Starting phenix.real_space_refine on Wed Mar 4 15:08:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mjp_23881/03_2026/7mjp_23881_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mjp_23881/03_2026/7mjp_23881.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/7mjp_23881/03_2026/7mjp_23881.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mjp_23881/03_2026/7mjp_23881.map" model { file = "/net/cci-nas-00/data/ceres_data/7mjp_23881/03_2026/7mjp_23881_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mjp_23881/03_2026/7mjp_23881_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: 6 Type Number sf(0) Gaussians P 15 5.49 5 S 1 5.16 5 Cl 1 4.86 5 C 8398 2.51 5 N 2849 2.21 5 O 2899 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: 14163 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 1812 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 319} Link IDs: {'PTRANS': 12, 'TRANS': 353} Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1137 Unresolved non-hydrogen angles: 1460 Unresolved non-hydrogen dihedrals: 934 Unresolved non-hydrogen chiralities: 128 Planarities with less than four sites: {'ARG:plan': 25, 'GLU:plan': 24, 'TYR:plan': 7, 'ASN:plan1': 12, 'ASP:plan': 13, 'PHE:plan': 18, 'HIS:plan': 8, 'GLN:plan1': 11, 'TRP:plan': 5} Unresolved non-hydrogen planarities: 582 Chain: "B" 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: "C" Number of atoms: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 1677 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 296} Link IDs: {'PTRANS': 10, 'TRANS': 328} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1046 Unresolved non-hydrogen angles: 1348 Unresolved non-hydrogen dihedrals: 859 Unresolved non-hydrogen chiralities: 121 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: 1677 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 1677 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 296} Link IDs: {'PTRANS': 10, 'TRANS': 328} Unresolved chain link angles: 10 Unresolved non-hydrogen bonds: 1046 Unresolved non-hydrogen angles: 1348 Unresolved non-hydrogen dihedrals: 859 Unresolved non-hydrogen chiralities: 121 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: "E" Number of atoms: 7107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1436, 7107 Classifications: {'peptide': 1436} Incomplete info: {'truncation_to_alanine': 1248} Link IDs: {'PTRANS': 47, 'TRANS': 1388} Chain breaks: 4 Unresolved chain link angles: 45 Unresolved non-hydrogen bonds: 4520 Unresolved non-hydrogen angles: 5845 Unresolved non-hydrogen dihedrals: 3784 Unresolved non-hydrogen chiralities: 497 Planarities with less than four sites: {'PHE:plan': 75, 'ASN:plan1': 65, 'TYR:plan': 44, 'HIS:plan': 33, 'GLN:plan1': 48, 'ASP:plan': 56, 'TRP:plan': 28, 'ARG:plan': 61, 'GLU:plan': 65} Unresolved non-hydrogen planarities: 2295 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: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 62 Unusual residues: {'ATP': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'ATP': 1, 'GBM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.75, per 1000 atoms: 0.26 Number of scatterers: 14163 At special positions: 0 Unit cell: (125.54, 170.734, 156.925, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 1 16.00 P 15 15.00 O 2899 8.00 N 2849 7.00 C 8398 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=1, symmetry=0 Links applied BETA1-4 " NAG N 1 " - " NAG N 2 " NAG-ASN " NAG N 1 " - " ASN E 9 " Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.36 Conformation dependent library (CDL) restraints added in 786.2 milliseconds 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5332 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 21 sheets defined 50.7% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 16 through 21 removed outlier: 4.263A pdb=" N GLU A 20 " --> pdb=" O ARG A 16 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ASN A 21 " --> pdb=" O ILE A 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 16 through 21' Processing helix chain 'A' and resid 56 through 66 removed outlier: 3.776A pdb=" N ILE A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 98 removed outlier: 3.853A pdb=" N LEU A 73 " --> pdb=" O TRP A 69 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N VAL A 74 " --> pdb=" O ARG A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 110 removed outlier: 3.583A pdb=" N ALA A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N THR A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 139 removed outlier: 4.577A pdb=" N ILE A 135 " --> pdb=" O PHE A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 183 removed outlier: 3.623A pdb=" N ILE A 156 " --> pdb=" O CYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 4.171A pdb=" N ASP A 279 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ILE A 280 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'B' and resid 56 through 66 removed outlier: 3.870A pdb=" N ILE B 60 " --> pdb=" O PHE B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 98 removed outlier: 4.144A pdb=" N VAL B 74 " --> pdb=" O ARG B 70 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N PHE B 80 " --> pdb=" O PHE B 76 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N HIS B 98 " --> pdb=" O VAL B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 removed outlier: 3.920A pdb=" N GLY B 108 " --> pdb=" O TYR B 104 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ILE B 109 " --> pdb=" O MET B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 139 Processing helix chain 'B' and resid 152 through 183 Processing helix chain 'B' and resid 282 through 286 removed outlier: 4.122A pdb=" N VAL B 286 " --> pdb=" O THR B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 342 No H-bonds generated for 'chain 'B' and resid 340 through 342' Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.917A pdb=" N LYS B 361 " --> pdb=" O GLU B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'C' and resid 57 through 66 removed outlier: 3.686A pdb=" N PHE C 61 " --> pdb=" O LEU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 68 through 97 removed outlier: 4.625A pdb=" N VAL C 74 " --> pdb=" O ARG C 70 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N THR C 77 " --> pdb=" O LEU C 73 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE C 80 " --> pdb=" O PHE C 76 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LEU C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 108 Processing helix chain 'C' and resid 114 through 118 Processing helix chain 'C' and resid 126 through 139 removed outlier: 3.660A pdb=" N ALA C 130 " --> pdb=" O SER C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 152 through 183 removed outlier: 3.901A pdb=" N ILE C 156 " --> pdb=" O CYS C 152 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLN C 183 " --> pdb=" O MET C 179 " (cutoff:3.500A) Processing helix chain 'C' and resid 340 through 342 No H-bonds generated for 'chain 'C' and resid 340 through 342' Processing helix chain 'C' and resid 354 through 361 removed outlier: 4.007A pdb=" N ASP C 359 " --> pdb=" O ALA C 355 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 66 Processing helix chain 'D' and resid 68 through 98 removed outlier: 4.183A pdb=" N VAL D 74 " --> pdb=" O ARG D 70 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D 80 " --> pdb=" O PHE D 76 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N HIS D 98 " --> pdb=" O VAL D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 110 removed outlier: 4.006A pdb=" N ALA D 103 " --> pdb=" O GLY D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 113 through 119 removed outlier: 3.542A pdb=" N ALA D 118 " --> pdb=" O LEU D 115 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N VAL D 119 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 139 removed outlier: 3.793A pdb=" N VAL D 139 " --> pdb=" O ILE D 135 " (cutoff:3.500A) Processing helix chain 'D' and resid 152 through 183 removed outlier: 4.014A pdb=" N ILE D 156 " --> pdb=" O CYS D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 275 through 280 removed outlier: 4.271A pdb=" N ASP D 279 " --> pdb=" O PRO D 276 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 286 removed outlier: 3.579A pdb=" N LEU D 285 " --> pdb=" O ALA D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 361 removed outlier: 3.680A pdb=" N LYS D 361 " --> pdb=" O GLU D 357 " (cutoff:3.500A) Processing helix chain 'E' and resid 9 through 13 Processing helix chain 'E' and resid 22 through 47 Proline residue: E 33 - end of helix Proline residue: E 43 - end of helix Processing helix chain 'E' and resid 69 through 96 Processing helix chain 'E' and resid 101 through 104 removed outlier: 4.291A pdb=" N LEU E 104 " --> pdb=" O HIS E 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 101 through 104' Processing helix chain 'E' and resid 105 through 127 Processing helix chain 'E' and resid 130 through 133 Processing helix chain 'E' and resid 134 through 159 removed outlier: 3.636A pdb=" N LEU E 158 " --> pdb=" O LYS E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 192 Processing helix chain 'E' and resid 216 through 220 removed outlier: 3.906A pdb=" N VAL E 220 " --> pdb=" O GLN E 217 " (cutoff:3.500A) Processing helix chain 'E' and resid 221 through 227 removed outlier: 3.963A pdb=" N THR E 227 " --> pdb=" O LEU E 223 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 237 Processing helix chain 'E' and resid 244 through 248 Processing helix chain 'E' and resid 256 through 278 removed outlier: 3.710A pdb=" N ASN E 260 " --> pdb=" O ARG E 256 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP E 277 " --> pdb=" O LYS E 273 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS E 278 " --> pdb=" O LYS E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 285 through 290 Processing helix chain 'E' and resid 294 through 312 removed outlier: 3.939A pdb=" N PHE E 312 " --> pdb=" O ASP E 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 312 through 326 removed outlier: 3.714A pdb=" N LEU E 316 " --> pdb=" O PHE E 312 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.993A pdb=" N LEU E 345 " --> pdb=" O SER E 341 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU E 346 " --> pdb=" O LYS E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 347 through 394 removed outlier: 3.642A pdb=" N ALA E 352 " --> pdb=" O ALA E 348 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 353 " --> pdb=" O HIS E 349 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N THR E 364 " --> pdb=" O ILE E 360 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N ARG E 394 " --> pdb=" O ASN E 390 " (cutoff:3.500A) Processing helix chain 'E' and resid 406 through 416 removed outlier: 3.579A pdb=" N ILE E 410 " --> pdb=" O THR E 406 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 427 removed outlier: 3.545A pdb=" N LEU E 427 " --> pdb=" O TRP E 423 " (cutoff:3.500A) Processing helix chain 'E' and resid 428 through 432 Processing helix chain 'E' and resid 433 through 450 removed outlier: 4.245A pdb=" N LEU E 448 " --> pdb=" O LEU E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 451 through 462 removed outlier: 4.051A pdb=" N VAL E 455 " --> pdb=" O SER E 451 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LEU E 462 " --> pdb=" O ALA E 458 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 498 removed outlier: 3.523A pdb=" N ILE E 466 " --> pdb=" O LEU E 462 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLY E 498 " --> pdb=" O GLU E 494 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 506 removed outlier: 4.010A pdb=" N LEU E 502 " --> pdb=" O GLY E 498 " (cutoff:3.500A) Processing helix chain 'E' and resid 511 through 559 removed outlier: 4.146A pdb=" N VAL E 515 " --> pdb=" O PHE E 511 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N THR E 528 " --> pdb=" O SER E 524 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE E 529 " --> pdb=" O SER E 525 " (cutoff:3.500A) Proline residue: E 544 - end of helix removed outlier: 4.174A pdb=" N HIS E 555 " --> pdb=" O THR E 551 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N ALA E 556 " --> pdb=" O PHE E 552 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR E 557 " --> pdb=" O VAL E 553 " (cutoff:3.500A) Processing helix chain 'E' and resid 564 through 606 removed outlier: 3.699A pdb=" N ALA E 568 " --> pdb=" O LYS E 564 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N SER E 571 " --> pdb=" O GLU E 567 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU E 572 " --> pdb=" O ALA E 568 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER E 573 " --> pdb=" O PHE E 569 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N HIS E 576 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE E 577 " --> pdb=" O SER E 573 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU E 578 " --> pdb=" O LEU E 574 " (cutoff:3.500A) Proline residue: E 581 - end of helix removed outlier: 3.804A pdb=" N LEU E 584 " --> pdb=" O THR E 580 " (cutoff:3.500A) Processing helix chain 'E' and resid 706 through 716 Processing helix chain 'E' and resid 761 through 768 Processing helix chain 'E' and resid 773 through 784 Processing helix chain 'E' and resid 785 through 793 removed outlier: 4.592A pdb=" N ASP E 789 " --> pdb=" O SER E 785 " (cutoff:3.500A) Processing helix chain 'E' and resid 795 through 799 Processing helix chain 'E' and resid 809 through 823 removed outlier: 3.509A pdb=" N TYR E 823 " --> pdb=" O ALA E 819 " (cutoff:3.500A) Processing helix chain 'E' and resid 840 through 855 Processing helix chain 'E' and resid 891 through 897 removed outlier: 3.518A pdb=" N THR E 897 " --> pdb=" O LYS E 893 " (cutoff:3.500A) Processing helix chain 'E' and resid 900 through 910 removed outlier: 4.168A pdb=" N GLU E 904 " --> pdb=" O VAL E 900 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N MET E 910 " --> pdb=" O TRP E 906 " (cutoff:3.500A) Processing helix chain 'E' and resid 976 through 983 Processing helix chain 'E' and resid 987 through 1018 removed outlier: 4.055A pdb=" N PHE E 991 " --> pdb=" O PHE E 987 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU E 992 " --> pdb=" O PHE E 988 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N MET E 993 " --> pdb=" O LEU E 989 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ASP E1008 " --> pdb=" O ILE E1004 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR E1018 " --> pdb=" O TRP E1014 " (cutoff:3.500A) Processing helix chain 'E' and resid 1028 through 1073 removed outlier: 3.804A pdb=" N SER E1050 " --> pdb=" O CYS E1046 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU E1051 " --> pdb=" O LEU E1047 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE E1073 " --> pdb=" O LEU E1069 " (cutoff:3.500A) Processing helix chain 'E' and resid 1076 through 1083 removed outlier: 3.793A pdb=" N PHE E1080 " --> pdb=" O PRO E1076 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N THR E1083 " --> pdb=" O PHE E1079 " (cutoff:3.500A) Processing helix chain 'E' and resid 1086 through 1102 removed outlier: 4.481A pdb=" N ASP E1095 " --> pdb=" O ARG E1091 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N THR E1096 " --> pdb=" O PHE E1092 " (cutoff:3.500A) Processing helix chain 'E' and resid 1102 through 1128 removed outlier: 3.721A pdb=" N THR E1106 " --> pdb=" O HIS E1102 " (cutoff:3.500A) Processing helix chain 'E' and resid 1129 through 1177 removed outlier: 3.736A pdb=" N ILE E1133 " --> pdb=" O PRO E1129 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA E1136 " --> pdb=" O LEU E1132 " (cutoff:3.500A) Proline residue: E1137 - end of helix removed outlier: 4.223A pdb=" N ARG E1150 " --> pdb=" O GLN E1146 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N LYS E1154 " --> pdb=" O ARG E1150 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP E1155 " --> pdb=" O VAL E1151 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N SER E1162 " --> pdb=" O GLU E1158 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LEU E1165 " --> pdb=" O ASP E1161 " (cutoff:3.500A) Proline residue: E1166 - end of helix removed outlier: 3.802A pdb=" N PHE E1171 " --> pdb=" O LEU E1167 " (cutoff:3.500A) Processing helix chain 'E' and resid 1177 through 1184 Processing helix chain 'E' and resid 1186 through 1236 removed outlier: 3.804A pdb=" N ARG E1193 " --> pdb=" O ARG E1189 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLU E1196 " --> pdb=" O GLN E1192 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA E1233 " --> pdb=" O THR E1229 " (cutoff:3.500A) Processing helix chain 'E' and resid 1241 through 1258 removed outlier: 3.598A pdb=" N GLY E1247 " --> pdb=" O LEU E1243 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR E1255 " --> pdb=" O ALA E1251 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ASN E1256 " --> pdb=" O LEU E1252 " (cutoff:3.500A) Processing helix chain 'E' and resid 1259 through 1282 removed outlier: 3.733A pdb=" N ARG E1263 " --> pdb=" O ASN E1259 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS E1277 " --> pdb=" O GLY E1273 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL E1278 " --> pdb=" O ALA E1274 " (cutoff:3.500A) Processing helix chain 'E' and resid 1294 through 1298 removed outlier: 3.558A pdb=" N VAL E1298 " --> pdb=" O PRO E1295 " (cutoff:3.500A) Processing helix chain 'E' and resid 1349 through 1356 removed outlier: 3.947A pdb=" N PHE E1356 " --> pdb=" O SER E1352 " (cutoff:3.500A) Processing helix chain 'E' and resid 1367 through 1371 Processing helix chain 'E' and resid 1372 through 1376 removed outlier: 3.505A pdb=" N LYS E1375 " --> pdb=" O ASP E1372 " (cutoff:3.500A) Processing helix chain 'E' and resid 1377 through 1383 Processing helix chain 'E' and resid 1414 through 1420 Processing helix chain 'E' and resid 1442 through 1461 removed outlier: 4.774A pdb=" N GLY E1448 " --> pdb=" O ASN E1444 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN E1451 " --> pdb=" O VAL E1447 " (cutoff:3.500A) Processing helix chain 'E' and resid 1475 through 1489 Processing helix chain 'E' and resid 1505 through 1509 removed outlier: 4.489A pdb=" N THR E1508 " --> pdb=" O THR E1505 " (cutoff:3.500A) Processing helix chain 'E' and resid 1528 through 1533 removed outlier: 3.994A pdb=" N GLU E1533 " --> pdb=" O LEU E1529 " (cutoff:3.500A) Processing helix chain 'E' and resid 1534 through 1540 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 48 removed outlier: 3.604A pdb=" N LYS A 48 " --> pdb=" O VAL B 337 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 192 through 193 removed outlier: 3.819A pdb=" N VAL A 212 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 265 " --> pdb=" O VAL A 212 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 201 through 202 Processing sheet with id=AA4, first strand: chain 'A' and resid 240 through 248 removed outlier: 5.444A pdb=" N THR A 233 " --> pdb=" O PRO A 242 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N ILE A 227 " --> pdb=" O ILE A 248 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 223 " --> pdb=" O GLU A 297 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU A 297 " --> pdb=" O ALA A 223 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N VAL A 225 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N ILE A 295 " --> pdb=" O VAL A 225 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ILE A 227 " --> pdb=" O ILE A 293 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE A 293 " --> pdb=" O ILE A 227 " (cutoff:3.500A) removed outlier: 4.950A pdb=" N VAL A 229 " --> pdb=" O GLU A 291 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N GLU A 291 " --> pdb=" O VAL A 229 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL A 294 " --> pdb=" O THR A 311 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL A 300 " --> pdb=" O ILE A 305 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 305 " --> pdb=" O VAL A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 322 through 324 Processing sheet with id=AA6, first strand: chain 'A' and resid 336 through 338 removed outlier: 6.175A pdb=" N VAL A 337 " --> pdb=" O LYS D 48 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 47 through 48 Processing sheet with id=AA8, first strand: chain 'B' and resid 191 through 193 Processing sheet with id=AA9, first strand: chain 'B' and resid 191 through 193 removed outlier: 6.686A pdb=" N ALA B 197 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 220 through 230 removed outlier: 5.428A pdb=" N SER B 222 " --> pdb=" O VAL B 299 " (cutoff:3.500A) removed outlier: 5.247A pdb=" N VAL B 299 " --> pdb=" O SER B 222 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 233 through 234 Processing sheet with id=AB3, first strand: chain 'B' and resid 322 through 324 Processing sheet with id=AB4, first strand: chain 'C' and resid 47 through 48 removed outlier: 4.095A pdb=" N LYS C 48 " --> pdb=" O VAL D 337 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 265 through 270 removed outlier: 5.471A pdb=" N ALA C 197 " --> pdb=" O GLN C 319 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 244 through 248 removed outlier: 4.512A pdb=" N ILE C 227 " --> pdb=" O ILE C 248 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N ALA C 223 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU C 297 " --> pdb=" O ALA C 223 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N VAL C 225 " --> pdb=" O ILE C 295 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ILE C 295 " --> pdb=" O VAL C 225 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE C 227 " --> pdb=" O ILE C 293 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 293 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N VAL C 229 " --> pdb=" O GLU C 291 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLU C 291 " --> pdb=" O VAL C 229 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 322 through 323 removed outlier: 3.508A pdb=" N ARG C 323 " --> pdb=" O VAL C 346 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL C 346 " --> pdb=" O ARG C 323 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 191 through 193 Processing sheet with id=AB9, first strand: chain 'D' and resid 191 through 193 removed outlier: 4.342A pdb=" N ILE D 199 " --> pdb=" O GLN D 319 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 244 through 248 removed outlier: 4.440A pdb=" N ILE D 227 " --> pdb=" O ILE D 248 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ALA D 223 " --> pdb=" O GLU D 297 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N GLU D 297 " --> pdb=" O ALA D 223 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N VAL D 225 " --> pdb=" O ILE D 295 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N ILE D 295 " --> pdb=" O VAL D 225 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ILE D 227 " --> pdb=" O ILE D 293 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE D 293 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N LEU D 296 " --> pdb=" O ALA D 309 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA D 309 " --> pdb=" O LEU D 296 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY D 298 " --> pdb=" O THR D 307 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 322 through 324 Processing sheet with id=AC3, first strand: chain 'E' and resid 880 through 881 removed outlier: 7.029A pdb=" N ALA E 880 " --> pdb=" O VAL E 886 " (cutoff:3.500A) 1060 hydrogen bonds defined for protein. 3054 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: 2.70 Time building geometry restraints manager: 1.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2829 1.30 - 1.43: 2898 1.43 - 1.56: 8407 1.56 - 1.69: 32 1.69 - 1.81: 3 Bond restraints: 14169 Sorted by residual: bond pdb=" O5 GBM E1602 " pdb=" S2 GBM E1602 " ideal model delta sigma weight residual 1.448 1.643 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" O4 GBM E1602 " pdb=" S2 GBM E1602 " ideal model delta sigma weight residual 1.453 1.645 -0.192 2.00e-02 2.50e+03 9.23e+01 bond pdb=" C4 ATP A 501 " pdb=" C5 ATP A 501 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.38e+01 bond pdb=" C4 ATP B 501 " pdb=" C5 ATP B 501 " ideal model delta sigma weight residual 1.388 1.467 -0.079 1.00e-02 1.00e+04 6.25e+01 bond pdb=" C4 ATP E1601 " pdb=" C5 ATP E1601 " ideal model delta sigma weight residual 1.388 1.466 -0.078 1.00e-02 1.00e+04 6.11e+01 ... (remaining 14164 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 19542 4.16 - 8.31: 180 8.31 - 12.47: 28 12.47 - 16.62: 3 16.62 - 20.78: 7 Bond angle restraints: 19760 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 139.87 119.09 20.78 1.00e+00 1.00e+00 4.32e+02 angle pdb=" PB ATP B 502 " pdb=" O3B ATP B 502 " pdb=" PG ATP B 502 " ideal model delta sigma weight residual 139.87 120.60 19.27 1.00e+00 1.00e+00 3.71e+02 angle pdb=" PB ATP E1601 " pdb=" O3B ATP E1601 " pdb=" PG ATP E1601 " ideal model delta sigma weight residual 139.87 121.14 18.73 1.00e+00 1.00e+00 3.51e+02 angle pdb=" PB ATP B 501 " pdb=" O3B ATP B 501 " pdb=" PG ATP B 501 " ideal model delta sigma weight residual 139.87 122.38 17.49 1.00e+00 1.00e+00 3.06e+02 angle pdb=" PB ATP A 501 " pdb=" O3B ATP A 501 " pdb=" PG ATP A 501 " ideal model delta sigma weight residual 139.87 122.73 17.14 1.00e+00 1.00e+00 2.94e+02 ... (remaining 19755 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.45: 8282 23.45 - 46.90: 65 46.90 - 70.35: 27 70.35 - 93.80: 5 93.80 - 117.24: 3 Dihedral angle restraints: 8382 sinusoidal: 241 harmonic: 8141 Sorted by residual: dihedral pdb=" CA LEU E1325 " pdb=" C LEU E1325 " pdb=" N LYS E1326 " pdb=" CA LYS E1326 " ideal model delta harmonic sigma weight residual 180.00 155.84 24.16 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CA VAL E1298 " pdb=" C VAL E1298 " pdb=" N PRO E1299 " pdb=" CA PRO E1299 " ideal model delta harmonic sigma weight residual 180.00 -155.96 -24.04 0 5.00e+00 4.00e-02 2.31e+01 dihedral pdb=" CA VAL E1496 " pdb=" C VAL E1496 " pdb=" N VAL E1497 " pdb=" CA VAL E1497 " ideal model delta harmonic sigma weight residual 180.00 158.58 21.42 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 8379 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.381: 2695 0.381 - 0.762: 1 0.762 - 1.143: 0 1.143 - 1.524: 0 1.524 - 1.905: 1 Chirality restraints: 2697 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 -0.49 -1.91 2.00e-01 2.50e+01 9.07e+01 chirality pdb=" CA CYS E 263 " pdb=" N CYS E 263 " pdb=" C CYS E 263 " pdb=" CB CYS E 263 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.18e+00 chirality pdb=" CA VAL A 241 " pdb=" N VAL A 241 " pdb=" C VAL A 241 " pdb=" CB VAL A 241 " both_signs ideal model delta sigma weight residual False 2.44 2.82 -0.38 2.00e-01 2.50e+01 3.54e+00 ... (remaining 2694 not shown) Planarity restraints: 2825 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN E 9 " 0.052 2.00e-02 2.50e+03 7.86e-02 7.72e+01 pdb=" CG ASN E 9 " -0.026 2.00e-02 2.50e+03 pdb=" OD1 ASN E 9 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN E 9 " -0.132 2.00e-02 2.50e+03 pdb=" C1 NAG N 1 " 0.100 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 104 " 0.028 2.00e-02 2.50e+03 5.70e-02 3.25e+01 pdb=" C TYR C 104 " -0.099 2.00e-02 2.50e+03 pdb=" O TYR C 104 " 0.036 2.00e-02 2.50e+03 pdb=" N MET C 105 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 581 " -0.027 2.00e-02 2.50e+03 5.24e-02 2.75e+01 pdb=" C PRO E 581 " 0.091 2.00e-02 2.50e+03 pdb=" O PRO E 581 " -0.032 2.00e-02 2.50e+03 pdb=" N LEU E 582 " -0.031 2.00e-02 2.50e+03 ... (remaining 2822 not shown) Histogram of nonbonded interaction distances: 1.48 - 2.16: 4 2.16 - 2.85: 5605 2.85 - 3.53: 19564 3.53 - 4.22: 23383 4.22 - 4.90: 39819 Nonbonded interactions: 88375 Sorted by model distance: nonbonded pdb=" CD PRO E1392 " pdb=" CB ARG E1450 " model vdw 1.477 3.840 nonbonded pdb=" O GLY E1397 " pdb=" O THR E1437 " model vdw 1.985 3.040 nonbonded pdb=" ND2 ASN E 9 " pdb=" N2 NAG N 1 " model vdw 2.004 2.560 nonbonded pdb=" CG PRO E1392 " pdb=" CB ARG E1450 " model vdw 2.150 3.840 nonbonded pdb=" N ARG B 195 " pdb=" O2A ATP B 501 " model vdw 2.228 3.120 ... (remaining 88370 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 366) selection = (chain 'B' 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)) selection = (chain 'C' and resid 30 through 366) selection = (chain 'D' and resid 30 through 366) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.110 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.190 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 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 : 0.009 0.394 14172 Z= 0.644 Angle : 1.223 54.326 19766 Z= 0.829 Chirality : 0.073 1.905 2697 Planarity : 0.005 0.057 2824 Dihedral : 10.540 117.245 3050 Min Nonbonded Distance : 1.477 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % 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: -1.16 (0.16), residues: 2800 helix: 0.86 (0.15), residues: 1291 sheet: -0.22 (0.35), residues: 210 loop : -2.70 (0.16), residues: 1299 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 12 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00754 (14169) covalent geometry : angle 1.11436 (19760) hydrogen bonds : bond 0.15321 ( 1056) hydrogen bonds : angle 6.27012 ( 3054) Misc. bond : bond 0.39353 ( 1) link_BETA1-4 : bond 0.00441 ( 1) link_BETA1-4 : angle 2.02792 ( 3) link_NAG-ASN : bond 0.36914 ( 1) link_NAG-ASN : angle 40.90356 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.480 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0542 time to fit residues: 8.5246 Evaluate side-chains 78 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 197 optimal weight: 50.0000 chunk 215 optimal weight: 40.0000 chunk 20 optimal weight: 0.5980 chunk 132 optimal weight: 30.0000 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 40.0000 chunk 207 optimal weight: 30.0000 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 50.0000 chunk 111 optimal weight: 20.0000 overall best weight: 9.7192 ------------------------------------------------------------------------------- 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 = 0.4390 r_free = 0.4390 target = 0.238049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.233251 restraints weight = 21671.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.223063 restraints weight = 36506.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.219814 restraints weight = 47281.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.219903 restraints weight = 48035.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.220057 restraints weight = 38285.806| |-----------------------------------------------------------------------------| r_work (final): 0.4150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 14172 Z= 0.233 Angle : 0.648 12.025 19766 Z= 0.394 Chirality : 0.049 0.214 2697 Planarity : 0.004 0.034 2824 Dihedral : 9.880 82.238 3039 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 1.02 Ramachandran Plot: Outliers : 0.04 % Allowed : 9.82 % Favored : 90.14 % 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: -1.15 (0.16), residues: 2800 helix: 0.94 (0.14), residues: 1281 sheet: -0.45 (0.34), residues: 228 loop : -2.73 (0.16), residues: 1291 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 12 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00354 (14169) covalent geometry : angle 0.64043 (19760) hydrogen bonds : bond 0.06308 ( 1056) hydrogen bonds : angle 5.29867 ( 3054) Misc. bond : bond 0.00383 ( 1) link_BETA1-4 : bond 0.00169 ( 1) link_BETA1-4 : angle 2.54062 ( 3) link_NAG-ASN : bond 0.00937 ( 1) link_NAG-ASN : angle 7.68066 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.344 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.0600 time to fit residues: 9.2635 Evaluate side-chains 78 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 230 optimal weight: 40.0000 chunk 241 optimal weight: 20.0000 chunk 203 optimal weight: 20.0000 chunk 67 optimal weight: 30.0000 chunk 208 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 275 optimal weight: 50.0000 chunk 184 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 overall best weight: 9.9792 ------------------------------------------------------------------------------- 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 = 0.4329 r_free = 0.4329 target = 0.231131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.228499 restraints weight = 21903.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.215788 restraints weight = 50962.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.212773 restraints weight = 66383.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.212726 restraints weight = 55404.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.212539 restraints weight = 49011.254| |-----------------------------------------------------------------------------| r_work (final): 0.4088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 14172 Z= 0.229 Angle : 0.622 11.648 19766 Z= 0.383 Chirality : 0.048 0.233 2697 Planarity : 0.003 0.023 2824 Dihedral : 9.815 87.825 3039 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 0.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % 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: -1.42 (0.16), residues: 2800 helix: 0.67 (0.14), residues: 1288 sheet: -0.59 (0.38), residues: 176 loop : -2.77 (0.16), residues: 1336 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 12 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00339 (14169) covalent geometry : angle 0.61869 (19760) hydrogen bonds : bond 0.06484 ( 1056) hydrogen bonds : angle 5.34626 ( 3054) Misc. bond : bond 0.00043 ( 1) link_BETA1-4 : bond 0.00679 ( 1) link_BETA1-4 : angle 3.78311 ( 3) link_NAG-ASN : bond 0.01681 ( 1) link_NAG-ASN : angle 3.94725 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.628 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0604 time to fit residues: 9.7465 Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 107 optimal weight: 7.9990 chunk 105 optimal weight: 5.9990 chunk 166 optimal weight: 7.9990 chunk 263 optimal weight: 50.0000 chunk 256 optimal weight: 50.0000 chunk 148 optimal weight: 7.9990 chunk 216 optimal weight: 30.0000 chunk 192 optimal weight: 30.0000 chunk 251 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.4316 r_free = 0.4316 target = 0.229673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.225273 restraints weight = 21535.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.223312 restraints weight = 36478.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.211641 restraints weight = 42730.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.4126 r_free = 0.4126 target = 0.208796 restraints weight = 53813.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.208853 restraints weight = 46460.864| |-----------------------------------------------------------------------------| r_work (final): 0.4065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14172 Z= 0.175 Angle : 0.566 15.518 19766 Z= 0.330 Chirality : 0.048 0.435 2697 Planarity : 0.002 0.018 2824 Dihedral : 9.590 87.285 3039 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 0.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.43 % Favored : 90.57 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % 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: -1.09 (0.16), residues: 2800 helix: 1.12 (0.15), residues: 1297 sheet: -0.83 (0.36), residues: 190 loop : -2.78 (0.16), residues: 1313 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 12 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00258 (14169) covalent geometry : angle 0.54165 (19760) hydrogen bonds : bond 0.05407 ( 1056) hydrogen bonds : angle 4.78325 ( 3054) Misc. bond : bond 0.00088 ( 1) link_BETA1-4 : bond 0.00568 ( 1) link_BETA1-4 : angle 6.08971 ( 3) link_NAG-ASN : bond 0.02462 ( 1) link_NAG-ASN : angle 12.02000 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.423 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0598 time to fit residues: 9.4733 Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 194 optimal weight: 40.0000 chunk 154 optimal weight: 20.0000 chunk 218 optimal weight: 50.0000 chunk 173 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 208 optimal weight: 20.0000 chunk 170 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 101 optimal weight: 1.9990 chunk 164 optimal weight: 20.0000 chunk 88 optimal weight: 7.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- 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 = 0.4361 r_free = 0.4361 target = 0.233689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.229084 restraints weight = 23881.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.226738 restraints weight = 39595.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.4269 r_free = 0.4269 target = 0.223431 restraints weight = 46961.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.209007 restraints weight = 66132.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.208544 restraints weight = 60488.962| |-----------------------------------------------------------------------------| r_work (final): 0.4056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.2838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14172 Z= 0.172 Angle : 0.542 12.441 19766 Z= 0.323 Chirality : 0.047 0.355 2697 Planarity : 0.003 0.018 2824 Dihedral : 9.498 87.983 3039 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 0.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 0.00 % Allowed : 25.00 % Favored : 75.00 % 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: -1.08 (0.16), residues: 2800 helix: 1.15 (0.15), residues: 1301 sheet: -1.05 (0.37), residues: 190 loop : -2.77 (0.16), residues: 1309 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 12 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00250 (14169) covalent geometry : angle 0.52722 (19760) hydrogen bonds : bond 0.05408 ( 1056) hydrogen bonds : angle 4.74908 ( 3054) Misc. bond : bond 0.00070 ( 1) link_BETA1-4 : bond 0.00874 ( 1) link_BETA1-4 : angle 6.16098 ( 3) link_NAG-ASN : bond 0.00122 ( 1) link_NAG-ASN : angle 8.19503 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.379 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0551 time to fit residues: 8.7930 Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 202 optimal weight: 50.0000 chunk 185 optimal weight: 10.0000 chunk 89 optimal weight: 40.0000 chunk 197 optimal weight: 50.0000 chunk 51 optimal weight: 7.9990 chunk 87 optimal weight: 20.0000 chunk 191 optimal weight: 6.9990 chunk 104 optimal weight: 50.0000 chunk 32 optimal weight: 9.9990 chunk 200 optimal weight: 50.0000 chunk 218 optimal weight: 50.0000 overall best weight: 10.9994 ------------------------------------------------------------------------------- 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 = 0.4321 r_free = 0.4321 target = 0.228885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.223274 restraints weight = 24040.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4094 r_free = 0.4094 target = 0.204566 restraints weight = 47790.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.201943 restraints weight = 51584.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.202216 restraints weight = 52880.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.202689 restraints weight = 39943.239| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6953 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 14172 Z= 0.242 Angle : 0.656 14.834 19766 Z= 0.399 Chirality : 0.051 0.584 2697 Planarity : 0.003 0.020 2824 Dihedral : 9.776 88.910 3039 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 1.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.29 % Favored : 87.71 % 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: -1.80 (0.15), residues: 2800 helix: 0.43 (0.14), residues: 1296 sheet: -1.26 (0.38), residues: 180 loop : -3.00 (0.15), residues: 1324 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 12 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00355 (14169) covalent geometry : angle 0.63904 (19760) hydrogen bonds : bond 0.06548 ( 1056) hydrogen bonds : angle 5.52628 ( 3054) Misc. bond : bond 0.00115 ( 1) link_BETA1-4 : bond 0.00223 ( 1) link_BETA1-4 : angle 5.76165 ( 3) link_NAG-ASN : bond 0.02207 ( 1) link_NAG-ASN : angle 10.75850 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.465 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0579 time to fit residues: 9.1741 Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 176 optimal weight: 20.0000 chunk 8 optimal weight: 40.0000 chunk 127 optimal weight: 30.0000 chunk 276 optimal weight: 30.0000 chunk 42 optimal weight: 20.0000 chunk 214 optimal weight: 50.0000 chunk 40 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 chunk 122 optimal weight: 50.0000 chunk 78 optimal weight: 6.9990 chunk 125 optimal weight: 0.0570 overall best weight: 11.4110 ------------------------------------------------------------------------------- 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 = 0.4311 r_free = 0.4311 target = 0.227816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.223317 restraints weight = 23973.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.221090 restraints weight = 35335.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.4099 r_free = 0.4099 target = 0.205231 restraints weight = 53163.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.203713 restraints weight = 60735.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.203831 restraints weight = 48723.559| |-----------------------------------------------------------------------------| r_work (final): 0.4043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6926 moved from start: 0.3451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 14172 Z= 0.249 Angle : 0.652 12.443 19766 Z= 0.401 Chirality : 0.050 0.460 2697 Planarity : 0.003 0.022 2824 Dihedral : 9.842 88.447 3039 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % 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: -2.06 (0.15), residues: 2800 helix: 0.29 (0.14), residues: 1280 sheet: -1.54 (0.38), residues: 180 loop : -3.15 (0.15), residues: 1340 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 12 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00363 (14169) covalent geometry : angle 0.63917 (19760) hydrogen bonds : bond 0.06545 ( 1056) hydrogen bonds : angle 5.62886 ( 3054) Misc. bond : bond 0.00112 ( 1) link_BETA1-4 : bond 0.00322 ( 1) link_BETA1-4 : angle 6.34427 ( 3) link_NAG-ASN : bond 0.01032 ( 1) link_NAG-ASN : angle 8.39042 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.470 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0543 time to fit residues: 8.6271 Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 27 optimal weight: 0.0270 chunk 134 optimal weight: 30.0000 chunk 217 optimal weight: 20.0000 chunk 141 optimal weight: 0.2980 chunk 234 optimal weight: 20.0000 chunk 102 optimal weight: 30.0000 chunk 209 optimal weight: 40.0000 chunk 231 optimal weight: 9.9990 chunk 194 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 163 optimal weight: 0.0670 overall best weight: 3.0780 ------------------------------------------------------------------------------- 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 = 0.4394 r_free = 0.4394 target = 0.237392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.222927 restraints weight = 23730.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.215051 restraints weight = 43641.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.212299 restraints weight = 31380.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.212663 restraints weight = 29499.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.213456 restraints weight = 22421.191| |-----------------------------------------------------------------------------| r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6771 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.028 14172 Z= 0.106 Angle : 0.454 9.746 19766 Z= 0.263 Chirality : 0.046 0.248 2697 Planarity : 0.002 0.015 2824 Dihedral : 8.792 88.053 3039 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 0.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % 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: -0.75 (0.17), residues: 2800 helix: 1.76 (0.15), residues: 1284 sheet: -1.51 (0.37), residues: 184 loop : -2.83 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 12 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00148 (14169) covalent geometry : angle 0.43853 (19760) hydrogen bonds : bond 0.04143 ( 1056) hydrogen bonds : angle 4.11008 ( 3054) Misc. bond : bond 0.00032 ( 1) link_BETA1-4 : bond 0.00329 ( 1) link_BETA1-4 : angle 6.10976 ( 3) link_NAG-ASN : bond 0.01056 ( 1) link_NAG-ASN : angle 7.26521 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.518 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0523 time to fit residues: 8.5124 Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 40 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 chunk 102 optimal weight: 50.0000 chunk 51 optimal weight: 40.0000 chunk 270 optimal weight: 50.0000 chunk 263 optimal weight: 0.0570 chunk 33 optimal weight: 40.0000 chunk 221 optimal weight: 40.0000 chunk 247 optimal weight: 20.0000 chunk 224 optimal weight: 50.0000 chunk 11 optimal weight: 0.9980 overall best weight: 10.4106 ------------------------------------------------------------------------------- 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 = 0.4322 r_free = 0.4322 target = 0.229210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.223998 restraints weight = 24013.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.205913 restraints weight = 55728.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.202858 restraints weight = 61893.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.202900 restraints weight = 54995.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.203503 restraints weight = 40327.039| |-----------------------------------------------------------------------------| r_work (final): 0.4027 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6933 moved from start: 0.3567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 14172 Z= 0.230 Angle : 0.608 10.566 19766 Z= 0.374 Chirality : 0.048 0.257 2697 Planarity : 0.003 0.022 2824 Dihedral : 9.417 87.887 3039 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 1.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.07 % Favored : 86.93 % 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 : 0.00 % 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: -1.59 (0.16), residues: 2800 helix: 0.84 (0.14), residues: 1279 sheet: -1.50 (0.38), residues: 180 loop : -3.07 (0.16), residues: 1341 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 12 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00336 (14169) covalent geometry : angle 0.59571 (19760) hydrogen bonds : bond 0.06137 ( 1056) hydrogen bonds : angle 5.25446 ( 3054) Misc. bond : bond 0.00115 ( 1) link_BETA1-4 : bond 0.00357 ( 1) link_BETA1-4 : angle 6.55607 ( 3) link_NAG-ASN : bond 0.00621 ( 1) link_NAG-ASN : angle 7.26787 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.307 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0575 time to fit residues: 8.9413 Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 28 optimal weight: 30.0000 chunk 93 optimal weight: 30.0000 chunk 236 optimal weight: 20.0000 chunk 55 optimal weight: 30.0000 chunk 22 optimal weight: 0.0270 chunk 224 optimal weight: 50.0000 chunk 115 optimal weight: 8.9990 chunk 103 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 overall best weight: 7.0050 ------------------------------------------------------------------------------- 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 = 0.4349 r_free = 0.4349 target = 0.232197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.224065 restraints weight = 23954.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.209550 restraints weight = 51074.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.205583 restraints weight = 56333.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.206497 restraints weight = 54695.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.207011 restraints weight = 39371.229| |-----------------------------------------------------------------------------| r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6872 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 14172 Z= 0.166 Angle : 0.526 10.213 19766 Z= 0.317 Chirality : 0.047 0.243 2697 Planarity : 0.002 0.018 2824 Dihedral : 9.172 88.328 3039 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.86 % Favored : 90.14 % 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: -1.29 (0.16), residues: 2800 helix: 1.21 (0.15), residues: 1271 sheet: -1.64 (0.38), residues: 180 loop : -2.98 (0.16), residues: 1349 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 12 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00242 (14169) covalent geometry : angle 0.51296 (19760) hydrogen bonds : bond 0.05299 ( 1056) hydrogen bonds : angle 4.78706 ( 3054) Misc. bond : bond 0.00045 ( 1) link_BETA1-4 : bond 0.00533 ( 1) link_BETA1-4 : angle 6.40919 ( 3) link_NAG-ASN : bond 0.00696 ( 1) link_NAG-ASN : angle 6.94444 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5600 Ramachandran restraints generated. 2800 Oldfield, 0 Emsley, 2800 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.493 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.0561 time to fit residues: 8.9654 Evaluate side-chains 79 residues out of total 2457 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 278 random chunks: chunk 96 optimal weight: 8.9990 chunk 277 optimal weight: 40.0000 chunk 26 optimal weight: 50.0000 chunk 215 optimal weight: 50.0000 chunk 255 optimal weight: 50.0000 chunk 166 optimal weight: 10.0000 chunk 51 optimal weight: 30.0000 chunk 27 optimal weight: 6.9990 chunk 170 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 1 optimal weight: 40.0000 overall best weight: 15.1996 ------------------------------------------------------------------------------- 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 = 0.4277 r_free = 0.4277 target = 0.224053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4233 r_free = 0.4233 target = 0.219240 restraints weight = 23999.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.201379 restraints weight = 56364.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.197869 restraints weight = 62242.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.197749 restraints weight = 55719.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.198695 restraints weight = 44548.774| |-----------------------------------------------------------------------------| r_work (final): 0.3985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7010 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 14172 Z= 0.319 Angle : 0.744 11.684 19766 Z= 0.469 Chirality : 0.051 0.292 2697 Planarity : 0.004 0.025 2824 Dihedral : 10.162 89.640 3039 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 1.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.14 % Favored : 83.86 % 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 : 0.04 % 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: -2.50 (0.15), residues: 2800 helix: -0.08 (0.14), residues: 1265 sheet: -1.82 (0.39), residues: 162 loop : -3.34 (0.15), residues: 1373 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.000 0.000 TYR A 12 PHE 0.000 0.000 PHE A 36 TRP 0.000 0.000 TRP A 69 Details of bonding type rmsd covalent geometry : bond 0.00465 (14169) covalent geometry : angle 0.73429 (19760) hydrogen bonds : bond 0.07523 ( 1056) hydrogen bonds : angle 6.25196 ( 3054) Misc. bond : bond 0.00127 ( 1) link_BETA1-4 : bond 0.00305 ( 1) link_BETA1-4 : angle 7.14720 ( 3) link_NAG-ASN : bond 0.00383 ( 1) link_NAG-ASN : angle 6.97979 ( 3) =============================================================================== Job complete usr+sys time: 1671.08 seconds wall clock time: 29 minutes 12.01 seconds (1752.01 seconds total)