18, 314.64, 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 136 16.00 O 7277 8.00 N 6865 7.00 C 25983 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: 3.16 Conformation dependent library (CDL) restraints added in 2.1 seconds 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10842 Finding SS restraints... Secondary structure from input PDB file: 254 helices and 24 sheets defined 62.5% alpha, 6.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'G' and resid 36 through 51 Processing helix chain 'G' and resid 53 through 72 removed outlier: 3.601A pdb=" N LYS G 57 " --> pdb=" O SER G 53 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR G 63 " --> pdb=" O ASP G 59 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N PHE G 71 " --> pdb=" O GLU G 67 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE G 72 " --> pdb=" O LEU G 68 " (cutoff:3.500A) Processing helix chain 'G' and resid 86 through 101 removed outlier: 3.978A pdb=" N SER G 101 " --> pdb=" O GLU G 97 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 115 removed outlier: 3.912A pdb=" N MET G 109 " --> pdb=" O ILE G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 132 Processing helix chain 'G' and resid 135 through 143 Processing helix chain 'G' and resid 151 through 166 Processing helix chain 'G' and resid 178 through 194 Processing helix chain 'G' and resid 197 through 200 Processing helix chain 'G' and resid 201 through 216 Processing helix chain 'G' and resid 219 through 233 removed outlier: 3.563A pdb=" N THR G 223 " --> pdb=" O ASP G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 249 removed outlier: 8.202A pdb=" N LYS G 240 " --> pdb=" O THR G 236 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE G 241 " --> pdb=" O GLU G 237 " (cutoff:3.500A) Processing helix chain 'G' and resid 262 through 266 removed outlier: 3.916A pdb=" N LEU G 266 " --> pdb=" O TYR G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 271 through 282 Processing helix chain 'G' and resid 289 through 292 removed outlier: 3.609A pdb=" N GLU G 292 " --> pdb=" O VAL G 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 289 through 292' Processing helix chain 'G' and resid 293 through 305 Processing helix chain 'G' and resid 312 through 317 Processing helix chain 'G' and resid 322 through 343 Processing helix chain 'G' and resid 395 through 402 Processing helix chain 'G' and resid 403 through 414 Processing helix chain 'G' and resid 416 through 425 removed outlier: 4.702A pdb=" N VAL G 420 " --> pdb=" O CYS G 416 " (cutoff:3.500A) Processing helix chain 'G' and resid 427 through 433 Processing helix chain 'G' and resid 435 through 456 removed outlier: 3.553A pdb=" N ARG G 439 " --> pdb=" O GLU G 435 " (cutoff:3.500A) Proline residue: G 451 - end of helix Processing helix chain 'G' and resid 510 through 514 removed outlier: 3.563A pdb=" N SER G 513 " --> pdb=" O GLU G 510 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN G 514 " --> pdb=" O TRP G 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 510 through 514' Processing helix chain 'G' and resid 520 through 536 removed outlier: 4.379A pdb=" N ILE G 530 " --> pdb=" O GLU G 526 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER G 533 " --> pdb=" O HIS G 529 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE G 534 " --> pdb=" O ILE G 530 " (cutoff:3.500A) Processing helix chain 'G' and resid 537 through 541 removed outlier: 4.008A pdb=" N GLY G 540 " --> pdb=" O PRO G 537 " (cutoff:3.500A) Processing helix chain 'G' and resid 542 through 560 removed outlier: 4.092A pdb=" N LEU G 546 " --> pdb=" O ILE G 542 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N ASN G 560 " --> pdb=" O ASP G 556 " (cutoff:3.500A) Processing helix chain 'G' and resid 565 through 580 removed outlier: 3.632A pdb=" N THR G 569 " --> pdb=" O SER G 565 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 586 Processing helix chain 'G' and resid 591 through 603 removed outlier: 4.003A pdb=" N THR G 595 " --> pdb=" O ASN G 591 " (cutoff:3.500A) Processing helix chain 'G' and resid 606 through 620 Processing helix chain 'G' and resid 625 through 644 Processing helix chain 'G' and resid 650 through 665 removed outlier: 4.645A pdb=" N ARG G 656 " --> pdb=" O ALA G 652 " (cutoff:3.500A) Processing helix chain 'G' and resid 665 through 670 removed outlier: 3.563A pdb=" N SER G 669 " --> pdb=" O ASN G 665 " (cutoff:3.500A) Processing helix chain 'G' and resid 670 through 680 Processing helix chain 'G' and resid 682 through 691 Processing helix chain 'G' and resid 692 through 694 No H-bonds generated for 'chain 'G' and resid 692 through 694' Processing helix chain 'G' and resid 695 through 712 Processing helix chain 'G' and resid 727 through 742 Processing helix chain 'G' and resid 747 through 758 Processing helix chain 'G' and resid 759 through 761 No H-bonds generated for 'chain 'G' and resid 759 through 761' Processing helix chain 'G' and resid 762 through 776 removed outlier: 3.547A pdb=" N VAL G 766 " --> pdb=" O ASN G 762 " (cutoff:3.500A) Processing helix chain 'G' and resid 786 through 793 Processing helix chain 'G' and resid 796 through 807 Processing helix chain 'G' and resid 814 through 827 Processing helix chain 'G' and resid 830 through 847 removed outlier: 3.521A pdb=" N LEU G 843 " --> pdb=" O TYR G 839 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS G 844 " --> pdb=" O THR G 840 " (cutoff:3.500A) Processing helix chain 'G' and resid 851 through 877 removed outlier: 4.345A pdb=" N THR G 857 " --> pdb=" O LYS G 853 " (cutoff:3.500A) Processing helix chain 'G' and resid 878 through 885 removed outlier: 3.754A pdb=" N PHE G 882 " --> pdb=" O LYS G 878 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU G 883 " --> pdb=" O GLY G 879 " (cutoff:3.500A) Processing helix chain 'G' and resid 888 through 895 Processing helix chain 'G' and resid 899 through 917 removed outlier: 5.653A pdb=" N ASP G 909 " --> pdb=" O HIS G 905 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR G 910 " --> pdb=" O ILE G 906 " (cutoff:3.500A) Processing helix chain 'G' and resid 941 through 951 removed outlier: 3.855A pdb=" N LEU G 951 " --> pdb=" O THR G 947 " (cutoff:3.500A) Processing helix chain 'G' and resid 960 through 970 removed outlier: 3.770A pdb=" N ASP G 964 " --> pdb=" O LYS G 960 " (cutoff:3.500A) Processing helix chain 'G' and resid 984 through 993 Processing helix chain 'G' and resid 993 through 1018 removed outlier: 4.062A pdb=" N GLY G 997 " --> pdb=" O ILE G 993 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU G1013 " --> pdb=" O GLU G1009 " (cutoff:3.500A) Processing helix chain 'G' and resid 1025 through 1034 removed outlier: 4.030A pdb=" N LEU G1031 " --> pdb=" O ILE G1027 " (cutoff:3.500A) Processing helix chain 'G' and resid 1035 through 1040 Processing helix chain 'G' and resid 1042 through 1054 removed outlier: 3.546A pdb=" N ALA G1046 " --> pdb=" O SER G1042 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE G1054 " --> pdb=" O SER G1050 " (cutoff:3.500A) Processing helix chain 'G' and resid 1058 through 1071 Processing helix chain 'G' and resid 1074 through 1082 removed outlier: 3.519A pdb=" N PHE G1080 " --> pdb=" O LYS G1076 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N CYS G1082 " --> pdb=" O LEU G1078 " (cutoff:3.500A) Processing helix chain 'G' and resid 1083 through 1107 Processing helix chain 'G' and resid 1113 through 1133 Processing helix chain 'G' and resid 1137 through 1152 removed outlier: 4.015A pdb=" N ILE G1141 " --> pdb=" O ASN G1137 " (cutoff:3.500A) Processing helix chain 'G' and resid 1153 through 1155 No H-bonds generated for 'chain 'G' and resid 1153 through 1155' Processing helix chain 'H' and resid 3 through 22 removed outlier: 3.791A pdb=" N LEU H 22 " --> pdb=" O THR H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 32 removed outlier: 3.960A pdb=" N HIS H 31 " --> pdb=" O ASP H 27 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 39 removed outlier: 3.511A pdb=" N MET H 38 " --> pdb=" O PRO H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 43 through 47 removed outlier: 3.950A pdb=" N PHE H 46 " --> pdb=" O VAL H 43 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU H 47 " --> pdb=" O LEU H 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 43 through 47' Processing helix chain 'H' and resid 55 through 59 removed outlier: 3.647A pdb=" N HIS H 59 " --> pdb=" O SER H 56 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 78 Processing helix chain 'H' and resid 91 through 106 removed outlier: 3.747A pdb=" N TYR H 104 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 112 through 114 No H-bonds generated for 'chain 'H' and resid 112 through 114' Processing helix chain 'H' and resid 115 through 131 removed outlier: 3.551A pdb=" N LEU H 131 " --> pdb=" O ILE H 127 " (cutoff:3.500A) Processing helix chain 'H' and resid 133 through 147 Proline residue: H 142 - end of helix Processing helix chain 'H' and resid 147 through 152 removed outlier: 3.882A pdb=" N PHE H 151 " --> pdb=" O ARG H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 191 removed outlier: 4.346A pdb=" N LYS H 177 " --> pdb=" O PRO H 173 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ARG H 179 " --> pdb=" O TYR H 175 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASN H 191 " --> pdb=" O LYS H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 196 through 214 removed outlier: 3.505A pdb=" N LEU H 214 " --> pdb=" O LEU H 210 " (cutoff:3.500A) Processing helix chain 'H' and resid 251 through 268 Processing helix chain 'H' and resid 271 through 275 Processing helix chain 'H' and resid 279 through 320 Proline residue: H 290 - end of helix Processing helix chain 'H' and resid 336 through 341 removed outlier: 3.671A pdb=" N HIS H 341 " --> pdb=" O VAL H 337 " (cutoff:3.500A) Processing helix chain 'H' and resid 343 through 361 Processing helix chain 'H' and resid 378 through 387 Processing helix chain 'H' and resid 392 through 416 removed outlier: 4.071A pdb=" N ASP H 416 " --> pdb=" O LEU H 412 " (cutoff:3.500A) Processing helix chain 'H' and resid 417 through 430 removed outlier: 3.667A pdb=" N PHE H 421 " --> pdb=" O GLU H 417 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU H 429 " --> pdb=" O CYS H 425 " (cutoff:3.500A) Processing helix chain 'H' and resid 442 through 456 Processing helix chain 'H' and resid 459 through 464 Processing helix chain 'H' and resid 470 through 491 removed outlier: 3.910A pdb=" N ASP H 491 " --> pdb=" O THR H 487 " (cutoff:3.500A) Processing helix chain 'H' and resid 493 through 497 removed outlier: 3.714A pdb=" N PHE H 496 " --> pdb=" O PHE H 493 " (cutoff:3.500A) Processing helix chain 'H' and resid 525 through 532 Processing helix chain 'H' and resid 577 through 587 Processing helix chain 'K' and resid 23 through 32 Processing helix chain 'K' and resid 42 through 53 Processing helix chain 'K' and resid 200 through 206 removed outlier: 3.694A pdb=" N ILE K 204 " --> pdb=" O ASN K 200 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 68 removed outlier: 3.520A pdb=" N LEU L 68 " --> pdb=" O LYS L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 70 through 79 Processing helix chain 'L' and resid 86 through 97 Proline residue: L 94 - end of helix Processing helix chain 'L' and resid 111 through 124 removed outlier: 3.847A pdb=" N VAL L 115 " --> pdb=" O GLY L 111 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE L 116 " --> pdb=" O LYS L 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 154 Processing helix chain 'L' and resid 170 through 180 Processing helix chain 'L' and resid 191 through 201 removed outlier: 3.595A pdb=" N GLU L 201 " --> pdb=" O ALA L 197 " (cutoff:3.500A) Processing helix chain 'L' and resid 216 through 223 Processing helix chain 'L' and resid 223 through 236 removed outlier: 3.577A pdb=" N ALA L 236 " --> pdb=" O GLU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 289 through 291 No H-bonds generated for 'chain 'L' and resid 289 through 291' Processing helix chain 'L' and resid 292 through 304 removed outlier: 3.794A pdb=" N ASP L 302 " --> pdb=" O ALA L 298 " (cutoff:3.500A) Processing helix chain 'L' and resid 315 through 329 Processing helix chain 'L' and resid 341 through 354 Processing helix chain 'L' and resid 364 through 367 Processing helix chain 'L' and resid 386 through 395 Processing helix chain 'L' and resid 412 through 427 removed outlier: 3.970A pdb=" N GLN L 423 " --> pdb=" O LEU L 419 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU L 424 " --> pdb=" O ALA L 420 " (cutoff:3.500A) Processing helix chain 'L' and resid 439 through 443 Processing helix chain 'A' and resid 36 through 51 Processing helix chain 'A' and resid 53 through 72 removed outlier: 3.601A pdb=" N LYS A 57 " --> pdb=" O SER A 53 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A 63 " --> pdb=" O ASP A 59 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE A 72 " --> pdb=" O LEU A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 101 removed outlier: 3.979A pdb=" N SER A 101 " --> pdb=" O GLU A 97 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 115 removed outlier: 3.911A pdb=" N MET A 109 " --> pdb=" O ILE A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 135 through 143 Processing helix chain 'A' and resid 151 through 166 Processing helix chain 'A' and resid 178 through 194 Processing helix chain 'A' and resid 197 through 200 Processing helix chain 'A' and resid 201 through 216 Processing helix chain 'A' and resid 219 through 233 removed outlier: 3.564A pdb=" N THR A 223 " --> pdb=" O ASP A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 249 removed outlier: 8.204A pdb=" N LYS A 240 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N PHE A 241 " --> pdb=" O GLU A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 266 removed outlier: 3.916A pdb=" N LEU A 266 " --> pdb=" O TYR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 289 through 292 removed outlier: 3.609A pdb=" N GLU A 292 " --> pdb=" O VAL A 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 289 through 292' Processing helix chain 'A' and resid 293 through 305 Processing helix chain 'A' and resid 312 through 317 Processing helix chain 'A' and resid 322 through 343 Processing helix chain 'A' and resid 395 through 402 Processing helix chain 'A' and resid 403 through 414 Processing helix chain 'A' and resid 416 through 425 removed outlier: 4.703A pdb=" N VAL A 420 " --> pdb=" O CYS A 416 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 433 Processing helix chain 'A' and resid 435 through 456 removed outlier: 3.553A pdb=" N ARG A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 510 through 514 removed outlier: 3.564A pdb=" N SER A 513 " --> pdb=" O GLU A 510 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N ASN A 514 " --> pdb=" O TRP A 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 510 through 514' Processing helix chain 'A' and resid 520 through 536 removed outlier: 4.380A pdb=" N ILE A 530 " --> pdb=" O GLU A 526 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER A 533 " --> pdb=" O HIS A 529 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ILE A 534 " --> pdb=" O ILE A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 541 removed outlier: 4.008A pdb=" N GLY A 540 " --> pdb=" O PRO A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 560 removed outlier: 4.093A pdb=" N LEU A 546 " --> pdb=" O ILE A 542 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ASN A 560 " --> pdb=" O ASP A 556 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 580 removed outlier: 3.631A pdb=" N THR A 569 " --> pdb=" O SER A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 586 Processing helix chain 'A' and resid 591 through 603 removed outlier: 4.003A pdb=" N THR A 595 " --> pdb=" O ASN A 591 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 620 Processing helix chain 'A' and resid 625 through 644 Processing helix chain 'A' and resid 650 through 665 removed outlier: 4.645A pdb=" N ARG A 656 " --> pdb=" O ALA A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 670 removed outlier: 3.563A pdb=" N SER A 669 " --> pdb=" O ASN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 680 Processing helix chain 'A' and resid 682 through 691 Processing helix chain 'A' and resid 692 through 694 No H-bonds generated for 'chain 'A' and resid 692 through 694' Processing helix chain 'A' and resid 695 through 712 Processing helix chain 'A' and resid 727 through 742 Processing helix chain 'A' and resid 747 through 758 Processing helix chain 'A' and resid 759 through 761 No H-bonds generated for 'chain 'A' and resid 759 through 761' Processing helix chain 'A' and resid 762 through 776 removed outlier: 3.546A pdb=" N VAL A 766 " --> pdb=" O ASN A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 786 through 793 Processing helix chain 'A' and resid 796 through 807 Processing helix chain 'A' and resid 814 through 827 Processing helix chain 'A' and resid 830 through 847 removed outlier: 3.521A pdb=" N LEU A 843 " --> pdb=" O TYR A 839 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 844 " --> pdb=" O THR A 840 " (cutoff:3.500A) Processing helix chain 'A' and resid 851 through 877 removed outlier: 4.345A pdb=" N THR A 857 " --> pdb=" O LYS A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 878 through 885 removed outlier: 3.754A pdb=" N PHE A 882 " --> pdb=" O LYS A 878 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU A 883 " --> pdb=" O GLY A 879 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 895 Processing helix chain 'A' and resid 899 through 917 removed outlier: 5.652A pdb=" N ASP A 909 " --> pdb=" O HIS A 905 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N TYR A 910 " --> pdb=" O ILE A 906 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 951 removed outlier: 3.854A pdb=" N LEU A 951 " --> pdb=" O THR A 947 " (cutoff:3.500A) Processing helix chain 'A' and resid 960 through 970 removed outlier: 3.771A pdb=" N ASP A 964 " --> pdb=" O LYS A 960 " (cutoff:3.500A) Processing helix chain 'A' and resid 984 through 993 Processing helix chain 'A' and resid 993 through 1018 removed outlier: 4.062A pdb=" N GLY A 997 " --> pdb=" O ILE A 993 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU A1013 " --> pdb=" O GLU A1009 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1034 removed outlier: 4.031A pdb=" N LEU A1031 " --> pdb=" O ILE A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1040 Processing helix chain 'A' and resid 1042 through 1054 removed outlier: 3.546A pdb=" N ALA A1046 " --> pdb=" O SER A1042 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A1054 " --> pdb=" O SER A1050 " (cutoff:3.500A) Processing helix chain 'A' and resid 1058 through 1071 Processing helix chain 'A' and resid 1074 through 1082 removed outlier: 3.519A pdb=" N PHE A1080 " --> pdb=" O LYS A1076 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N CYS A1082 " --> pdb=" O LEU A1078 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1107 Processing helix chain 'A' and resid 1113 through 1133 Processing helix chain 'A' and resid 1137 through 1152 removed outlier: 4.015A pdb=" N ILE A1141 " --> pdb=" O ASN A1137 " (cutoff:3.500A) Processing helix chain 'A' and resid 1153 through 1155 No H-bonds generated for 'chain 'A' and resid 1153 through 1155' Processing helix chain 'B' and resid 3 through 22 removed outlier: 3.791A pdb=" N LEU B 22 " --> pdb=" O THR B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 32 removed outlier: 3.960A pdb=" N HIS B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 39 removed outlier: 3.511A pdb=" N MET B 38 " --> pdb=" O PRO B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 47 removed outlier: 3.949A pdb=" N PHE B 46 " --> pdb=" O VAL B 43 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU B 47 " --> pdb=" O LEU B 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 43 through 47' Processing helix chain 'B' and resid 55 through 59 removed outlier: 3.647A pdb=" N HIS B 59 " --> pdb=" O SER B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 78 Processing helix chain 'B' and resid 91 through 106 removed outlier: 3.748A pdb=" N TYR B 104 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 114 No H-bonds generated for 'chain 'B' and resid 112 through 114' Processing helix chain 'B' and resid 115 through 131 removed outlier: 3.551A pdb=" N LEU B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 133 through 147 Proline residue: B 142 - end of helix Processing helix chain 'B' and resid 147 through 152 removed outlier: 3.881A pdb=" N PHE B 151 " --> pdb=" O ARG B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 191 removed outlier: 4.346A pdb=" N LYS B 177 " --> pdb=" O PRO B 173 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N ARG B 179 " --> pdb=" O TYR B 175 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ASN B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 196 through 214 removed outlier: 3.504A pdb=" N LEU B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 268 Processing helix chain 'B' and resid 271 through 275 Processing helix chain 'B' and resid 279 through 320 Proline residue: B 290 - end of helix Processing helix chain 'B' and resid 336 through 341 removed outlier: 3.671A pdb=" N HIS B 341 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 343 through 361 Processing helix chain 'B' and resid 378 through 387 Processing helix chain 'B' and resid 392 through 416 removed outlier: 4.071A pdb=" N ASP B 416 " --> pdb=" O LEU B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 417 through 430 removed outlier: 3.667A pdb=" N PHE B 421 " --> pdb=" O GLU B 417 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU B 429 " --> pdb=" O CYS B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 456 Processing helix chain 'B' and resid 459 through 464 Processing helix chain 'B' and resid 470 through 491 removed outlier: 3.909A pdb=" N ASP B 491 " --> pdb=" O THR B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 493 through 497 removed outlier: 3.713A pdb=" N PHE B 496 " --> pdb=" O PHE B 493 " (cutoff:3.500A) Processing helix chain 'B' and resid 525 through 532 Processing helix chain 'B' and resid 577 through 587 Processing helix chain 'E' and resid 23 through 32 Processing helix chain 'E' and resid 42 through 53 Processing helix chain 'E' and resid 200 through 206 removed outlier: 3.694A pdb=" N ILE E 204 " --> pdb=" O ASN E 200 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 68 removed outlier: 3.519A pdb=" N LEU F 68 " --> pdb=" O LYS F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 70 through 79 Processing helix chain 'F' and resid 86 through 97 Proline residue: F 94 - end of helix Processing helix chain 'F' and resid 111 through 124 removed outlier: 3.847A pdb=" N VAL F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE F 116 " --> pdb=" O LYS F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 154 Processing helix chain 'F' and resid 170 through 180 Processing helix chain 'F' and resid 191 through 201 removed outlier: 3.595A pdb=" N GLU F 201 " --> pdb=" O ALA F 197 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 223 Processing helix chain 'F' and resid 223 through 236 removed outlier: 3.576A pdb=" N ALA F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) Processing helix chain 'F' and resid 289 through 291 No H-bonds generated for 'chain 'F' and resid 289 through 291' Processing helix chain 'F' and resid 292 through 304 removed outlier: 3.794A pdb=" N ASP F 302 " --> pdb=" O ALA F 298 " (cutoff:3.500A) Processing helix chain 'F' and resid 315 through 329 Processing helix chain 'F' and resid 341 through 354 Processing helix chain 'F' and resid 364 through 367 Processing helix chain 'F' and resid 386 through 395 Processing helix chain 'F' and resid 412 through 427 removed outlier: 3.969A pdb=" N GLN F 423 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N GLU F 424 " --> pdb=" O ALA F 420 " (cutoff:3.500A) Processing helix chain 'F' and resid 439 through 443 Processing helix chain 'J' and resid 8 through 39 removed outlier: 3.679A pdb=" N GLU J 22 " --> pdb=" O GLN J 18 " (cutoff:3.500A) Processing helix chain 'J' and resid 45 through 84 Proline residue: J 55 - end of helix removed outlier: 4.491A pdb=" N GLU J 60 " --> pdb=" O ASP J 56 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE J 62 " --> pdb=" O HIS J 58 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN J 63 " --> pdb=" O ARG J 59 " (cutoff:3.500A) Processing helix chain 'J' and resid 86 through 91 removed outlier: 3.724A pdb=" N VAL J 90 " --> pdb=" O THR J 86 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 94 No H-bonds generated for 'chain 'J' and resid 92 through 94' Processing helix chain 'J' and resid 96 through 120 removed outlier: 3.932A pdb=" N ILE J 100 " --> pdb=" O ASN J 96 " (cutoff:3.500A) Processing helix chain 'J' and resid 150 through 159 removed outlier: 3.566A pdb=" N ILE J 156 " --> pdb=" O LYS J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 160 through 162 No H-bonds generated for 'chain 'J' and resid 160 through 162' Processing helix chain 'J' and resid 166 through 235 removed outlier: 3.635A pdb=" N VAL J 170 " --> pdb=" O ASP J 166 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N TYR J 194 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing helix chain 'J' and resid 237 through 238 No H-bonds generated for 'chain 'J' and resid 237 through 238' Processing helix chain 'I' and resid 4 through 16 Processing helix chain 'I' and resid 21 through 44 removed outlier: 3.935A pdb=" N LEU I 37 " --> pdb=" O LYS I 33 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 102 Processing helix chain 'I' and resid 103 through 105 No H-bonds generated for 'chain 'I' and resid 103 through 105' Processing helix chain 'I' and resid 106 through 143 Processing helix chain 'I' and resid 153 through 160 Processing helix chain 'I' and resid 163 through 169 removed outlier: 4.092A pdb=" N LEU I 167 " --> pdb=" O LEU I 163 " (cutoff:3.500A) Processing helix chain 'I' and resid 198 through 249 removed outlier: 3.831A pdb=" N SER I 239 " --> pdb=" O GLY I 235 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE I 240 " --> pdb=" O LYS I 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 8 through 39 removed outlier: 3.679A pdb=" N GLU C 22 " --> pdb=" O GLN C 18 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 84 Proline residue: C 55 - end of helix removed outlier: 4.491A pdb=" N GLU C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ILE C 62 " --> pdb=" O HIS C 58 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N ASN C 63 " --> pdb=" O ARG C 59 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 91 removed outlier: 3.724A pdb=" N VAL C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 94 No H-bonds generated for 'chain 'C' and resid 92 through 94' Processing helix chain 'C' and resid 96 through 120 removed outlier: 3.932A pdb=" N ILE C 100 " --> pdb=" O ASN C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 159 removed outlier: 3.566A pdb=" N ILE C 156 " --> pdb=" O LYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 160 through 162 No H-bonds generated for 'chain 'C' and resid 160 through 162' Processing helix chain 'C' and resid 166 through 194 removed outlier: 3.634A pdb=" N VAL C 170 " --> pdb=" O ASP C 166 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N TYR C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 235 removed outlier: 3.526A pdb=" N MET C 229 " --> pdb=" O ASP C 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 4 through 16 Processing helix chain 'D' and resid 21 through 44 removed outlier: 3.936A pdb=" N LEU D 37 " --> pdb=" O LYS D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 102 Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 106 through 143 Processing helix chain 'D' and resid 153 through 160 Processing helix chain 'D' and resid 163 through 169 removed outlier: 4.092A pdb=" N LEU D 167 " --> pdb=" O LEU D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 247 removed outlier: 3.659A pdb=" N ILE D 240 " --> pdb=" O LYS D 236 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N PHE D 241 " --> pdb=" O ILE D 237 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'G' and resid 471 through 475 Processing sheet with id=AA2, first strand: chain 'G' and resid 484 through 485 removed outlier: 6.525A pdb=" N ARG G 484 " --> pdb=" O TYR J 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'G' and resid 487 through 491 removed outlier: 3.641A pdb=" N SER G 497 " --> pdb=" O TYR G 504 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'K' and resid 66 through 71 removed outlier: 6.722A pdb=" N SER K 81 " --> pdb=" O LEU K 67 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N LEU K 69 " --> pdb=" O ALA K 79 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA K 79 " --> pdb=" O LEU K 69 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL K 101 " --> pdb=" O PHE K 91 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'K' and resid 117 through 119 removed outlier: 3.553A pdb=" N ASP K 117 " --> pdb=" O VAL K 131 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU K 141 " --> pdb=" O LYS K 151 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS K 151 " --> pdb=" O LEU K 141 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 163 through 168 removed outlier: 6.740A pdb=" N ALA K 178 " --> pdb=" O ASN K 164 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N CYS K 166 " --> pdb=" O LEU K 176 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N LEU K 176 " --> pdb=" O CYS K 166 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N TYR K 168 " --> pdb=" O TRP K 174 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP K 174 " --> pdb=" O TYR K 168 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP K 188 " --> pdb=" O SER K 195 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER K 195 " --> pdb=" O ASP K 188 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 214 through 217 removed outlier: 6.260A pdb=" N LYS K 237 " --> pdb=" O VAL K 245 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL K 245 " --> pdb=" O LYS K 237 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 256 through 261 removed outlier: 4.404A pdb=" N CYS K 277 " --> pdb=" O ILE K 291 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K 289 " --> pdb=" O VAL K 279 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASN K 281 " --> pdb=" O CYS K 287 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N CYS K 287 " --> pdb=" O ASN K 281 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 298 through 303 removed outlier: 3.549A pdb=" N THR K 300 " --> pdb=" O CYS K 313 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N ASP K 323 " --> pdb=" O LEU K 329 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU K 329 " --> pdb=" O ASP K 323 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 344 through 346 Processing sheet with id=AB2, first strand: chain 'L' and resid 102 through 104 removed outlier: 6.135A pdb=" N VAL L 102 " --> pdb=" O MET L 245 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N PHE L 212 " --> pdb=" O MET L 244 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE L 246 " --> pdb=" O PHE L 212 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N ILE L 214 " --> pdb=" O PHE L 246 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N VAL L 134 " --> pdb=" O VAL L 213 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N ASP L 215 " --> pdb=" O VAL L 134 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE L 136 " --> pdb=" O ASP L 215 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA L 163 " --> pdb=" O VAL L 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 333 through 336 removed outlier: 6.208A pdb=" N VAL L 309 " --> pdb=" O CYS L 360 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N SER L 362 " --> pdb=" O VAL L 309 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE L 311 " --> pdb=" O SER L 362 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N GLN L 308 " --> pdb=" O LEU L 377 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE L 379 " --> pdb=" O GLN L 308 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE L 310 " --> pdb=" O ILE L 379 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN L 282 " --> pdb=" O ALA L 406 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N SER L 408 " --> pdb=" O GLN L 282 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR L 284 " --> pdb=" O SER L 408 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL L 410 " --> pdb=" O TYR L 284 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ILE L 286 " --> pdb=" O VAL L 410 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA L 431 " --> pdb=" O GLN L 283 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TYR L 285 " --> pdb=" O ALA L 431 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 471 through 475 Processing sheet with id=AB5, first strand: chain 'A' and resid 484 through 485 removed outlier: 6.591A pdb=" N ARG A 484 " --> pdb=" O TYR C 142 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'A' and resid 487 through 491 removed outlier: 3.640A pdb=" N SER A 497 " --> pdb=" O TYR A 504 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 66 through 71 removed outlier: 6.722A pdb=" N SER E 81 " --> pdb=" O LEU E 67 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU E 69 " --> pdb=" O ALA E 79 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ALA E 79 " --> pdb=" O LEU E 69 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL E 101 " --> pdb=" O PHE E 91 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 117 through 119 removed outlier: 3.553A pdb=" N ASP E 117 " --> pdb=" O VAL E 131 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N LEU E 141 " --> pdb=" O LYS E 151 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N LYS E 151 " --> pdb=" O LEU E 141 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 163 through 168 removed outlier: 6.740A pdb=" N ALA E 178 " --> pdb=" O ASN E 164 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N CYS E 166 " --> pdb=" O LEU E 176 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU E 176 " --> pdb=" O CYS E 166 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N TYR E 168 " --> pdb=" O TRP E 174 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TRP E 174 " --> pdb=" O TYR E 168 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ASP E 188 " --> pdb=" O SER E 195 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N SER E 195 " --> pdb=" O ASP E 188 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 214 through 217 removed outlier: 6.260A pdb=" N LYS E 237 " --> pdb=" O VAL E 245 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N VAL E 245 " --> pdb=" O LYS E 237 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 256 through 261 removed outlier: 4.403A pdb=" N CYS E 277 " --> pdb=" O ILE E 291 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU E 289 " --> pdb=" O VAL E 279 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N ASN E 281 " --> pdb=" O CYS E 287 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N CYS E 287 " --> pdb=" O ASN E 281 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 298 through 303 removed outlier: 3.547A pdb=" N THR E 300 " --> pdb=" O CYS E 313 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ASP E 323 " --> pdb=" O LEU E 329 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU E 329 " --> pdb=" O ASP E 323 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'E' and resid 344 through 346 Processing sheet with id=AC5, first strand: chain 'F' and resid 102 through 104 removed outlier: 6.135A pdb=" N VAL F 102 " --> pdb=" O MET F 245 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE F 212 " --> pdb=" O MET F 244 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N PHE F 246 " --> pdb=" O PHE F 212 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE F 214 " --> pdb=" O PHE F 246 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N VAL F 134 " --> pdb=" O VAL F 213 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N ASP F 215 " --> pdb=" O VAL F 134 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE F 136 " --> pdb=" O ASP F 215 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA F 163 " --> pdb=" O VAL F 189 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 333 through 336 removed outlier: 6.208A pdb=" N VAL F 309 " --> pdb=" O CYS F 360 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N SER F 362 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ILE F 311 " --> pdb=" O SER F 362 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N GLN F 308 " --> pdb=" O LEU F 377 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N ILE F 379 " --> pdb=" O GLN F 308 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N ILE F 310 " --> pdb=" O ILE F 379 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLN F 282 " --> pdb=" O ALA F 406 " (cutoff:3.500A) removed outlier: 8.066A pdb=" N SER F 408 " --> pdb=" O GLN F 282 " (cutoff:3.500A) removed outlier: 7.225A pdb=" N TYR F 284 " --> pdb=" O SER F 408 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N VAL F 410 " --> pdb=" O TYR F 284 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE F 286 " --> pdb=" O VAL F 410 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N ALA F 431 " --> pdb=" O GLN F 283 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N TYR F 285 " --> pdb=" O ALA F 431 " (cutoff:3.500A) 2506 hydrogen bonds defined for protein. 7374 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: 10.16 Time building geometry restraints manager: 4.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 6536 1.30 - 1.43: 10737 1.43 - 1.56: 23585 1.56 - 1.68: 0 1.68 - 1.81: 210 Bond restraints: 41068 Sorted by residual: bond pdb=" C LYS D 236 " pdb=" O LYS D 236 " ideal model delta sigma weight residual 1.236 1.322 -0.085 1.15e-02 7.56e+03 5.51e+01 bond pdb=" C ARG D 229 " pdb=" O ARG D 229 " ideal model delta sigma weight residual 1.236 1.318 -0.081 1.15e-02 7.56e+03 4.98e+01 bond pdb=" C ILE D 233 " pdb=" O ILE D 233 " ideal model delta sigma weight residual 1.237 1.315 -0.078 1.17e-02 7.31e+03 4.39e+01 bond pdb=" C LYS I 236 " pdb=" O LYS I 236 " ideal model delta sigma weight residual 1.237 1.304 -0.067 1.19e-02 7.06e+03 3.21e+01 bond pdb=" C TYR C 194 " pdb=" O TYR C 194 " ideal model delta sigma weight residual 1.235 1.306 -0.070 1.26e-02 6.30e+03 3.12e+01 ... (remaining 41063 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.10: 54957 3.10 - 6.19: 1084 6.19 - 9.29: 64 9.29 - 12.38: 7 12.38 - 15.48: 2 Bond angle restraints: 56114 Sorted by residual: angle pdb=" C THR I 81 " pdb=" CA THR I 81 " pdb=" CB THR I 81 " ideal model delta sigma weight residual 110.88 95.40 15.48 1.57e+00 4.06e-01 9.72e+01 angle pdb=" C THR D 81 " pdb=" CA THR D 81 " pdb=" CB THR D 81 " ideal model delta sigma weight residual 110.88 95.47 15.41 1.57e+00 4.06e-01 9.64e+01 angle pdb=" N ASN G 36 " pdb=" CA ASN G 36 " pdb=" C ASN G 36 " ideal model delta sigma weight residual 112.58 103.26 9.32 1.22e+00 6.72e-01 5.84e+01 angle pdb=" N ASN A 36 " pdb=" CA ASN A 36 " pdb=" C ASN A 36 " ideal model delta sigma weight residual 112.58 103.28 9.30 1.22e+00 6.72e-01 5.81e+01 angle pdb=" C THR C 114 " pdb=" CA THR C 114 " pdb=" CB THR C 114 " ideal model delta sigma weight residual 110.79 99.80 10.99 1.66e+00 3.63e-01 4.39e+01 ... (remaining 56109 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 21463 17.91 - 35.83: 2091 35.83 - 53.74: 624 53.74 - 71.65: 92 71.65 - 89.57: 30 Dihedral angle restraints: 24300 sinusoidal: 7676 harmonic: 16624 Sorted by residual: dihedral pdb=" C THR I 81 " pdb=" N THR I 81 " pdb=" CA THR I 81 " pdb=" CB THR I 81 " ideal model delta harmonic sigma weight residual -122.00 -104.62 -17.38 0 2.50e+00 1.60e-01 4.83e+01 dihedral pdb=" C THR D 81 " pdb=" N THR D 81 " pdb=" CA THR D 81 " pdb=" CB THR D 81 " ideal model delta harmonic sigma weight residual -122.00 -104.75 -17.25 0 2.50e+00 1.60e-01 4.76e+01 dihedral pdb=" CA PHE G 932 " pdb=" C PHE G 932 " pdb=" N SER G 933 " pdb=" CA SER G 933 " ideal model delta harmonic sigma weight residual -180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 24297 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 5794 0.083 - 0.167: 746 0.167 - 0.250: 193 0.250 - 0.333: 26 0.333 - 0.417: 10 Chirality restraints: 6769 Sorted by residual: chirality pdb=" CA ILE J 66 " pdb=" N ILE J 66 " pdb=" C ILE J 66 " pdb=" CB ILE J 66 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" CA ILE C 66 " pdb=" N ILE C 66 " pdb=" C ILE C 66 " pdb=" CB ILE C 66 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.28e+00 chirality pdb=" CA THR I 81 " pdb=" N THR I 81 " pdb=" C THR I 81 " pdb=" CB THR I 81 " both_signs ideal model delta sigma weight residual False 2.53 2.90 -0.37 2.00e-01 2.50e+01 3.50e+00 ... (remaining 6766 not shown) Planarity restraints: 7146 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN I 206 " -0.031 2.00e-02 2.50e+03 6.14e-02 3.77e+01 pdb=" C ASN I 206 " 0.106 2.00e-02 2.50e+03 pdb=" O ASN I 206 " -0.039 2.00e-02 2.50e+03 pdb=" N ALA I 207 " -0.037 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU C 46 " -0.027 2.00e-02 2.50e+03 5.51e-02 3.04e+01 pdb=" C LEU C 46 " 0.095 2.00e-02 2.50e+03 pdb=" O LEU C 46 " -0.035 2.00e-02 2.50e+03 pdb=" N ALEU C 47 " -0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU J 46 " -0.027 2.00e-02 2.50e+03 5.50e-02 3.02e+01 pdb=" C LEU J 46 " 0.095 2.00e-02 2.50e+03 pdb=" O LEU J 46 " -0.035 2.00e-02 2.50e+03 pdb=" N ALEU J 47 " -0.033 2.00e-02 2.50e+03 ... (remaining 7143 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 35 2.22 - 2.89: 17012 2.89 - 3.56: 57862 3.56 - 4.23: 82676 4.23 - 4.90: 143721 Nonbonded interactions: 301306 Sorted by model distance: nonbonded pdb=" CB THR D 151 " pdb=" CB TRP D 155 " model vdw 1.547 3.870 nonbonded pdb=" CB THR I 151 " pdb=" CB TRP I 155 " model vdw 1.548 3.870 nonbonded pdb=" O ARG C 67 " pdb=" OD1 ASP C 71 " model vdw 1.577 3.040 nonbonded pdb=" O ARG J 67 " pdb=" OD1 ASP J 71 " model vdw 1.578 3.040 nonbonded pdb=" O LEU G 524 " pdb=" OG SER G 528 " model vdw 2.091 3.040 ... (remaining 301301 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 'G' } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = (chain 'C' and (resid 6 through 46 or resid 48 through 235)) selection = (chain 'J' and (resid 6 through 46 or resid 48 through 235)) } ncs_group { reference = chain 'D' selection = (chain 'I' and resid 2 through 247) } ncs_group { reference = chain 'E' selection = chain 'K' } ncs_group { reference = chain 'F' 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=0.00 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 42.850 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4869 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 : 0.008 0.085 41068 Z= 0.496 Angle : 1.019 15.480 56114 Z= 0.715 Chirality : 0.065 0.417 6769 Planarity : 0.006 0.061 7146 Dihedral : 16.269 89.567 13458 Min Nonbonded Distance : 1.547 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.18 % Favored : 93.59 % Rotamer: Outliers : 10.45 % Allowed : 19.19 % Favored : 70.36 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.71 (0.11), residues: 5543 helix: -0.15 (0.09), residues: 3197 sheet: -1.05 (0.23), residues: 462 loop : -2.85 (0.12), residues: 1884 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 76 TYR 0.022 0.002 TYR D 17 PHE 0.029 0.002 PHE G 694 TRP 0.039 0.002 TRP J 147 HIS 0.005 0.001 HIS G 414 Details of bonding type rmsd covalent geometry : bond 0.00788 (41068) covalent geometry : angle 1.01942 (56114) hydrogen bonds : bond 0.15466 ( 2506) hydrogen bonds : angle 6.31575 ( 7374) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 708 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 373 poor density : 335 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 MET cc_start: 0.3309 (mtt) cc_final: 0.2181 (mtt) REVERT: G 285 TYR cc_start: -0.0110 (OUTLIER) cc_final: -0.1046 (t80) REVERT: G 411 LEU cc_start: -0.1254 (OUTLIER) cc_final: -0.1604 (tp) REVERT: G 552 ILE cc_start: -0.1594 (OUTLIER) cc_final: -0.2306 (mt) REVERT: G 711 THR cc_start: 0.0406 (OUTLIER) cc_final: -0.0017 (p) REVERT: G 724 GLN cc_start: 0.0482 (OUTLIER) cc_final: -0.0076 (mp10) REVERT: G 790 LEU cc_start: 0.4807 (tt) cc_final: 0.4538 (tp) REVERT: G 842 ASN cc_start: -0.4349 (OUTLIER) cc_final: -0.5508 (t0) REVERT: G 1036 VAL cc_start: 0.5015 (OUTLIER) cc_final: 0.4812 (t) REVERT: G 1081 CYS cc_start: 0.0229 (t) cc_final: -0.0217 (p) REVERT: G 1151 VAL cc_start: 0.3707 (p) cc_final: 0.3422 (m) REVERT: H 376 LEU cc_start: 0.3817 (OUTLIER) cc_final: 0.3598 (pt) REVERT: H 443 VAL cc_start: 0.2271 (OUTLIER) cc_final: 0.1273 (t) REVERT: H 479 MET cc_start: 0.0509 (mtm) cc_final: -0.0209 (mtt) REVERT: L 227 ARG cc_start: 0.4240 (ptm160) cc_final: 0.4019 (ptm160) REVERT: L 244 MET cc_start: 0.2249 (mpp) cc_final: 0.0497 (mpp) REVERT: L 245 MET cc_start: 0.2865 (mmt) cc_final: 0.2580 (mmt) REVERT: L 307 ASN cc_start: 0.6482 (m-40) cc_final: 0.5065 (m110) REVERT: A 136 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7673 (t70) REVERT: A 137 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8730 (pm20) REVERT: A 138 GLU cc_start: 0.8079 (tp30) cc_final: 0.7783 (tm-30) REVERT: A 154 GLN cc_start: 0.7226 (OUTLIER) cc_final: 0.6886 (mm-40) REVERT: A 217 SER cc_start: 0.8916 (OUTLIER) cc_final: 0.8169 (t) REVERT: A 300 MET cc_start: 0.8726 (ttp) cc_final: 0.8471 (tmm) REVERT: A 323 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8603 (tpp) REVERT: A 572 LYS cc_start: 0.9560 (OUTLIER) cc_final: 0.9342 (ttmt) REVERT: A 619 THR cc_start: 0.9260 (OUTLIER) cc_final: 0.8982 (t) REVERT: A 738 LEU cc_start: 0.8890 (mt) cc_final: 0.8604 (tp) REVERT: A 745 MET cc_start: 0.8000 (tpp) cc_final: 0.7769 (tpt) REVERT: A 747 ILE cc_start: 0.9203 (OUTLIER) cc_final: 0.8998 (mm) REVERT: A 1092 LEU cc_start: 0.9133 (OUTLIER) cc_final: 0.8840 (tt) REVERT: A 1148 MET cc_start: 0.9107 (mmm) cc_final: 0.8874 (mmm) REVERT: B 196 THR cc_start: 0.9448 (OUTLIER) cc_final: 0.9224 (t) REVERT: B 278 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7746 (mt) REVERT: B 371 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9118 (tp) REVERT: B 528 ILE cc_start: 0.8842 (OUTLIER) cc_final: 0.8582 (mt) REVERT: F 284 TYR cc_start: 0.7800 (m-80) cc_final: 0.7334 (m-80) REVERT: F 326 LEU cc_start: 0.9484 (tp) cc_final: 0.9272 (tt) REVERT: F 339 HIS cc_start: 0.9306 (t-170) cc_final: 0.9062 (m90) REVERT: C 156 ILE cc_start: 0.8597 (OUTLIER) cc_final: 0.8339 (mm) REVERT: C 178 LEU cc_start: 0.9152 (mt) cc_final: 0.8730 (tp) REVERT: D 107 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8926 (tt) REVERT: D 133 VAL cc_start: 0.9165 (OUTLIER) cc_final: 0.8353 (p) outliers start: 373 outliers final: 65 residues processed: 685 average time/residue: 0.2037 time to fit residues: 239.1266 Evaluate side-chains 301 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 211 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 394 optimal weight: 3.9990 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 265 optimal weight: 30.0000 chunk 523 optimal weight: 8.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.9990 chunk 488 optimal weight: 5.9990 chunk 366 optimal weight: 8.9990 chunk 223 optimal weight: 8.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 154 GLN G 318 ASN G 414 HIS G 422 HIS G 529 HIS G 703 GLN G 744 ASN G 759 HIS G 893 ASN G1032 GLN G1033 ASN G1150 HIS H 9 GLN H 180 HIS H 221 ASN H 260 ASN H 282 ASN H 385 GLN H 401 GLN K 281 ASN L 122 GLN L 123 GLN ** L 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 385 ASN ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 318 ASN A 414 HIS A 487 HIS A 529 HIS A 615 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 801 GLN A 893 ASN A1032 GLN A1033 ASN B 9 GLN B 180 HIS B 221 ASN B 260 ASN B 282 ASN B 350 ASN B 385 GLN ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 223 HIS E 252 HIS F 122 GLN F 123 GLN F 385 ASN J 79 GLN J 109 HIS J 180 GLN I 25 ASN C 74 GLN C 79 GLN C 109 HIS C 176 ASN C 180 GLN D 25 ASN D 93 GLN D 94 GLN D 114 HIS Total number of N/Q/H flips: 57 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.112406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.082676 restraints weight = 431338.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.079046 restraints weight = 364149.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.078844 restraints weight = 319937.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.079071 restraints weight = 242082.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.078993 restraints weight = 207884.048| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3180 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3180 r_free = 0.3180 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3180 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 41068 Z= 0.209 Angle : 0.686 9.871 56114 Z= 0.362 Chirality : 0.044 0.258 6769 Planarity : 0.005 0.064 7146 Dihedral : 4.693 23.872 5930 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.42 % Favored : 95.54 % Rotamer: Outliers : 0.34 % Allowed : 4.73 % Favored : 94.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.32 (0.11), residues: 5543 helix: 0.89 (0.09), residues: 3209 sheet: -0.51 (0.24), residues: 496 loop : -2.13 (0.14), residues: 1838 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 443 TYR 0.023 0.002 TYR J 9 PHE 0.027 0.002 PHE G 110 TRP 0.025 0.002 TRP A 949 HIS 0.012 0.002 HIS G 136 Details of bonding type rmsd covalent geometry : bond 0.00442 (41068) covalent geometry : angle 0.68615 (56114) hydrogen bonds : bond 0.05031 ( 2506) hydrogen bonds : angle 4.51111 ( 7374) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 242 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 MET cc_start: -0.0590 (mtt) cc_final: -0.1002 (mtt) REVERT: G 862 MET cc_start: 0.2437 (tpp) cc_final: 0.1846 (ptt) REVERT: G 948 PHE cc_start: 0.5253 (t80) cc_final: 0.4870 (t80) REVERT: G 1081 CYS cc_start: 0.0447 (t) cc_final: -0.0377 (p) REVERT: G 1151 VAL cc_start: 0.1122 (p) cc_final: 0.0907 (m) REVERT: H 339 MET cc_start: 0.7473 (mpp) cc_final: 0.6770 (mpp) REVERT: H 479 MET cc_start: -0.0966 (mtm) cc_final: -0.1183 (mtt) REVERT: H 581 GLN cc_start: 0.1185 (mm-40) cc_final: 0.0658 (pt0) REVERT: L 244 MET cc_start: 0.3160 (mpp) cc_final: 0.2767 (mpp) REVERT: L 245 MET cc_start: 0.2068 (mmt) cc_final: 0.1676 (ptt) REVERT: A 135 LEU cc_start: 0.9178 (pt) cc_final: 0.8508 (pt) REVERT: A 745 MET cc_start: 0.8345 (tpp) cc_final: 0.7877 (tpp) REVERT: A 1148 MET cc_start: 0.9310 (mmm) cc_final: 0.9062 (mmm) REVERT: B 221 ASN cc_start: 0.9273 (OUTLIER) cc_final: 0.9071 (t0) REVERT: E 355 MET cc_start: 0.8759 (ttp) cc_final: 0.8415 (ptm) REVERT: F 244 MET cc_start: 0.3417 (mmp) cc_final: 0.2964 (mmm) REVERT: J 144 MET cc_start: 0.4307 (mmm) cc_final: 0.3935 (mmm) REVERT: C 178 LEU cc_start: 0.9471 (mt) cc_final: 0.9260 (tp) outliers start: 12 outliers final: 4 residues processed: 254 average time/residue: 0.2023 time to fit residues: 89.4062 Evaluate side-chains 181 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 176 time to evaluate : 1.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 137 optimal weight: 50.0000 chunk 489 optimal weight: 7.9990 chunk 138 optimal weight: 7.9990 chunk 525 optimal weight: 8.9990 chunk 312 optimal weight: 5.9990 chunk 259 optimal weight: 1.9990 chunk 401 optimal weight: 8.9990 chunk 462 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 349 optimal weight: 0.8980 chunk 299 optimal weight: 8.9990 overall best weight: 4.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 529 HIS G 744 ASN G 794 ASN G1032 GLN ** H 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 397 GLN K 143 ASN K 325 ASN L 91 HIS A 154 GLN A 160 HIS A 615 ASN ** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1150 HIS B 265 HIS ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS J 21 GLN J 79 GLN I 16 HIS C 131 GLN D 93 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.109778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.097162 restraints weight = 562954.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.096791 restraints weight = 1168923.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.095998 restraints weight = 446719.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.096261 restraints weight = 314106.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.095986 restraints weight = 273879.558| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3811 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3811 r_free = 0.3811 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3811 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5791 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 41068 Z= 0.235 Angle : 0.666 9.017 56114 Z= 0.352 Chirality : 0.043 0.204 6769 Planarity : 0.004 0.051 7146 Dihedral : 4.573 22.310 5930 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.95 % Favored : 95.02 % Rotamer: Outliers : 0.08 % Allowed : 4.96 % Favored : 94.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.06 (0.11), residues: 5543 helix: 1.09 (0.09), residues: 3235 sheet: -0.10 (0.24), residues: 478 loop : -1.84 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 410 TYR 0.021 0.002 TYR C 103 PHE 0.025 0.002 PHE G1004 TRP 0.023 0.002 TRP C 147 HIS 0.013 0.002 HIS G1000 Details of bonding type rmsd covalent geometry : bond 0.00504 (41068) covalent geometry : angle 0.66592 (56114) hydrogen bonds : bond 0.04897 ( 2506) hydrogen bonds : angle 4.41787 ( 7374) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 207 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 MET cc_start: 0.3492 (mtt) cc_final: 0.2969 (mtt) REVERT: G 862 MET cc_start: -0.0038 (tpp) cc_final: -0.0827 (ptt) REVERT: G 1081 CYS cc_start: 0.0859 (t) cc_final: -0.0615 (p) REVERT: G 1151 VAL cc_start: 0.4362 (p) cc_final: 0.3987 (m) REVERT: H 95 ASN cc_start: 0.4679 (m-40) cc_final: 0.4321 (m-40) REVERT: H 479 MET cc_start: -0.1481 (mtm) cc_final: -0.2519 (mtt) REVERT: A 300 MET cc_start: 0.8654 (tmm) cc_final: 0.8281 (tmm) REVERT: A 787 MET cc_start: 0.8433 (tpp) cc_final: 0.8018 (tpp) REVERT: B 38 MET cc_start: 0.7040 (tpt) cc_final: 0.6813 (tpt) REVERT: C 178 LEU cc_start: 0.9402 (mt) cc_final: 0.9145 (tt) REVERT: D 25 ASN cc_start: 0.8535 (m-40) cc_final: 0.8268 (m-40) outliers start: 3 outliers final: 1 residues processed: 209 average time/residue: 0.2064 time to fit residues: 74.6763 Evaluate side-chains 171 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 170 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 268 optimal weight: 0.9990 chunk 218 optimal weight: 40.0000 chunk 348 optimal weight: 2.9990 chunk 341 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 308 optimal weight: 0.2980 chunk 279 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 256 optimal weight: 0.9990 chunk 24 optimal weight: 40.0000 chunk 165 optimal weight: 40.0000 overall best weight: 1.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 271 ASN G 293 ASN G 331 GLN ** G 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 223 ASN H 581 GLN ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 HIS A 615 ASN A 703 GLN ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 GLN J 79 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.111298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.082926 restraints weight = 505969.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.078319 restraints weight = 395887.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.078055 restraints weight = 407237.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.078071 restraints weight = 316316.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.078256 restraints weight = 298274.866| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3171 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3171 r_free = 0.3171 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3171 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 41068 Z= 0.113 Angle : 0.528 7.425 56114 Z= 0.279 Chirality : 0.040 0.222 6769 Planarity : 0.003 0.056 7146 Dihedral : 4.110 19.842 5930 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.01 % Favored : 95.95 % Rotamer: Outliers : 0.06 % Allowed : 2.46 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.12), residues: 5543 helix: 1.67 (0.09), residues: 3226 sheet: 0.18 (0.24), residues: 486 loop : -1.67 (0.14), residues: 1831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 61 TYR 0.023 0.001 TYR F 349 PHE 0.024 0.001 PHE C 107 TRP 0.013 0.001 TRP C 147 HIS 0.013 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00228 (41068) covalent geometry : angle 0.52752 (56114) hydrogen bonds : bond 0.03816 ( 2506) hydrogen bonds : angle 3.93927 ( 7374) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 211 time to evaluate : 1.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 465 MET cc_start: -0.1303 (ttt) cc_final: -0.1698 (tpp) REVERT: G 862 MET cc_start: 0.1940 (tpp) cc_final: 0.1244 (ptt) REVERT: G 1151 VAL cc_start: -0.0855 (p) cc_final: -0.1086 (m) REVERT: H 479 MET cc_start: -0.0760 (mtm) cc_final: -0.1184 (mtt) REVERT: L 244 MET cc_start: 0.2995 (mpp) cc_final: 0.2340 (mpp) REVERT: L 245 MET cc_start: 0.2813 (mmt) cc_final: 0.2377 (ptt) REVERT: B 122 GLU cc_start: 0.7861 (tm-30) cc_final: 0.7622 (tm-30) REVERT: E 355 MET cc_start: 0.8621 (ttp) cc_final: 0.8271 (ptm) REVERT: F 244 MET cc_start: 0.2291 (mmm) cc_final: 0.1864 (mmm) REVERT: D 25 ASN cc_start: 0.8803 (m-40) cc_final: 0.8591 (m-40) outliers start: 2 outliers final: 0 residues processed: 212 average time/residue: 0.2022 time to fit residues: 74.8210 Evaluate side-chains 170 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 370 optimal weight: 10.0000 chunk 521 optimal weight: 6.9990 chunk 261 optimal weight: 2.9990 chunk 300 optimal weight: 5.9990 chunk 206 optimal weight: 50.0000 chunk 106 optimal weight: 30.0000 chunk 486 optimal weight: 50.0000 chunk 294 optimal weight: 5.9990 chunk 335 optimal weight: 10.0000 chunk 386 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 581 GLN K 223 HIS ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1122 HIS ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 392 HIS J 21 GLN J 58 HIS C 131 GLN D 10 GLN ** D 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.108572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.095515 restraints weight = 496472.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.094790 restraints weight = 1103794.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.094078 restraints weight = 415785.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.094245 restraints weight = 311190.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.093962 restraints weight = 269307.902| |-----------------------------------------------------------------------------| r_work (final): 0.3772 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3772 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3772 r_free = 0.3772 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3772 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 moved from start: 0.5902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 41068 Z= 0.215 Angle : 0.644 8.575 56114 Z= 0.339 Chirality : 0.042 0.193 6769 Planarity : 0.004 0.059 7146 Dihedral : 4.445 21.418 5930 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.02 % Favored : 94.94 % Rotamer: Outliers : 0.06 % Allowed : 2.69 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.11), residues: 5543 helix: 1.39 (0.09), residues: 3264 sheet: 0.15 (0.24), residues: 486 loop : -1.66 (0.14), residues: 1793 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 76 TYR 0.030 0.002 TYR B 204 PHE 0.042 0.002 PHE A 632 TRP 0.023 0.002 TRP C 147 HIS 0.013 0.001 HIS G1000 Details of bonding type rmsd covalent geometry : bond 0.00463 (41068) covalent geometry : angle 0.64382 (56114) hydrogen bonds : bond 0.04650 ( 2506) hydrogen bonds : angle 4.36237 ( 7374) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 193 time to evaluate : 1.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 323 MET cc_start: 0.0849 (mmm) cc_final: -0.0696 (mmt) REVERT: G 862 MET cc_start: -0.0922 (tpp) cc_final: -0.1638 (ptt) REVERT: G 1151 VAL cc_start: 0.4290 (p) cc_final: 0.3922 (m) REVERT: H 38 MET cc_start: -0.0176 (mtp) cc_final: -0.1045 (mtp) REVERT: H 95 ASN cc_start: 0.4404 (m-40) cc_final: 0.4025 (m110) REVERT: H 479 MET cc_start: -0.1233 (mtm) cc_final: -0.2619 (mtt) REVERT: L 245 MET cc_start: 0.2504 (mmt) cc_final: 0.1578 (ptt) REVERT: A 300 MET cc_start: 0.8689 (tmm) cc_final: 0.8357 (tmm) outliers start: 2 outliers final: 0 residues processed: 195 average time/residue: 0.2028 time to fit residues: 70.3432 Evaluate side-chains 162 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 426 optimal weight: 10.0000 chunk 61 optimal weight: 7.9990 chunk 166 optimal weight: 30.0000 chunk 514 optimal weight: 0.0570 chunk 317 optimal weight: 0.9990 chunk 293 optimal weight: 0.5980 chunk 41 optimal weight: 20.0000 chunk 439 optimal weight: 2.9990 chunk 353 optimal weight: 1.9990 chunk 328 optimal weight: 4.9990 chunk 58 optimal weight: 30.0000 overall best weight: 1.3304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 265 HIS ** H 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 160 HIS A 615 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.109916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.097565 restraints weight = 559792.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.097262 restraints weight = 1158692.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.096498 restraints weight = 433259.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.096854 restraints weight = 296779.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.096577 restraints weight = 250014.765| |-----------------------------------------------------------------------------| r_work (final): 0.3832 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3832 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3832 r_free = 0.3832 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3832 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5755 moved from start: 0.6046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 41068 Z= 0.112 Angle : 0.522 8.273 56114 Z= 0.275 Chirality : 0.040 0.214 6769 Planarity : 0.003 0.060 7146 Dihedral : 4.026 22.991 5930 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.14 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.12), residues: 5543 helix: 1.79 (0.09), residues: 3248 sheet: 0.31 (0.24), residues: 496 loop : -1.55 (0.14), residues: 1799 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 76 TYR 0.018 0.001 TYR F 349 PHE 0.020 0.001 PHE G1051 TRP 0.014 0.001 TRP K 280 HIS 0.011 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00231 (41068) covalent geometry : angle 0.52221 (56114) hydrogen bonds : bond 0.03652 ( 2506) hydrogen bonds : angle 3.92658 ( 7374) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 323 MET cc_start: 0.0356 (mmm) cc_final: -0.1252 (mmt) REVERT: G 862 MET cc_start: -0.1129 (tpp) cc_final: -0.1655 (ptt) REVERT: G 1151 VAL cc_start: 0.3742 (p) cc_final: 0.3402 (m) REVERT: H 38 MET cc_start: 0.0163 (mtp) cc_final: -0.0677 (mtp) REVERT: H 95 ASN cc_start: 0.4443 (m-40) cc_final: 0.4073 (m110) REVERT: H 372 MET cc_start: 0.3866 (pmm) cc_final: 0.3666 (pmm) REVERT: H 479 MET cc_start: -0.0495 (mtm) cc_final: -0.1631 (mtt) REVERT: L 245 MET cc_start: 0.1934 (mmt) cc_final: 0.1184 (ptt) REVERT: B 122 GLU cc_start: 0.8172 (tm-30) cc_final: 0.7947 (tm-30) REVERT: I 33 LYS cc_start: 0.7012 (mppt) cc_final: 0.6698 (mmmt) outliers start: 0 outliers final: 0 residues processed: 191 average time/residue: 0.1975 time to fit residues: 66.7721 Evaluate side-chains 158 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 505 optimal weight: 50.0000 chunk 474 optimal weight: 7.9990 chunk 386 optimal weight: 7.9990 chunk 16 optimal weight: 20.0000 chunk 437 optimal weight: 30.0000 chunk 458 optimal weight: 6.9990 chunk 267 optimal weight: 4.9990 chunk 148 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 195 optimal weight: 30.0000 chunk 154 optimal weight: 40.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 136 HIS ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 281 ASN ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 341 HIS ** H 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 233 GLN A 615 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 401 GLN ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 GLN I 93 GLN D 10 GLN D 114 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.106758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.088323 restraints weight = 483650.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.088004 restraints weight = 1089355.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.088897 restraints weight = 536215.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.089634 restraints weight = 327017.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.089841 restraints weight = 254903.018| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6458 moved from start: 0.6999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 41068 Z= 0.311 Angle : 0.761 12.369 56114 Z= 0.399 Chirality : 0.045 0.266 6769 Planarity : 0.005 0.062 7146 Dihedral : 4.837 22.687 5930 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.63 % Favored : 94.33 % Rotamer: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.11), residues: 5543 helix: 1.13 (0.09), residues: 3259 sheet: 0.15 (0.25), residues: 472 loop : -1.69 (0.15), residues: 1812 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 410 TYR 0.036 0.003 TYR G 839 PHE 0.032 0.002 PHE A 632 TRP 0.027 0.002 TRP B 532 HIS 0.010 0.001 HIS A 422 Details of bonding type rmsd covalent geometry : bond 0.00665 (41068) covalent geometry : angle 0.76100 (56114) hydrogen bonds : bond 0.05224 ( 2506) hydrogen bonds : angle 4.78713 ( 7374) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 1.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 MET cc_start: 0.2097 (ttm) cc_final: 0.0835 (ptt) REVERT: G 323 MET cc_start: 0.0761 (mmm) cc_final: 0.0290 (tpp) REVERT: G 456 MET cc_start: 0.5692 (ptt) cc_final: 0.5021 (ppp) REVERT: G 862 MET cc_start: -0.1558 (tpp) cc_final: -0.2021 (ptt) REVERT: G 1085 SER cc_start: 0.7801 (m) cc_final: 0.7400 (p) REVERT: G 1151 VAL cc_start: 0.3291 (p) cc_final: 0.2898 (m) REVERT: H 38 MET cc_start: 0.0142 (mtp) cc_final: -0.0355 (mtp) REVERT: H 95 ASN cc_start: 0.5574 (m-40) cc_final: 0.5241 (m110) REVERT: H 339 MET cc_start: 0.7921 (mpp) cc_final: 0.7681 (mpp) REVERT: H 372 MET cc_start: 0.4911 (pmm) cc_final: 0.4476 (pmm) REVERT: H 479 MET cc_start: -0.2230 (mtm) cc_final: -0.3178 (mtt) REVERT: L 244 MET cc_start: 0.2364 (mpp) cc_final: 0.1977 (mpp) REVERT: L 245 MET cc_start: 0.2015 (mmt) cc_final: 0.1536 (ptt) REVERT: A 301 CYS cc_start: 0.9255 (m) cc_final: 0.8959 (m) REVERT: A 745 MET cc_start: 0.8337 (tpp) cc_final: 0.8012 (tpp) outliers start: 0 outliers final: 0 residues processed: 188 average time/residue: 0.2001 time to fit residues: 66.4541 Evaluate side-chains 159 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 465 optimal weight: 1.9990 chunk 250 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 chunk 170 optimal weight: 40.0000 chunk 163 optimal weight: 6.9990 chunk 351 optimal weight: 0.5980 chunk 193 optimal weight: 30.0000 chunk 175 optimal weight: 7.9990 chunk 328 optimal weight: 1.9990 chunk 361 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 341 HIS ** H 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 193 HIS K 325 ASN A 615 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 HIS ** 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 = 0.4185 r_free = 0.4185 target = 0.108634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.092553 restraints weight = 447299.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.091867 restraints weight = 809698.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.091858 restraints weight = 387460.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.091825 restraints weight = 288241.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.091837 restraints weight = 289918.712| |-----------------------------------------------------------------------------| r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3723 r_free = 0.3723 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.7045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 41068 Z= 0.121 Angle : 0.549 8.642 56114 Z= 0.290 Chirality : 0.041 0.198 6769 Planarity : 0.003 0.061 7146 Dihedral : 4.231 26.201 5930 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.14 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.12), residues: 5543 helix: 1.68 (0.09), residues: 3258 sheet: 0.10 (0.25), residues: 462 loop : -1.49 (0.15), residues: 1823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 76 TYR 0.022 0.001 TYR J 103 PHE 0.028 0.001 PHE A 110 TRP 0.028 0.001 TRP K 280 HIS 0.007 0.001 HIS C 109 Details of bonding type rmsd covalent geometry : bond 0.00254 (41068) covalent geometry : angle 0.54933 (56114) hydrogen bonds : bond 0.03818 ( 2506) hydrogen bonds : angle 4.10179 ( 7374) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 1.506 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 323 MET cc_start: 0.0961 (mmm) cc_final: 0.0298 (tpp) REVERT: G 456 MET cc_start: 0.4003 (ptt) cc_final: 0.3620 (ppp) REVERT: G 862 MET cc_start: -0.1496 (tpp) cc_final: -0.1926 (ptt) REVERT: G 1148 MET cc_start: 0.1251 (ppp) cc_final: 0.0270 (ttt) REVERT: G 1151 VAL cc_start: 0.3829 (p) cc_final: 0.3489 (m) REVERT: H 38 MET cc_start: -0.0250 (mtp) cc_final: -0.0888 (mtp) REVERT: H 95 ASN cc_start: 0.4915 (m-40) cc_final: 0.4614 (m110) REVERT: H 372 MET cc_start: 0.3952 (pmm) cc_final: 0.3633 (pmm) REVERT: H 479 MET cc_start: -0.0892 (mtm) cc_final: -0.2079 (mtt) REVERT: L 244 MET cc_start: 0.2545 (mpp) cc_final: 0.2063 (mpp) REVERT: L 245 MET cc_start: 0.2118 (mmt) cc_final: 0.1470 (ptt) REVERT: A 225 ASP cc_start: 0.9191 (t70) cc_final: 0.8943 (t70) REVERT: A 301 CYS cc_start: 0.9171 (m) cc_final: 0.8940 (m) REVERT: B 372 MET cc_start: 0.8465 (mmm) cc_final: 0.8200 (mmm) REVERT: B 479 MET cc_start: 0.9211 (mmm) cc_final: 0.8991 (mmt) REVERT: C 30 ILE cc_start: 0.8696 (mt) cc_final: 0.8467 (tp) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1957 time to fit residues: 65.0631 Evaluate side-chains 159 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 282 optimal weight: 5.9990 chunk 266 optimal weight: 3.9990 chunk 187 optimal weight: 50.0000 chunk 445 optimal weight: 9.9990 chunk 66 optimal weight: 40.0000 chunk 90 optimal weight: 9.9990 chunk 501 optimal weight: 5.9990 chunk 333 optimal weight: 9.9990 chunk 154 optimal weight: 8.9990 chunk 452 optimal weight: 9.9990 chunk 87 optimal weight: 50.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 325 ASN ** A 276 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 376 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 21 GLN ** D 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.106036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.089608 restraints weight = 600637.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.090870 restraints weight = 870875.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.090822 restraints weight = 328321.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.091073 restraints weight = 261851.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.091152 restraints weight = 137092.294| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3432 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3432 r_free = 0.3432 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3432 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.7880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 41068 Z= 0.302 Angle : 0.752 12.287 56114 Z= 0.396 Chirality : 0.046 0.248 6769 Planarity : 0.005 0.067 7146 Dihedral : 4.982 25.697 5930 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.18 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.11), residues: 5543 helix: 1.09 (0.09), residues: 3217 sheet: 0.00 (0.25), residues: 460 loop : -1.61 (0.15), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 820 TYR 0.036 0.003 TYR G 839 PHE 0.054 0.003 PHE A 632 TRP 0.022 0.002 TRP B 532 HIS 0.013 0.002 HIS G1000 Details of bonding type rmsd covalent geometry : bond 0.00655 (41068) covalent geometry : angle 0.75206 (56114) hydrogen bonds : bond 0.05257 ( 2506) hydrogen bonds : angle 4.89125 ( 7374) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 298 MET cc_start: -0.5939 (tmm) cc_final: -0.6497 (ttp) REVERT: G 323 MET cc_start: 0.1836 (mmm) cc_final: 0.1163 (tpp) REVERT: G 456 MET cc_start: 0.5959 (ptt) cc_final: 0.5516 (ppp) REVERT: G 465 MET cc_start: -0.4336 (tpt) cc_final: -0.4570 (tpp) REVERT: G 862 MET cc_start: -0.1695 (tpp) cc_final: -0.2052 (ptt) REVERT: G 1148 MET cc_start: 0.0917 (ppp) cc_final: 0.0197 (ttt) REVERT: G 1151 VAL cc_start: 0.2787 (p) cc_final: 0.2442 (m) REVERT: H 38 MET cc_start: 0.0571 (mtp) cc_final: 0.0058 (mtp) REVERT: H 95 ASN cc_start: 0.5510 (m-40) cc_final: 0.5303 (m110) REVERT: H 339 MET cc_start: 0.8001 (mpp) cc_final: 0.7733 (mpp) REVERT: H 479 MET cc_start: -0.2335 (mtm) cc_final: -0.3272 (mtt) REVERT: L 244 MET cc_start: 0.2770 (mpp) cc_final: 0.2271 (mpp) REVERT: L 245 MET cc_start: 0.2064 (mmt) cc_final: 0.1742 (ptt) REVERT: A 301 CYS cc_start: 0.9217 (m) cc_final: 0.8993 (m) REVERT: B 77 MET cc_start: 0.8764 (mmm) cc_final: 0.8395 (mmm) REVERT: C 30 ILE cc_start: 0.9210 (mt) cc_final: 0.8974 (tp) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.1970 time to fit residues: 63.5681 Evaluate side-chains 158 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 328 optimal weight: 2.9990 chunk 68 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 307 optimal weight: 1.9990 chunk 161 optimal weight: 9.9990 chunk 213 optimal weight: 6.9990 chunk 229 optimal weight: 10.0000 chunk 434 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 350 optimal weight: 5.9990 chunk 474 optimal weight: 0.0010 overall best weight: 3.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 397 GLN ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 16 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.106979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.090245 restraints weight = 488755.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.090360 restraints weight = 1075047.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.091620 restraints weight = 439680.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.091688 restraints weight = 264510.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.091689 restraints weight = 174547.082| |-----------------------------------------------------------------------------| r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3564 r_free = 0.3564 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6301 moved from start: 0.8000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 41068 Z= 0.171 Angle : 0.597 8.928 56114 Z= 0.314 Chirality : 0.042 0.198 6769 Planarity : 0.004 0.061 7146 Dihedral : 4.498 24.313 5930 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.07 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.12), residues: 5543 helix: 1.46 (0.09), residues: 3222 sheet: -0.13 (0.25), residues: 452 loop : -1.48 (0.15), residues: 1869 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 76 TYR 0.025 0.002 TYR J 103 PHE 0.019 0.002 PHE A 694 TRP 0.026 0.002 TRP K 280 HIS 0.014 0.001 HIS G1000 Details of bonding type rmsd covalent geometry : bond 0.00369 (41068) covalent geometry : angle 0.59670 (56114) hydrogen bonds : bond 0.04188 ( 2506) hydrogen bonds : angle 4.38333 ( 7374) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11086 Ramachandran restraints generated. 5543 Oldfield, 0 Emsley, 5543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 185 time to evaluate : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 109 MET cc_start: 0.2624 (ttt) cc_final: 0.1507 (tpt) REVERT: G 298 MET cc_start: -0.5635 (tmm) cc_final: -0.6331 (ttp) REVERT: G 323 MET cc_start: 0.1842 (mmm) cc_final: 0.1239 (tpp) REVERT: G 456 MET cc_start: 0.5796 (ptt) cc_final: 0.5324 (ppp) REVERT: G 465 MET cc_start: -0.4156 (tpt) cc_final: -0.4419 (tpp) REVERT: G 862 MET cc_start: -0.1651 (tpp) cc_final: -0.1966 (ptt) REVERT: G 1148 MET cc_start: 0.1027 (ppp) cc_final: 0.0418 (mmm) REVERT: H 38 MET cc_start: 0.0170 (mtp) cc_final: -0.0363 (mtp) REVERT: H 372 MET cc_start: 0.4907 (pmm) cc_final: 0.4370 (pmm) REVERT: H 479 MET cc_start: -0.2393 (mtm) cc_final: -0.3511 (mtt) REVERT: L 244 MET cc_start: 0.2738 (mpp) cc_final: 0.2192 (mpp) REVERT: L 245 MET cc_start: 0.2041 (mmt) cc_final: 0.1736 (ptt) REVERT: A 300 MET cc_start: 0.8642 (tmm) cc_final: 0.8293 (tmm) REVERT: A 301 CYS cc_start: 0.9287 (m) cc_final: 0.9014 (m) REVERT: B 77 MET cc_start: 0.8807 (mmm) cc_final: 0.8472 (mmm) REVERT: F 150 TYR cc_start: 0.4133 (m-10) cc_final: 0.3457 (m-80) REVERT: F 203 TYR cc_start: 0.5934 (m-80) cc_final: 0.5712 (m-10) REVERT: C 30 ILE cc_start: 0.9216 (mt) cc_final: 0.8945 (tp) outliers start: 0 outliers final: 0 residues processed: 185 average time/residue: 0.2034 time to fit residues: 66.6484 Evaluate side-chains 158 residues out of total 5175 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 555 random chunks: chunk 421 optimal weight: 1.9990 chunk 358 optimal weight: 0.9990 chunk 474 optimal weight: 0.9990 chunk 101 optimal weight: 30.0000 chunk 425 optimal weight: 2.9990 chunk 295 optimal weight: 6.9990 chunk 413 optimal weight: 9.9990 chunk 106 optimal weight: 40.0000 chunk 318 optimal weight: 4.9990 chunk 508 optimal weight: 9.9990 chunk 548 optimal weight: 30.0000 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 271 ASN A 615 ASN ** A1032 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 365 HIS ** F 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 93 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.107367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.094728 restraints weight = 508667.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.093950 restraints weight = 1026064.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.093247 restraints weight = 384261.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.093365 restraints weight = 293957.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.093156 restraints weight = 254400.315| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3774 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3774 r_free = 0.3774 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 28 | |-----------------------------------------------------------------------------| r_final: 0.3774 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5892 moved from start: 0.8121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 41068 Z= 0.134 Angle : 0.559 8.632 56114 Z= 0.293 Chirality : 0.041 0.196 6769 Planarity : 0.004 0.060 7146 Dihedral : 4.252 23.451 5930 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.97 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.12), residues: 5543 helix: 1.73 (0.09), residues: 3221 sheet: -0.05 (0.26), residues: 440 loop : -1.47 (0.14), residues: 1882 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 76 TYR 0.024 0.001 TYR J 103 PHE 0.017 0.001 PHE A 694 TRP 0.021 0.001 TRP K 280 HIS 0.011 0.001 HIS G1000 Details of bonding type rmsd covalent geometry : bond 0.00287 (41068) covalent geometry : angle 0.55875 (56114) hydrogen bonds : bond 0.03800 ( 2506) hydrogen bonds : angle 4.15700 ( 7374) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7308.73 seconds wall clock time: 126 minutes 32.39 seconds (7592.39 seconds total)