Starting phenix.real_space_refine on Wed Mar 4 17:25:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mjq_23882/03_2026/7mjq_23882_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjq_23882/03_2026/7mjq_23882.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mjq_23882/03_2026/7mjq_23882.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjq_23882/03_2026/7mjq_23882.map" model { file = "/net/cci-nas-00/data/ceres_data/7mjq_23882/03_2026/7mjq_23882_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjq_23882/03_2026/7mjq_23882_neut.cif" } resolution = 4.2 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians K 1 8.98 5 P 15 5.49 5 C 8878 2.51 5 N 3013 2.21 5 O 3069 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 14976 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 1714 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 302} Link IDs: {'PTRANS': 11, 'TRANS': 334} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1074 Unresolved non-hydrogen angles: 1381 Unresolved non-hydrogen dihedrals: 882 Unresolved non-hydrogen chiralities: 122 Planarities with less than four sites: {'ARG:plan': 23, 'ASP:plan': 13, 'PHE:plan': 18, 'ASN:plan1': 11, 'HIS:plan': 8, 'GLU:plan': 21, 'GLN:plan1': 12, 'TRP:plan': 5, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 554 Chain: "B" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 1667 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1040 Unresolved non-hydrogen angles: 1340 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'ARG:plan': 20, 'PHE:plan': 18, 'ASN:plan1': 11, 'HIS:plan': 8, 'GLU:plan': 21, 'GLN:plan1': 11, 'ASP:plan': 12, 'TRP:plan': 5, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 532 Chain: "C" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 1674 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PTRANS': 10, 'TRANS': 327} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 1041 Unresolved non-hydrogen angles: 1341 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'ARG:plan': 20, 'PHE:plan': 18, 'ASN:plan1': 11, 'HIS:plan': 8, 'GLU:plan': 21, 'GLN:plan1': 12, 'ASP:plan': 12, 'TRP:plan': 5, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 536 Chain: "D" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 1667 Classifications: {'peptide': 337} Incomplete info: {'truncation_to_alanine': 294} Link IDs: {'PTRANS': 10, 'TRANS': 326} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1040 Unresolved non-hydrogen angles: 1340 Unresolved non-hydrogen dihedrals: 855 Unresolved non-hydrogen chiralities: 120 Planarities with less than four sites: {'ARG:plan': 20, 'PHE:plan': 18, 'ASN:plan1': 11, 'HIS:plan': 8, 'GLU:plan': 21, 'GLN:plan1': 11, 'ASP:plan': 12, 'TRP:plan': 5, 'TYR:plan': 6} Unresolved non-hydrogen planarities: 532 Chain: "E" Number of atoms: 7060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1426, 7060 Classifications: {'peptide': 1426} Incomplete info: {'truncation_to_alanine': 1237} Link IDs: {'PTRANS': 44, 'TRANS': 1381} Chain breaks: 6 Unresolved chain link angles: 41 Unresolved non-hydrogen bonds: 4489 Unresolved non-hydrogen angles: 5807 Unresolved non-hydrogen dihedrals: 3756 Unresolved non-hydrogen chiralities: 493 Planarities with less than four sites: {'PHE:plan': 75, 'ASN:plan1': 66, 'TYR:plan': 44, 'HIS:plan': 33, 'GLN:plan1': 47, 'ASP:plan': 56, 'TRP:plan': 28, 'ARG:plan': 61, 'GLU:plan': 66} Unresolved non-hydrogen planarities: 2298 Chain: "G" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 982 Classifications: {'peptide': 198} Incomplete info: {'truncation_to_alanine': 177} Link IDs: {'PTRANS': 6, 'TRANS': 191} Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 684 Unresolved non-hydrogen angles: 896 Unresolved non-hydrogen dihedrals: 595 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'PHE:plan': 17, 'ASN:plan1': 11, 'TYR:plan': 7, 'HIS:plan': 10, 'GLN:plan1': 5, 'ASP:plan': 3, 'TRP:plan': 6, 'ARG:plan': 7, 'GLU:plan': 4} Unresolved non-hydrogen planarities: 368 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' K': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.36, per 1000 atoms: 0.29 Number of scatterers: 14976 At special positions: 0 Unit cell: (110.751, 153.729, 153.729, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 1 19.00 P 15 15.00 O 3069 8.00 N 3013 7.00 C 8878 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=3, symmetry=0 Links applied BETA1-4 " NAG F 1 " - " NAG F 2 " " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG F 1 " - " ASN G 9 " " NAG N 1 " - " ASN E 9 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 1.1 seconds 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5640 Finding SS restraints... Secondary structure from input PDB file: 91 helices and 19 sheets defined 49.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.56 Creating SS restraints... Processing helix chain 'A' and resid 23 through 29 Processing helix chain 'A' and resid 57 through 66 removed outlier: 4.186A pdb=" N PHE A 61 " --> pdb=" O LEU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 98 Processing helix chain 'A' and resid 100 through 106 Processing helix chain 'A' and resid 126 through 139 Processing helix chain 'A' and resid 152 through 183 Processing helix chain 'A' and resid 281 through 288 removed outlier: 3.597A pdb=" N LEU A 285 " --> pdb=" O ALA A 282 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 286 " --> pdb=" O THR A 283 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 Processing helix chain 'A' and resid 353 through 358 removed outlier: 4.142A pdb=" N GLU A 357 " --> pdb=" O CYS A 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 66 Processing helix chain 'B' and resid 68 through 98 removed outlier: 4.712A pdb=" N VAL B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR B 77 " --> pdb=" O LEU B 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N HIS B 98 " --> pdb=" O VAL B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 106 removed outlier: 4.238A pdb=" N GLU B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 138 Processing helix chain 'B' and resid 152 through 184 Processing helix chain 'B' and resid 281 through 286 removed outlier: 4.382A pdb=" N VAL B 286 " --> pdb=" O ALA B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 316 No H-bonds generated for 'chain 'B' and resid 314 through 316' Processing helix chain 'B' and resid 355 through 361 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.954A pdb=" N PHE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 94 removed outlier: 3.900A pdb=" N LEU C 73 " --> pdb=" O TRP C 69 " (cutoff:3.500A) removed outlier: 5.476A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 107 removed outlier: 3.527A pdb=" N LYS C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 118 removed outlier: 3.744A pdb=" N GLU C 116 " --> pdb=" O LYS C 112 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 139 Processing helix chain 'C' and resid 152 through 182 removed outlier: 3.852A pdb=" N ILE C 156 " --> pdb=" O CYS C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 280 removed outlier: 4.291A pdb=" N ASP C 279 " --> pdb=" O PRO C 276 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE C 280 " --> pdb=" O LEU C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 316 No H-bonds generated for 'chain 'C' and resid 314 through 316' Processing helix chain 'C' and resid 354 through 360 Processing helix chain 'D' and resid 58 through 66 removed outlier: 3.872A pdb=" N ASP D 66 " --> pdb=" O THR D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 68 through 73 Processing helix chain 'D' and resid 74 through 98 removed outlier: 3.666A pdb=" N LEU D 93 " --> pdb=" O ILE D 89 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N HIS D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 107 removed outlier: 3.707A pdb=" N ALA D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N TYR D 104 " --> pdb=" O ASP D 100 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 138 removed outlier: 3.684A pdb=" N GLU D 136 " --> pdb=" O LEU D 132 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL D 137 " --> pdb=" O PHE D 133 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 183 Processing helix chain 'D' and resid 276 through 280 removed outlier: 3.858A pdb=" N ASP D 279 " --> pdb=" O PRO D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 283 through 287 Processing helix chain 'D' and resid 314 through 318 removed outlier: 3.664A pdb=" N ILE D 318 " --> pdb=" O ALA D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 361 through 366 Processing helix chain 'E' and resid 24 through 45 Proline residue: E 33 - end of helix Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 68 through 97 removed outlier: 4.276A pdb=" N TRP E 73 " --> pdb=" O HIS E 69 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N SER E 95 " --> pdb=" O ILE E 91 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N GLN E 96 " --> pdb=" O VAL E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 128 Processing helix chain 'E' and resid 130 through 159 removed outlier: 4.286A pdb=" N LEU E 134 " --> pdb=" O PHE E 130 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N LEU E 135 " --> pdb=" O PRO E 131 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA E 136 " --> pdb=" O LYS E 132 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ALA E 144 " --> pdb=" O TYR E 140 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE E 145 " --> pdb=" O TRP E 141 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE E 146 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N THR E 147 " --> pdb=" O MET E 143 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY E 159 " --> pdb=" O TYR E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 191 Processing helix chain 'E' and resid 218 through 225 Processing helix chain 'E' and resid 231 through 237 Processing helix chain 'E' and resid 245 through 249 Processing helix chain 'E' and resid 250 through 255 removed outlier: 3.584A pdb=" N ALA E 254 " --> pdb=" O LYS E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 276 removed outlier: 3.679A pdb=" N TYR E 261 " --> pdb=" O ALA E 257 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LEU E 264 " --> pdb=" O ASN E 260 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS E 265 " --> pdb=" O TYR E 261 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU E 266 " --> pdb=" O VAL E 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 294 removed outlier: 4.242A pdb=" N TYR E 290 " --> pdb=" O TRP E 286 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ARG E 291 " --> pdb=" O LEU E 287 " (cutoff:3.500A) Processing helix chain 'E' and resid 297 through 324 removed outlier: 3.853A pdb=" N PHE E 303 " --> pdb=" O LEU E 299 " (cutoff:3.500A) Proline residue: E 315 - end of helix removed outlier: 3.628A pdb=" N ARG E 324 " --> pdb=" O GLY E 320 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 347 removed outlier: 3.994A pdb=" N GLU E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN E 347 " --> pdb=" O GLU E 343 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 342 through 347' Processing helix chain 'E' and resid 347 through 394 removed outlier: 3.825A pdb=" N LEU E 351 " --> pdb=" O ASN E 347 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL E 353 " --> pdb=" O HIS E 349 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN E 379 " --> pdb=" O GLU E 375 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ARG E 394 " --> pdb=" O ASN E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 413 Processing helix chain 'E' and resid 417 through 434 Proline residue: E 429 - end of helix Processing helix chain 'E' and resid 434 through 449 removed outlier: 4.082A pdb=" N MET E 440 " --> pdb=" O VAL E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 452 through 497 removed outlier: 3.877A pdb=" N VAL E 459 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 5.267A pdb=" N ILE E 460 " --> pdb=" O GLY E 456 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL E 461 " --> pdb=" O ALA E 457 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU E 462 " --> pdb=" O ALA E 458 " (cutoff:3.500A) Proline residue: E 465 - end of helix removed outlier: 4.302A pdb=" N THR E 472 " --> pdb=" O TYR E 468 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LYS E 473 " --> pdb=" O PHE E 469 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 503 Processing helix chain 'E' and resid 509 through 511 No H-bonds generated for 'chain 'E' and resid 509 through 511' Processing helix chain 'E' and resid 512 through 556 removed outlier: 3.586A pdb=" N SER E 525 " --> pdb=" O LYS E 521 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR E 532 " --> pdb=" O THR E 528 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE E 543 " --> pdb=" O MET E 539 " (cutoff:3.500A) Proline residue: E 544 - end of helix removed outlier: 3.611A pdb=" N ALA E 556 " --> pdb=" O PHE E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 579 removed outlier: 3.578A pdb=" N PHE E 569 " --> pdb=" O PRO E 565 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N ALA E 570 " --> pdb=" O ALA E 566 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N SER E 571 " --> pdb=" O GLU E 567 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL E 579 " --> pdb=" O PHE E 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 580 through 607 removed outlier: 4.389A pdb=" N LEU E 584 " --> pdb=" O THR E 580 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ARG E 590 " --> pdb=" O SER E 586 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N VAL E 593 " --> pdb=" O VAL E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 715 removed outlier: 4.224A pdb=" N LEU E 715 " --> pdb=" O LEU E 711 " (cutoff:3.500A) Processing helix chain 'E' and resid 774 through 784 removed outlier: 4.118A pdb=" N ALA E 779 " --> pdb=" O GLN E 775 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N VAL E 780 " --> pdb=" O ARG E 776 " (cutoff:3.500A) Processing helix chain 'E' and resid 809 through 823 Processing helix chain 'E' and resid 843 through 855 Processing helix chain 'E' and resid 893 through 898 Processing helix chain 'E' and resid 900 through 907 Processing helix chain 'E' and resid 909 through 914 Processing helix chain 'E' and resid 962 through 969 Processing helix chain 'E' and resid 973 through 986 removed outlier: 4.506A pdb=" N THR E 977 " --> pdb=" O MET E 973 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N SER E 984 " --> pdb=" O TRP E 980 " (cutoff:3.500A) Processing helix chain 'E' and resid 988 through 993 Processing helix chain 'E' and resid 993 through 1015 removed outlier: 3.516A pdb=" N THR E1015 " --> pdb=" O LEU E1011 " (cutoff:3.500A) Processing helix chain 'E' and resid 1026 through 1073 removed outlier: 4.340A pdb=" N ILE E1037 " --> pdb=" O ALA E1033 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU E1069 " --> pdb=" O HIS E1065 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ILE E1072 " --> pdb=" O LEU E1068 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE E1073 " --> pdb=" O LEU E1069 " (cutoff:3.500A) Processing helix chain 'E' and resid 1076 through 1083 removed outlier: 3.838A pdb=" N PHE E1080 " --> pdb=" O PRO E1076 " (cutoff:3.500A) Processing helix chain 'E' and resid 1084 through 1102 removed outlier: 4.201A pdb=" N ILE E1088 " --> pdb=" O PRO E1084 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ASP E1095 " --> pdb=" O ARG E1091 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N THR E1096 " --> pdb=" O PHE E1092 " (cutoff:3.500A) Processing helix chain 'E' and resid 1102 through 1128 Processing helix chain 'E' and resid 1129 through 1135 removed outlier: 4.291A pdb=" N ILE E1133 " --> pdb=" O PRO E1129 " (cutoff:3.500A) Processing helix chain 'E' and resid 1135 through 1177 removed outlier: 4.154A pdb=" N GLY E1139 " --> pdb=" O LEU E1135 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL E1140 " --> pdb=" O ALA E1136 " (cutoff:3.500A) removed outlier: 5.064A pdb=" N LYS E1154 " --> pdb=" O ARG E1150 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN E1164 " --> pdb=" O ASP E1160 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LEU E1165 " --> pdb=" O ASP E1161 " (cutoff:3.500A) Proline residue: E1166 - end of helix removed outlier: 3.722A pdb=" N CYS E1169 " --> pdb=" O LEU E1165 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA E1175 " --> pdb=" O PHE E1171 " (cutoff:3.500A) Processing helix chain 'E' and resid 1186 through 1238 removed outlier: 3.866A pdb=" N LYS E1191 " --> pdb=" O GLU E1187 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN E1192 " --> pdb=" O THR E1188 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG E1193 " --> pdb=" O ARG E1189 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU E1196 " --> pdb=" O GLN E1192 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP E1199 " --> pdb=" O LEU E1195 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ALA E1204 " --> pdb=" O THR E1200 " (cutoff:3.500A) Processing helix chain 'E' and resid 1240 through 1280 removed outlier: 4.255A pdb=" N ASN E1256 " --> pdb=" O LEU E1252 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N TYR E1257 " --> pdb=" O THR E1253 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU E1258 " --> pdb=" O ILE E1254 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ASN E1259 " --> pdb=" O THR E1255 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N TRP E1260 " --> pdb=" O ASN E1256 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS E1277 " --> pdb=" O GLY E1273 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL E1278 " --> pdb=" O ALA E1274 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER E1280 " --> pdb=" O LYS E1276 " (cutoff:3.500A) Processing helix chain 'E' and resid 1343 through 1354 removed outlier: 4.150A pdb=" N LYS E1348 " --> pdb=" O THR E1344 " (cutoff:3.500A) removed outlier: 5.774A pdb=" N SER E1349 " --> pdb=" O GLY E1345 " (cutoff:3.500A) Processing helix chain 'E' and resid 1380 through 1385 Processing helix chain 'E' and resid 1415 through 1421 Processing helix chain 'E' and resid 1453 through 1459 Processing helix chain 'E' and resid 1475 through 1494 removed outlier: 4.091A pdb=" N ALA E1492 " --> pdb=" O MET E1488 " (cutoff:3.500A) Processing helix chain 'E' and resid 1527 through 1533 Processing helix chain 'E' and resid 1538 through 1542 removed outlier: 3.573A pdb=" N ARG E1542 " --> pdb=" O SER E1539 " (cutoff:3.500A) Processing helix chain 'G' and resid 23 through 42 removed outlier: 4.012A pdb=" N ALA G 28 " --> pdb=" O CYS G 24 " (cutoff:3.500A) removed outlier: 4.721A pdb=" N LEU G 29 " --> pdb=" O PHE G 25 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ASN G 30 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N LEU G 31 " --> pdb=" O ASP G 27 " (cutoff:3.500A) Proline residue: G 33 - end of helix Processing helix chain 'G' and resid 65 through 97 removed outlier: 3.688A pdb=" N ASN G 70 " --> pdb=" O PHE G 66 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU G 71 " --> pdb=" O PRO G 67 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N ILE G 74 " --> pdb=" O ASN G 70 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE G 77 " --> pdb=" O TRP G 73 " (cutoff:3.500A) Processing helix chain 'G' and resid 104 through 128 Processing helix chain 'G' and resid 135 through 158 removed outlier: 4.054A pdb=" N LEU G 139 " --> pdb=" O LEU G 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N PHE G 145 " --> pdb=" O TRP G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 192 Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 193 Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 202 removed outlier: 3.905A pdb=" N VAL A 198 " --> pdb=" O MET A 209 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 244 through 248 removed outlier: 4.629A pdb=" N ILE A 227 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N SER A 222 " --> pdb=" O VAL A 299 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N VAL A 299 " --> pdb=" O SER A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 323 through 324 Processing sheet with id=AA5, first strand: chain 'A' and resid 328 through 330 Processing sheet with id=AA6, first strand: chain 'B' and resid 265 through 270 removed outlier: 3.782A pdb=" N PHE B 210 " --> pdb=" O ILE B 267 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ILE B 199 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 246 through 248 removed outlier: 4.515A pdb=" N ILE B 227 " --> pdb=" O ILE B 248 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N SER B 222 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N VAL B 299 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 46 through 48 removed outlier: 3.718A pdb=" N LYS C 48 " --> pdb=" O VAL D 337 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 197 through 198 removed outlier: 5.845A pdb=" N ALA C 197 " --> pdb=" O GLN C 319 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 209 through 212 Processing sheet with id=AB2, first strand: chain 'C' and resid 245 through 248 removed outlier: 4.442A pdb=" N ILE C 227 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N ALA C 223 " --> pdb=" O ILE C 259 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE C 259 " --> pdb=" O ALA C 223 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 245 through 248 removed outlier: 4.442A pdb=" N ILE C 227 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N SER C 222 " --> pdb=" O VAL C 299 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N VAL C 299 " --> pdb=" O SER C 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 233 through 234 Processing sheet with id=AB5, first strand: chain 'C' and resid 323 through 324 Processing sheet with id=AB6, first strand: chain 'C' and resid 329 through 330 Processing sheet with id=AB7, first strand: chain 'D' and resid 201 through 202 Processing sheet with id=AB8, first strand: chain 'D' and resid 240 through 248 removed outlier: 4.554A pdb=" N THR D 233 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE D 227 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ALA D 223 " --> pdb=" O ILE D 259 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 240 through 248 removed outlier: 4.554A pdb=" N THR D 233 " --> pdb=" O PRO D 242 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ILE D 227 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N SER D 222 " --> pdb=" O VAL D 299 " (cutoff:3.500A) removed outlier: 5.794A pdb=" N VAL D 299 " --> pdb=" O SER D 222 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ILE D 305 " --> pdb=" O VAL D 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 1513 through 1516 removed outlier: 6.679A pdb=" N VAL E1514 " --> pdb=" O LEU E1521 " (cutoff:3.500A) 1112 hydrogen bonds defined for protein. 3222 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: 2.94 Time building geometry restraints manager: 2.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.25: 2972 1.25 - 1.34: 2995 1.34 - 1.43: 125 1.43 - 1.52: 5328 1.52 - 1.61: 3558 Bond restraints: 14978 Sorted by residual: bond pdb=" C4 ATP E1601 " pdb=" C5 ATP E1601 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.84e+01 bond pdb=" C4 ATP A3002 " pdb=" C5 ATP A3002 " ideal model delta sigma weight residual 1.388 1.464 -0.076 1.00e-02 1.00e+04 5.82e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.463 -0.075 1.00e-02 1.00e+04 5.66e+01 bond pdb=" C4 ATP C 501 " pdb=" C5 ATP C 501 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.23e+01 bond pdb=" C4 ATP D 501 " pdb=" C5 ATP D 501 " ideal model delta sigma weight residual 1.388 1.460 -0.072 1.00e-02 1.00e+04 5.22e+01 ... (remaining 14973 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.60: 20469 4.60 - 9.20: 357 9.20 - 13.80: 39 13.80 - 18.40: 7 18.40 - 23.00: 11 Bond angle restraints: 20883 Sorted by residual: angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 116.87 23.00 1.00e+00 1.00e+00 5.29e+02 angle pdb=" PA ATP B 501 " pdb=" O3A ATP B 501 " pdb=" PB ATP B 501 " ideal model delta sigma weight residual 136.83 114.87 21.96 1.00e+00 1.00e+00 4.82e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 118.03 21.84 1.00e+00 1.00e+00 4.77e+02 angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 118.41 21.46 1.00e+00 1.00e+00 4.61e+02 angle pdb=" PB ATP E1601 " pdb=" O3B ATP E1601 " pdb=" PG ATP E1601 " ideal model delta sigma weight residual 139.87 119.09 20.78 1.00e+00 1.00e+00 4.32e+02 ... (remaining 20878 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.67: 8786 23.67 - 47.33: 57 47.33 - 71.00: 10 71.00 - 94.67: 17 94.67 - 118.33: 13 Dihedral angle restraints: 8883 sinusoidal: 273 harmonic: 8610 Sorted by residual: dihedral pdb=" C ASN G 22 " pdb=" N ASN G 22 " pdb=" CA ASN G 22 " pdb=" CB ASN G 22 " ideal model delta harmonic sigma weight residual -122.60 -111.06 -11.54 0 2.50e+00 1.60e-01 2.13e+01 dihedral pdb=" CA CYS E1407 " pdb=" C CYS E1407 " pdb=" N LYS E1408 " pdb=" CA LYS E1408 " ideal model delta harmonic sigma weight residual 180.00 157.67 22.33 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA LYS C 48 " pdb=" C LYS C 48 " pdb=" N ASN C 49 " pdb=" CA ASN C 49 " ideal model delta harmonic sigma weight residual 180.00 159.11 20.89 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 8880 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.902: 2858 0.902 - 1.805: 0 1.805 - 2.707: 0 2.707 - 3.609: 0 3.609 - 4.511: 2 Chirality restraints: 2860 Sorted by residual: chirality pdb=" C1 NAG N 1 " pdb=" ND2 ASN E 9 " pdb=" C2 NAG N 1 " pdb=" O5 NAG N 1 " both_signs ideal model delta sigma weight residual False -2.40 2.11 -4.51 2.00e-01 2.50e+01 5.09e+02 chirality pdb=" C1 NAG F 1 " pdb=" ND2 ASN G 9 " pdb=" C2 NAG F 1 " pdb=" O5 NAG F 1 " both_signs ideal model delta sigma weight residual False -2.40 2.02 -4.42 2.00e-01 2.50e+01 4.89e+02 chirality pdb=" C1 NAG N 2 " pdb=" O4 NAG N 1 " pdb=" C2 NAG N 2 " pdb=" O5 NAG N 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-02 2.50e+03 1.84e+02 ... (remaining 2857 not shown) Planarity restraints: 2988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 1 " 0.355 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG N 1 " -0.085 2.00e-02 2.50e+03 pdb=" C8 NAG N 1 " 0.114 2.00e-02 2.50e+03 pdb=" N2 NAG N 1 " -0.545 2.00e-02 2.50e+03 pdb=" O7 NAG N 1 " 0.160 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG F 2 " -0.323 2.00e-02 2.50e+03 2.70e-01 9.12e+02 pdb=" C7 NAG F 2 " 0.088 2.00e-02 2.50e+03 pdb=" C8 NAG F 2 " -0.200 2.00e-02 2.50e+03 pdb=" N2 NAG F 2 " 0.460 2.00e-02 2.50e+03 pdb=" O7 NAG F 2 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG N 2 " 0.232 2.00e-02 2.50e+03 1.98e-01 4.89e+02 pdb=" C7 NAG N 2 " -0.049 2.00e-02 2.50e+03 pdb=" C8 NAG N 2 " -0.035 2.00e-02 2.50e+03 pdb=" N2 NAG N 2 " -0.326 2.00e-02 2.50e+03 pdb=" O7 NAG N 2 " 0.178 2.00e-02 2.50e+03 ... (remaining 2985 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.27: 4 2.27 - 2.99: 9314 2.99 - 3.70: 24739 3.70 - 4.42: 30177 4.42 - 5.14: 45188 Nonbonded interactions: 109422 Sorted by model distance: nonbonded pdb=" CB ASN E 672 " pdb=" O GLU E 722 " model vdw 1.552 3.440 nonbonded pdb=" O4 NAG F 2 " pdb=" O6 NAG F 2 " model vdw 2.104 3.040 nonbonded pdb=" O GLN E1336 " pdb=" N VAL E1496 " model vdw 2.219 3.120 nonbonded pdb=" N LYS E 707 " pdb=" O1A ATP E1601 " model vdw 2.250 3.120 nonbonded pdb=" O VAL E 153 " pdb=" CB TRP E 156 " model vdw 2.298 3.440 ... (remaining 109417 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' and ((resid 30 through 297 and (name N or name CA or name C or name O \ or name CB )) or resid 298 through 366 or resid 3002)) selection = chain 'B' selection = (chain 'C' and ((resid 30 through 40 and (name N or name CA or name C or name O \ or name CB )) or resid 41 through 366 or resid 501)) selection = chain 'D' } ncs_group { reference = chain 'F' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.130 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6425 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 : 0.013 0.770 14985 Z= 1.153 Angle : 1.555 22.995 20895 Z= 1.146 Chirality : 0.148 4.511 2860 Planarity : 0.012 0.306 2986 Dihedral : 11.990 118.331 3243 Min Nonbonded Distance : 1.552 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.25 (0.15), residues: 2958 helix: 1.11 (0.15), residues: 1307 sheet: -1.49 (0.34), residues: 239 loop : -2.74 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 102 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00932 (14978) covalent geometry : angle 1.55053 (20883) hydrogen bonds : bond 0.18252 ( 1104) hydrogen bonds : angle 7.32249 ( 3222) Misc. bond : bond 0.62763 ( 3) link_BETA1-4 : bond 0.01576 ( 2) link_BETA1-4 : angle 5.42577 ( 6) link_NAG-ASN : bond 0.01544 ( 2) link_NAG-ASN : angle 4.90077 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.528 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0596 time to fit residues: 10.4406 Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 50.0000 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 30.0000 chunk 183 optimal weight: 50.0000 chunk 111 optimal weight: 0.8980 overall best weight: 10.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.229108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.191638 restraints weight = 235189.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.196473 restraints weight = 148622.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.195990 restraints weight = 123682.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.196346 restraints weight = 123226.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.196128 restraints weight = 111185.806| |-----------------------------------------------------------------------------| r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7200 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 14985 Z= 0.287 Angle : 0.733 20.145 20895 Z= 0.428 Chirality : 0.052 0.678 2860 Planarity : 0.004 0.050 2986 Dihedral : 11.327 100.721 3224 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.79 % Favored : 91.21 % Rotamer: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % 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: -1.44 (0.15), residues: 2958 helix: 0.77 (0.14), residues: 1350 sheet: -0.99 (0.36), residues: 212 loop : -2.85 (0.15), residues: 1396 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 102 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00429 (14978) covalent geometry : angle 0.70841 (20883) hydrogen bonds : bond 0.06369 ( 1104) hydrogen bonds : angle 5.40688 ( 3222) Misc. bond : bond 0.01544 ( 3) link_BETA1-4 : bond 0.03443 ( 2) link_BETA1-4 : angle 3.89273 ( 6) link_NAG-ASN : bond 0.01997 ( 2) link_NAG-ASN : angle 10.52048 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.573 Fit side-chains REVERT: E 9 ASN cc_start: 0.5740 (p0) cc_final: 0.5411 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0586 time to fit residues: 10.3877 Evaluate side-chains 86 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 258 optimal weight: 0.0470 chunk 71 optimal weight: 6.9990 chunk 144 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 chunk 128 optimal weight: 40.0000 chunk 272 optimal weight: 50.0000 chunk 75 optimal weight: 50.0000 chunk 158 optimal weight: 20.0000 chunk 50 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 169 optimal weight: 20.0000 overall best weight: 10.6090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.222932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.185092 restraints weight = 235272.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.189757 restraints weight = 148733.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.189945 restraints weight = 121342.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.189412 restraints weight = 120276.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.189391 restraints weight = 114738.661| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 14985 Z= 0.238 Angle : 0.694 20.874 20895 Z= 0.396 Chirality : 0.050 0.376 2860 Planarity : 0.004 0.037 2986 Dihedral : 11.225 109.317 3224 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -1.25 (0.15), residues: 2958 helix: 1.04 (0.14), residues: 1355 sheet: -1.15 (0.37), residues: 202 loop : -2.84 (0.15), residues: 1401 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 102 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00359 (14978) covalent geometry : angle 0.64759 (20883) hydrogen bonds : bond 0.06165 ( 1104) hydrogen bonds : angle 5.23233 ( 3222) Misc. bond : bond 0.00750 ( 3) link_BETA1-4 : bond 0.02066 ( 2) link_BETA1-4 : angle 6.46563 ( 6) link_NAG-ASN : bond 0.03042 ( 2) link_NAG-ASN : angle 13.21116 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.339 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0597 time to fit residues: 10.3518 Evaluate side-chains 86 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 241 optimal weight: 9.9990 chunk 286 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 181 optimal weight: 40.0000 chunk 222 optimal weight: 10.0000 chunk 161 optimal weight: 30.0000 chunk 104 optimal weight: 20.0000 chunk 282 optimal weight: 20.0000 chunk 244 optimal weight: 40.0000 chunk 226 optimal weight: 30.0000 chunk 266 optimal weight: 40.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.218240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.181449 restraints weight = 239233.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.185976 restraints weight = 149292.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.185355 restraints weight = 124410.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.185197 restraints weight = 125331.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.185133 restraints weight = 118865.461| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7340 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 14985 Z= 0.231 Angle : 0.709 17.807 20895 Z= 0.396 Chirality : 0.049 0.399 2860 Planarity : 0.003 0.035 2986 Dihedral : 10.509 89.163 3224 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 0.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % 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: -1.44 (0.15), residues: 2958 helix: 0.96 (0.14), residues: 1339 sheet: -1.61 (0.36), residues: 210 loop : -2.92 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 102 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00343 (14978) covalent geometry : angle 0.65869 (20883) hydrogen bonds : bond 0.05867 ( 1104) hydrogen bonds : angle 5.26700 ( 3222) Misc. bond : bond 0.00526 ( 3) link_BETA1-4 : bond 0.00663 ( 2) link_BETA1-4 : angle 5.12019 ( 6) link_NAG-ASN : bond 0.03494 ( 2) link_NAG-ASN : angle 14.67605 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.492 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0565 time to fit residues: 9.8751 Evaluate side-chains 86 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 133 optimal weight: 40.0000 chunk 31 optimal weight: 20.0000 chunk 280 optimal weight: 50.0000 chunk 7 optimal weight: 9.9990 chunk 47 optimal weight: 20.0000 chunk 204 optimal weight: 0.0070 chunk 0 optimal weight: 70.0000 chunk 252 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 166 optimal weight: 50.0000 overall best weight: 10.6010 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.217276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.179874 restraints weight = 237805.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.184065 restraints weight = 152575.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.184285 restraints weight = 124924.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.183937 restraints weight = 127593.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.183896 restraints weight = 120497.261| |-----------------------------------------------------------------------------| r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.4934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14985 Z= 0.219 Angle : 0.646 17.657 20895 Z= 0.374 Chirality : 0.048 0.479 2860 Planarity : 0.003 0.040 2986 Dihedral : 10.458 100.616 3224 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 1.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.85 % Favored : 89.15 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.41 (0.16), residues: 2958 helix: 1.06 (0.14), residues: 1338 sheet: -1.76 (0.36), residues: 211 loop : -2.95 (0.15), residues: 1409 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 102 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00318 (14978) covalent geometry : angle 0.61592 (20883) hydrogen bonds : bond 0.05747 ( 1104) hydrogen bonds : angle 5.19572 ( 3222) Misc. bond : bond 0.00251 ( 3) link_BETA1-4 : bond 0.00937 ( 2) link_BETA1-4 : angle 4.40868 ( 6) link_NAG-ASN : bond 0.01647 ( 2) link_NAG-ASN : angle 10.75356 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.494 Fit side-chains REVERT: G 9 ASN cc_start: 0.6570 (t0) cc_final: 0.6214 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0580 time to fit residues: 10.1992 Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 32 optimal weight: 40.0000 chunk 97 optimal weight: 5.9990 chunk 290 optimal weight: 20.0000 chunk 113 optimal weight: 5.9990 chunk 122 optimal weight: 20.0000 chunk 72 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 229 optimal weight: 40.0000 chunk 46 optimal weight: 9.9990 chunk 41 optimal weight: 30.0000 chunk 163 optimal weight: 40.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4243 r_free = 0.4243 target = 0.220045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.183195 restraints weight = 237623.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.187677 restraints weight = 150507.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.187271 restraints weight = 124073.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.187400 restraints weight = 125966.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.187204 restraints weight = 116698.113| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 14985 Z= 0.165 Angle : 0.576 15.801 20895 Z= 0.326 Chirality : 0.047 0.364 2860 Planarity : 0.002 0.033 2986 Dihedral : 9.564 90.576 3224 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 1.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.60 % Favored : 90.40 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.04 (0.16), residues: 2958 helix: 1.50 (0.15), residues: 1340 sheet: -1.68 (0.36), residues: 201 loop : -2.90 (0.15), residues: 1417 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 102 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00239 (14978) covalent geometry : angle 0.53667 (20883) hydrogen bonds : bond 0.04980 ( 1104) hydrogen bonds : angle 4.73003 ( 3222) Misc. bond : bond 0.00207 ( 3) link_BETA1-4 : bond 0.00639 ( 2) link_BETA1-4 : angle 3.83215 ( 6) link_NAG-ASN : bond 0.01847 ( 2) link_NAG-ASN : angle 11.82694 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: G 9 ASN cc_start: 0.6557 (t0) cc_final: 0.6181 (t0) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0602 time to fit residues: 10.6008 Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 260 optimal weight: 6.9990 chunk 250 optimal weight: 50.0000 chunk 55 optimal weight: 2.9990 chunk 154 optimal weight: 40.0000 chunk 282 optimal weight: 40.0000 chunk 149 optimal weight: 10.0000 chunk 63 optimal weight: 50.0000 chunk 280 optimal weight: 9.9990 chunk 170 optimal weight: 30.0000 chunk 276 optimal weight: 40.0000 chunk 104 optimal weight: 6.9990 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4235 r_free = 0.4235 target = 0.219241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.181765 restraints weight = 239449.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.186040 restraints weight = 151901.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.185915 restraints weight = 125026.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.185804 restraints weight = 130580.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.185555 restraints weight = 120824.671| |-----------------------------------------------------------------------------| r_work (final): 0.3741 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7332 moved from start: 0.5405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 14985 Z= 0.165 Angle : 0.562 14.639 20895 Z= 0.321 Chirality : 0.046 0.333 2860 Planarity : 0.003 0.037 2986 Dihedral : 9.312 91.409 3224 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.45 % Favored : 89.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -0.89 (0.16), residues: 2958 helix: 1.63 (0.15), residues: 1342 sheet: -1.72 (0.36), residues: 201 loop : -2.82 (0.16), residues: 1415 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 102 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00238 (14978) covalent geometry : angle 0.53011 (20883) hydrogen bonds : bond 0.04898 ( 1104) hydrogen bonds : angle 4.63904 ( 3222) Misc. bond : bond 0.00144 ( 3) link_BETA1-4 : bond 0.00580 ( 2) link_BETA1-4 : angle 3.69909 ( 6) link_NAG-ASN : bond 0.01601 ( 2) link_NAG-ASN : angle 10.40174 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0604 time to fit residues: 10.5220 Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 280 optimal weight: 7.9990 chunk 147 optimal weight: 40.0000 chunk 227 optimal weight: 50.0000 chunk 46 optimal weight: 9.9990 chunk 197 optimal weight: 50.0000 chunk 162 optimal weight: 40.0000 chunk 123 optimal weight: 30.0000 chunk 148 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 96 optimal weight: 30.0000 chunk 95 optimal weight: 40.0000 overall best weight: 12.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.216280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.177930 restraints weight = 233828.635| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.181754 restraints weight = 153231.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.181789 restraints weight = 124587.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.181747 restraints weight = 128857.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.181524 restraints weight = 119317.023| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.5719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14985 Z= 0.258 Angle : 0.696 14.584 20895 Z= 0.412 Chirality : 0.048 0.290 2860 Planarity : 0.004 0.030 2986 Dihedral : 10.006 89.356 3224 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 1.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.95 % Favored : 87.05 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -1.66 (0.15), residues: 2958 helix: 0.84 (0.14), residues: 1336 sheet: -1.83 (0.37), residues: 197 loop : -3.07 (0.15), residues: 1425 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 102 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00373 (14978) covalent geometry : angle 0.66473 (20883) hydrogen bonds : bond 0.06240 ( 1104) hydrogen bonds : angle 5.53863 ( 3222) Misc. bond : bond 0.00228 ( 3) link_BETA1-4 : bond 0.00313 ( 2) link_BETA1-4 : angle 4.07197 ( 6) link_NAG-ASN : bond 0.01791 ( 2) link_NAG-ASN : angle 11.48422 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.558 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0604 time to fit residues: 10.6842 Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 16 optimal weight: 1.9990 chunk 133 optimal weight: 2.9990 chunk 243 optimal weight: 50.0000 chunk 35 optimal weight: 10.0000 chunk 45 optimal weight: 30.0000 chunk 66 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 19 optimal weight: 6.9990 chunk 41 optimal weight: 30.0000 chunk 276 optimal weight: 0.0050 chunk 200 optimal weight: 50.0000 overall best weight: 4.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.221217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.184800 restraints weight = 235781.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.189110 restraints weight = 149160.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.188148 restraints weight = 123837.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.188276 restraints weight = 120238.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.188406 restraints weight = 112879.904| |-----------------------------------------------------------------------------| r_work (final): 0.3775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.063 14985 Z= 0.126 Angle : 0.564 19.457 20895 Z= 0.303 Chirality : 0.047 0.497 2860 Planarity : 0.002 0.047 2986 Dihedral : 9.299 98.963 3224 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 0.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.76 (0.16), residues: 2958 helix: 1.78 (0.15), residues: 1345 sheet: -1.73 (0.36), residues: 201 loop : -2.79 (0.16), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 102 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00188 (14978) covalent geometry : angle 0.51313 (20883) hydrogen bonds : bond 0.04509 ( 1104) hydrogen bonds : angle 4.42024 ( 3222) Misc. bond : bond 0.00100 ( 3) link_BETA1-4 : bond 0.01021 ( 2) link_BETA1-4 : angle 3.83282 ( 6) link_NAG-ASN : bond 0.00502 ( 2) link_NAG-ASN : angle 13.35480 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.0572 time to fit residues: 10.1189 Evaluate side-chains 88 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 268 optimal weight: 50.0000 chunk 141 optimal weight: 40.0000 chunk 267 optimal weight: 20.0000 chunk 120 optimal weight: 3.9990 chunk 110 optimal weight: 6.9990 chunk 214 optimal weight: 50.0000 chunk 140 optimal weight: 7.9990 chunk 230 optimal weight: 7.9990 chunk 252 optimal weight: 8.9990 chunk 182 optimal weight: 0.0870 chunk 42 optimal weight: 30.0000 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.220857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.184025 restraints weight = 235734.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.188510 restraints weight = 147845.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.188640 restraints weight = 120456.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.188581 restraints weight = 122707.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.188353 restraints weight = 115015.681| |-----------------------------------------------------------------------------| r_work (final): 0.3770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.5867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14985 Z= 0.131 Angle : 0.524 11.703 20895 Z= 0.292 Chirality : 0.047 0.405 2860 Planarity : 0.002 0.028 2986 Dihedral : 8.860 84.353 3224 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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 (0.16), residues: 2958 helix: 2.00 (0.15), residues: 1352 sheet: -1.71 (0.36), residues: 207 loop : -2.73 (0.16), residues: 1399 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 102 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00191 (14978) covalent geometry : angle 0.49355 (20883) hydrogen bonds : bond 0.04319 ( 1104) hydrogen bonds : angle 4.25659 ( 3222) Misc. bond : bond 0.00113 ( 3) link_BETA1-4 : bond 0.00969 ( 2) link_BETA1-4 : angle 4.70727 ( 6) link_NAG-ASN : bond 0.00639 ( 2) link_NAG-ASN : angle 9.26135 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5916 Ramachandran restraints generated. 2958 Oldfield, 0 Emsley, 2958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.506 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0621 time to fit residues: 10.8696 Evaluate side-chains 87 residues out of total 2605 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 294 random chunks: chunk 166 optimal weight: 50.0000 chunk 59 optimal weight: 30.0000 chunk 249 optimal weight: 30.0000 chunk 171 optimal weight: 30.0000 chunk 97 optimal weight: 30.0000 chunk 124 optimal weight: 20.0000 chunk 8 optimal weight: 0.9990 chunk 138 optimal weight: 50.0000 chunk 112 optimal weight: 30.0000 chunk 190 optimal weight: 7.9990 chunk 87 optimal weight: 30.0000 overall best weight: 17.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.213167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.176136 restraints weight = 237830.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.179711 restraints weight = 154366.070| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.179445 restraints weight = 127383.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.179167 restraints weight = 128049.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.179348 restraints weight = 121854.023| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.6097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 14985 Z= 0.344 Angle : 0.797 13.083 20895 Z= 0.484 Chirality : 0.051 0.469 2860 Planarity : 0.004 0.033 2986 Dihedral : 10.128 89.288 3224 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 1.70 Ramachandran Plot: Outliers : 0.10 % Allowed : 14.30 % Favored : 85.60 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: -2.03 (0.15), residues: 2958 helix: 0.45 (0.14), residues: 1363 sheet: -1.84 (0.38), residues: 183 loop : -3.26 (0.15), residues: 1412 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 102 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00499 (14978) covalent geometry : angle 0.77538 (20883) hydrogen bonds : bond 0.06843 ( 1104) hydrogen bonds : angle 5.95947 ( 3222) Misc. bond : bond 0.00217 ( 3) link_BETA1-4 : bond 0.00564 ( 2) link_BETA1-4 : angle 6.64148 ( 6) link_NAG-ASN : bond 0.00924 ( 2) link_NAG-ASN : angle 8.57206 ( 6) =============================================================================== Job complete usr+sys time: 1529.81 seconds wall clock time: 26 minutes 48.69 seconds (1608.69 seconds total)