Starting phenix.real_space_refine on Wed Jun 18 09:03:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ii2_60588/06_2025/9ii2_60588.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ii2_60588/06_2025/9ii2_60588.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ii2_60588/06_2025/9ii2_60588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ii2_60588/06_2025/9ii2_60588.map" model { file = "/net/cci-nas-00/data/ceres_data/9ii2_60588/06_2025/9ii2_60588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ii2_60588/06_2025/9ii2_60588.cif" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 sd= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 6 5.49 5 S 108 5.16 5 C 13604 2.51 5 N 3506 2.21 5 O 3888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 21112 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 347, 2638 Classifications: {'peptide': 347} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 27, 'TRANS': 319} Chain breaks: 3 Unresolved non-hydrogen bonds: 133 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 80 Chain: "B" Number of atoms: 6205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 805, 6205 Classifications: {'peptide': 805} Incomplete info: {'truncation_to_alanine': 49} Link IDs: {'PTRANS': 34, 'TRANS': 770} Chain breaks: 3 Unresolved non-hydrogen bonds: 188 Unresolved non-hydrogen angles: 236 Unresolved non-hydrogen dihedrals: 150 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 1, 'ASN:plan1': 7, 'TPO:plan-1': 1, 'ASP:plan': 8, 'GLU:plan': 1, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 117 Chain: "D" Number of atoms: 1592 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1592 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 117 Unresolved non-hydrogen angles: 143 Unresolved non-hydrogen dihedrals: 91 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 6, 'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 61 Chain: "E" 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: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Chain: "B" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 84 Unusual residues: {'CLR': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Restraints were copied for chains: S, R, F, C Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" C1 NAG E 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG E 2 " occ=0.60 residue: pdb=" C1 NAG F 2 " occ=0.60 ... (12 atoms not shown) pdb=" O7 NAG F 2 " occ=0.60 Time building chain proxies: 19.51, per 1000 atoms: 0.92 Number of scatterers: 21112 At special positions: 0 Unit cell: (131.13, 116.25, 245.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 108 16.00 P 6 15.00 O 3888 8.00 N 3506 7.00 C 13604 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 24 " - pdb=" SG CYS S 89 " distance=2.03 Simple disulfide: pdb=" SG CYS S1025 " - pdb=" SG CYS S1099 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG E 1 " - " ASN R 209 " " NAG F 1 " - " ASN B 209 " Time building additional restraints: 5.38 Conformation dependent library (CDL) restraints added in 2.9 seconds 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5180 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 34 sheets defined 31.5% alpha, 23.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.59 Creating SS restraints... Processing helix chain 'R' and resid 64 through 82 Processing helix chain 'R' and resid 101 through 114 Processing helix chain 'R' and resid 115 through 121 removed outlier: 3.689A pdb=" N LYS R 119 " --> pdb=" O ALA R 115 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL R 120 " --> pdb=" O SER R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 162 Processing helix chain 'R' and resid 175 through 179 removed outlier: 3.720A pdb=" N LEU R 178 " --> pdb=" O SER R 175 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 208 removed outlier: 4.136A pdb=" N GLN R 197 " --> pdb=" O PRO R 193 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N PHE R 208 " --> pdb=" O ILE R 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 221 through 237 removed outlier: 3.868A pdb=" N THR R 225 " --> pdb=" O ASP R 221 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 265 removed outlier: 3.999A pdb=" N TYR R 256 " --> pdb=" O ILE R 252 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 291 Processing helix chain 'R' and resid 306 through 313 removed outlier: 4.097A pdb=" N ILE R 310 " --> pdb=" O GLN R 306 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER R 313 " --> pdb=" O ILE R 309 " (cutoff:3.500A) Processing helix chain 'R' and resid 330 through 339 Processing helix chain 'R' and resid 350 through 360 Processing helix chain 'R' and resid 389 through 412 Processing helix chain 'R' and resid 419 through 424 removed outlier: 4.264A pdb=" N ILE R 424 " --> pdb=" O ASP R 420 " (cutoff:3.500A) Processing helix chain 'R' and resid 426 through 435 Processing helix chain 'R' and resid 494 through 497 Processing helix chain 'R' and resid 499 through 503 removed outlier: 3.619A pdb=" N SER R 503 " --> pdb=" O SER R 500 " (cutoff:3.500A) Processing helix chain 'R' and resid 577 through 601 Processing helix chain 'R' and resid 604 through 611 Processing helix chain 'R' and resid 611 through 633 removed outlier: 4.534A pdb=" N PHE R 630 " --> pdb=" O TYR R 626 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE R 631 " --> pdb=" O CYS R 627 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE R 632 " --> pdb=" O MET R 628 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE R 633 " --> pdb=" O THR R 629 " (cutoff:3.500A) Processing helix chain 'R' and resid 637 through 672 removed outlier: 3.653A pdb=" N GLY R 672 " --> pdb=" O ARG R 668 " (cutoff:3.500A) Processing helix chain 'R' and resid 686 through 710 removed outlier: 3.792A pdb=" N TRP R 706 " --> pdb=" O MET R 702 " (cutoff:3.500A) Processing helix chain 'R' and resid 733 through 758 removed outlier: 4.593A pdb=" N TYR R 743 " --> pdb=" O ILE R 739 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP R 744 " --> pdb=" O SER R 740 " (cutoff:3.500A) Processing helix chain 'R' and resid 762 through 792 removed outlier: 6.327A pdb=" N ALA R 768 " --> pdb=" O ASN R 764 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS R 769 " --> pdb=" O PHE R 765 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE R 770 " --> pdb=" O ASN R 766 " (cutoff:3.500A) Proline residue: R 787 - end of helix Processing helix chain 'R' and resid 795 through 828 removed outlier: 3.546A pdb=" N VAL R 807 " --> pdb=" O MET R 803 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU R 818 " --> pdb=" O VAL R 814 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA R 820 " --> pdb=" O GLY R 816 " (cutoff:3.500A) Proline residue: R 821 - end of helix Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'A' and resid 243 through 246 removed outlier: 3.580A pdb=" N THR A 246 " --> pdb=" O LEU A 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 243 through 246' Processing helix chain 'S' and resid 1031 through 1033 No H-bonds generated for 'chain 'S' and resid 1031 through 1033' Processing helix chain 'B' and resid 64 through 82 Processing helix chain 'B' and resid 101 through 114 Processing helix chain 'B' and resid 115 through 121 removed outlier: 3.690A pdb=" N LYS B 119 " --> pdb=" O ALA B 115 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 120 " --> pdb=" O SER B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 162 Processing helix chain 'B' and resid 175 through 179 removed outlier: 3.719A pdb=" N LEU B 178 " --> pdb=" O SER B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 208 removed outlier: 4.136A pdb=" N GLN B 197 " --> pdb=" O PRO B 193 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N PHE B 208 " --> pdb=" O ILE B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.869A pdb=" N THR B 225 " --> pdb=" O ASP B 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 252 through 265 removed outlier: 3.999A pdb=" N TYR B 256 " --> pdb=" O ILE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 291 Processing helix chain 'B' and resid 306 through 313 removed outlier: 4.096A pdb=" N ILE B 310 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER B 313 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 339 Processing helix chain 'B' and resid 350 through 360 Processing helix chain 'B' and resid 389 through 412 Processing helix chain 'B' and resid 419 through 424 removed outlier: 4.264A pdb=" N ILE B 424 " --> pdb=" O ASP B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 426 through 435 Processing helix chain 'B' and resid 494 through 497 Processing helix chain 'B' and resid 499 through 503 removed outlier: 3.619A pdb=" N SER B 503 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 601 Processing helix chain 'B' and resid 604 through 611 Processing helix chain 'B' and resid 611 through 633 removed outlier: 4.534A pdb=" N PHE B 630 " --> pdb=" O TYR B 626 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N PHE B 631 " --> pdb=" O CYS B 627 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N PHE B 632 " --> pdb=" O MET B 628 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ILE B 633 " --> pdb=" O THR B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 637 through 672 removed outlier: 3.653A pdb=" N GLY B 672 " --> pdb=" O ARG B 668 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 710 removed outlier: 3.792A pdb=" N TRP B 706 " --> pdb=" O MET B 702 " (cutoff:3.500A) Processing helix chain 'B' and resid 733 through 758 removed outlier: 4.593A pdb=" N TYR B 743 " --> pdb=" O ILE B 739 " (cutoff:3.500A) removed outlier: 4.660A pdb=" N ASP B 744 " --> pdb=" O SER B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 792 removed outlier: 6.328A pdb=" N ALA B 768 " --> pdb=" O ASN B 764 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LYS B 769 " --> pdb=" O PHE B 765 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N PHE B 770 " --> pdb=" O ASN B 766 " (cutoff:3.500A) Proline residue: B 787 - end of helix Processing helix chain 'B' and resid 795 through 828 removed outlier: 3.546A pdb=" N VAL B 807 " --> pdb=" O MET B 803 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU B 818 " --> pdb=" O VAL B 814 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N ALA B 820 " --> pdb=" O GLY B 816 " (cutoff:3.500A) Proline residue: B 821 - end of helix Processing helix chain 'C' and resid 65 through 72 Processing helix chain 'C' and resid 98 through 109 Processing helix chain 'C' and resid 243 through 246 removed outlier: 3.580A pdb=" N THR C 246 " --> pdb=" O LEU C 243 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 243 through 246' Processing helix chain 'D' and resid 1031 through 1033 No H-bonds generated for 'chain 'D' and resid 1031 through 1033' Processing sheet with id=AA1, first strand: chain 'R' and resid 33 through 34 removed outlier: 6.886A pdb=" N LEU R 39 " --> pdb=" O GLY R 92 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS R 94 " --> pdb=" O LEU R 39 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU R 41 " --> pdb=" O HIS R 94 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU R 96 " --> pdb=" O LEU R 41 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY R 43 " --> pdb=" O LEU R 96 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL R 40 " --> pdb=" O GLY R 144 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE R 146 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 5.519A pdb=" N GLY R 42 " --> pdb=" O ILE R 146 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N ILE R 169 " --> pdb=" O ALA R 143 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL R 145 " --> pdb=" O ILE R 169 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 240 through 247 removed outlier: 7.736A pdb=" N VAL R 213 " --> pdb=" O ALA R 242 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA R 244 " --> pdb=" O VAL R 213 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR R 215 " --> pdb=" O ALA R 244 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N LYS R 246 " --> pdb=" O THR R 215 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA R 217 " --> pdb=" O LYS R 246 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL R 271 " --> pdb=" O TYR R 212 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL R 216 " --> pdb=" O VAL R 273 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N VAL R 272 " --> pdb=" O VAL R 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 321 through 325 removed outlier: 6.815A pdb=" N TYR R 466 " --> pdb=" O HIS R 485 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS R 485 " --> pdb=" O TYR R 466 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N VAL R 468 " --> pdb=" O VAL R 483 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU R 481 " --> pdb=" O ASN R 470 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'R' and resid 439 through 441 removed outlier: 3.597A pdb=" N PHE R 440 " --> pdb=" O VAL R 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'R' and resid 538 through 539 Processing sheet with id=AA6, first strand: chain 'R' and resid 553 through 555 Processing sheet with id=AA7, first strand: chain 'R' and resid 567 through 568 Processing sheet with id=AA8, first strand: chain 'R' and resid 857 through 862 removed outlier: 3.813A pdb=" N THR A 6 " --> pdb=" O VAL R 862 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 75 through 85 removed outlier: 6.667A pdb=" N VAL A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR A 144 " --> pdb=" O ILE A 168 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 75 through 85 removed outlier: 6.667A pdb=" N VAL A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU A 140 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 183 through 189 Processing sheet with id=AB3, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.824A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA A 254 " --> pdb=" O VAL A 235 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN A 237 " --> pdb=" O PRO A 252 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA A 239 " --> pdb=" O LYS A 250 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS A 250 " --> pdb=" O ALA A 239 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 6 through 8 Processing sheet with id=AB5, first strand: chain 'S' and resid 11 through 13 removed outlier: 7.301A pdb=" N VAL S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TYR S 50 " --> pdb=" O VAL S 34 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP S 36 " --> pdb=" O LEU S 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'S' and resid 1007 through 1010 Processing sheet with id=AB7, first strand: chain 'S' and resid 1013 through 1014 removed outlier: 6.212A pdb=" N GLY S1013 " --> pdb=" O THR S1120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'S' and resid 1060 through 1063 removed outlier: 5.237A pdb=" N TRP S1050 " --> pdb=" O ARG S1041 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ARG S1041 " --> pdb=" O TRP S1050 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 33 through 34 removed outlier: 6.887A pdb=" N LEU B 39 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N HIS B 94 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N LEU B 41 " --> pdb=" O HIS B 94 " (cutoff:3.500A) removed outlier: 7.693A pdb=" N LEU B 96 " --> pdb=" O LEU B 41 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLY B 43 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VAL B 40 " --> pdb=" O GLY B 144 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N ILE B 146 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N GLY B 42 " --> pdb=" O ILE B 146 " (cutoff:3.500A) removed outlier: 8.887A pdb=" N ILE B 169 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 145 " --> pdb=" O ILE B 169 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 240 through 247 removed outlier: 7.736A pdb=" N VAL B 213 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ALA B 244 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N THR B 215 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS B 246 " --> pdb=" O THR B 215 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ALA B 217 " --> pdb=" O LYS B 246 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N VAL B 271 " --> pdb=" O TYR B 212 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL B 216 " --> pdb=" O VAL B 273 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL B 272 " --> pdb=" O VAL B 298 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 321 through 325 removed outlier: 6.815A pdb=" N TYR B 466 " --> pdb=" O HIS B 485 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N HIS B 485 " --> pdb=" O TYR B 466 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL B 468 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LEU B 481 " --> pdb=" O ASN B 470 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 439 through 441 removed outlier: 3.597A pdb=" N PHE B 440 " --> pdb=" O VAL B 454 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 538 through 539 Processing sheet with id=AC5, first strand: chain 'B' and resid 553 through 555 Processing sheet with id=AC6, first strand: chain 'B' and resid 567 through 568 Processing sheet with id=AC7, first strand: chain 'B' and resid 857 through 862 removed outlier: 3.814A pdb=" N THR C 6 " --> pdb=" O VAL B 862 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 75 through 85 removed outlier: 6.668A pdb=" N VAL C 59 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL C 81 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 57 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN C 83 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 55 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N TYR C 144 " --> pdb=" O ILE C 168 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 75 through 85 removed outlier: 6.668A pdb=" N VAL C 59 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N VAL C 81 " --> pdb=" O LEU C 57 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N LEU C 57 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ASN C 83 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL C 55 " --> pdb=" O ASN C 83 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N LEU C 140 " --> pdb=" O LEU C 129 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 183 through 189 Processing sheet with id=AD2, first strand: chain 'C' and resid 207 through 208 removed outlier: 3.824A pdb=" N TYR C 321 " --> pdb=" O PHE C 349 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N LEU C 351 " --> pdb=" O VAL C 319 " (cutoff:3.500A) removed outlier: 9.332A pdb=" N VAL C 319 " --> pdb=" O LEU C 351 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ALA C 254 " --> pdb=" O VAL C 235 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N GLN C 237 " --> pdb=" O PRO C 252 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ALA C 239 " --> pdb=" O LYS C 250 " (cutoff:3.500A) removed outlier: 6.151A pdb=" N LYS C 250 " --> pdb=" O ALA C 239 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'D' and resid 6 through 8 Processing sheet with id=AD4, first strand: chain 'D' and resid 11 through 13 removed outlier: 7.301A pdb=" N VAL D 34 " --> pdb=" O TYR D 50 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N TYR D 50 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N TRP D 36 " --> pdb=" O LEU D 48 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 1007 through 1010 Processing sheet with id=AD6, first strand: chain 'D' and resid 1013 through 1014 removed outlier: 6.212A pdb=" N GLY D1013 " --> pdb=" O THR D1120 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 1060 through 1063 removed outlier: 5.236A pdb=" N TRP D1050 " --> pdb=" O ARG D1041 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ARG D1041 " --> pdb=" O TRP D1050 " (cutoff:3.500A) 972 hydrogen bonds defined for protein. 2754 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: 7.65 Time building geometry restraints manager: 6.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 3370 1.31 - 1.44: 5824 1.44 - 1.57: 12250 1.57 - 1.70: 22 1.70 - 1.82: 146 Bond restraints: 21612 Sorted by residual: bond pdb=" C7 NAG E 2 " pdb=" N2 NAG E 2 " ideal model delta sigma weight residual 1.346 1.467 -0.121 2.00e-02 2.50e+03 3.68e+01 bond pdb=" C7 NAG E 1 " pdb=" N2 NAG E 1 " ideal model delta sigma weight residual 1.346 1.467 -0.121 2.00e-02 2.50e+03 3.67e+01 bond pdb=" C7 NAG F 1 " pdb=" N2 NAG F 1 " ideal model delta sigma weight residual 1.346 1.467 -0.121 2.00e-02 2.50e+03 3.64e+01 bond pdb=" C7 NAG F 2 " pdb=" N2 NAG F 2 " ideal model delta sigma weight residual 1.346 1.467 -0.121 2.00e-02 2.50e+03 3.63e+01 bond pdb=" OG1 TPO R 860 " pdb=" P TPO R 860 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.95e+01 ... (remaining 21607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.53: 29266 2.53 - 5.07: 188 5.07 - 7.60: 12 7.60 - 10.13: 4 10.13 - 12.67: 2 Bond angle restraints: 29472 Sorted by residual: angle pdb=" CB TPO B 860 " pdb=" OG1 TPO B 860 " pdb=" P TPO B 860 " ideal model delta sigma weight residual 119.31 106.64 12.67 3.00e+00 1.11e-01 1.78e+01 angle pdb=" CB TPO R 860 " pdb=" OG1 TPO R 860 " pdb=" P TPO R 860 " ideal model delta sigma weight residual 119.31 106.72 12.59 3.00e+00 1.11e-01 1.76e+01 angle pdb=" OG1 TPO B 860 " pdb=" P TPO B 860 " pdb=" O1P TPO B 860 " ideal model delta sigma weight residual 100.43 109.48 -9.05 3.00e+00 1.11e-01 9.09e+00 angle pdb=" OG1 TPO R 860 " pdb=" P TPO R 860 " pdb=" O1P TPO R 860 " ideal model delta sigma weight residual 100.43 109.47 -9.04 3.00e+00 1.11e-01 9.09e+00 angle pdb=" CA LEU R 747 " pdb=" CB LEU R 747 " pdb=" CG LEU R 747 " ideal model delta sigma weight residual 116.30 125.95 -9.65 3.50e+00 8.16e-02 7.61e+00 ... (remaining 29467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 12036 17.89 - 35.78: 964 35.78 - 53.67: 138 53.67 - 71.56: 14 71.56 - 89.46: 14 Dihedral angle restraints: 13166 sinusoidal: 5128 harmonic: 8038 Sorted by residual: dihedral pdb=" CG ARG S 67 " pdb=" CD ARG S 67 " pdb=" NE ARG S 67 " pdb=" CZ ARG S 67 " ideal model delta sinusoidal sigma weight residual -180.00 -135.18 -44.82 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CG ARG D 67 " pdb=" CD ARG D 67 " pdb=" NE ARG D 67 " pdb=" CZ ARG D 67 " ideal model delta sinusoidal sigma weight residual -180.00 -135.18 -44.82 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CA VAL A 365 " pdb=" C VAL A 365 " pdb=" N PRO A 366 " pdb=" CA PRO A 366 " ideal model delta harmonic sigma weight residual 180.00 164.38 15.62 0 5.00e+00 4.00e-02 9.75e+00 ... (remaining 13163 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2239 0.032 - 0.064: 731 0.064 - 0.096: 252 0.096 - 0.128: 163 0.128 - 0.160: 17 Chirality restraints: 3402 Sorted by residual: chirality pdb=" CB ILE R 379 " pdb=" CA ILE R 379 " pdb=" CG1 ILE R 379 " pdb=" CG2 ILE R 379 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CB ILE B 379 " pdb=" CA ILE B 379 " pdb=" CG1 ILE B 379 " pdb=" CG2 ILE B 379 " both_signs ideal model delta sigma weight residual False 2.64 2.80 -0.16 2.00e-01 2.50e+01 6.12e-01 chirality pdb=" CA VAL C 59 " pdb=" N VAL C 59 " pdb=" C VAL C 59 " pdb=" CB VAL C 59 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.00e-01 ... (remaining 3399 not shown) Planarity restraints: 3708 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 88 " 0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO C 89 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 89 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO C 89 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 88 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 89 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 89 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 89 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 359 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO A 360 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 360 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 360 " 0.026 5.00e-02 4.00e+02 ... (remaining 3705 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 202 2.60 - 3.18: 17342 3.18 - 3.75: 32592 3.75 - 4.33: 43561 4.33 - 4.90: 74194 Nonbonded interactions: 167891 Sorted by model distance: nonbonded pdb=" SG CYS R 509 " pdb=" SG CYS R 528 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B 509 " pdb=" SG CYS B 528 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS R 549 " pdb=" SG CYS R 562 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS R 412 " pdb=" SG CYS R 419 " model vdw 2.030 3.760 nonbonded pdb=" SG CYS B 412 " pdb=" SG CYS B 419 " model vdw 2.030 3.760 ... (remaining 167886 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: 0.10 Found NCS groups: ncs_group { reference = chain 'D' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'A' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.320 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: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 54.930 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.121 21618 Z= 0.185 Angle : 0.514 12.668 29488 Z= 0.254 Chirality : 0.042 0.160 3402 Planarity : 0.003 0.051 3706 Dihedral : 12.872 89.455 7980 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.17), residues: 2696 helix: 2.09 (0.19), residues: 764 sheet: 0.84 (0.21), residues: 672 loop : -0.75 (0.17), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 355 HIS 0.002 0.000 HIS B 405 PHE 0.012 0.001 PHE R 275 TYR 0.006 0.001 TYR B 656 ARG 0.002 0.000 ARG B 68 Details of bonding type rmsd link_NAG-ASN : bond 0.00014 ( 2) link_NAG-ASN : angle 0.85214 ( 6) link_BETA1-4 : bond 0.00433 ( 2) link_BETA1-4 : angle 0.94815 ( 6) hydrogen bonds : bond 0.10607 ( 942) hydrogen bonds : angle 5.40727 ( 2754) SS BOND : bond 0.00112 ( 2) SS BOND : angle 0.27246 ( 4) covalent geometry : bond 0.00370 (21612) covalent geometry : angle 0.51416 (29472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 2.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 355 TRP cc_start: 0.8322 (t-100) cc_final: 0.7779 (t-100) REVERT: R 491 SER cc_start: 0.7669 (m) cc_final: 0.7241 (p) REVERT: R 748 VAL cc_start: 0.8546 (t) cc_final: 0.8345 (p) REVERT: R 813 VAL cc_start: 0.8120 (t) cc_final: 0.7638 (t) REVERT: A 143 ASP cc_start: 0.6045 (p0) cc_final: 0.5527 (p0) REVERT: A 273 THR cc_start: 0.6579 (m) cc_final: 0.6373 (p) REVERT: A 281 ASN cc_start: 0.7525 (m110) cc_final: 0.6904 (m-40) REVERT: S 1113 TRP cc_start: 0.7704 (m100) cc_final: 0.7021 (m100) REVERT: B 355 TRP cc_start: 0.8313 (t-100) cc_final: 0.7775 (t-100) REVERT: B 491 SER cc_start: 0.7659 (m) cc_final: 0.7229 (p) REVERT: B 748 VAL cc_start: 0.8537 (t) cc_final: 0.8331 (p) REVERT: B 813 VAL cc_start: 0.8116 (t) cc_final: 0.7632 (t) REVERT: C 143 ASP cc_start: 0.6044 (p0) cc_final: 0.5523 (p0) REVERT: C 273 THR cc_start: 0.6566 (m) cc_final: 0.6358 (p) REVERT: C 281 ASN cc_start: 0.7520 (m110) cc_final: 0.6889 (m-40) REVERT: D 1113 TRP cc_start: 0.7709 (m100) cc_final: 0.7003 (m100) outliers start: 0 outliers final: 0 residues processed: 583 average time/residue: 0.4044 time to fit residues: 349.7427 Evaluate side-chains 343 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 343 time to evaluate : 2.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 229 optimal weight: 0.8980 chunk 206 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 139 optimal weight: 2.9990 chunk 110 optimal weight: 5.9990 chunk 213 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 129 optimal weight: 3.9990 chunk 158 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 159 ASN R 292 ASN R 344 ASN R 472 GLN A 85 GLN A 111 HIS ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S1104 GLN B 159 ASN B 292 ASN B 344 ASN B 383 ASN B 472 GLN C 85 GLN C 111 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 299 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D1104 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.129844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.110634 restraints weight = 47724.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.110731 restraints weight = 59179.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.109898 restraints weight = 40430.735| |-----------------------------------------------------------------------------| r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3715 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3715 r_free = 0.3715 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6817 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 21618 Z= 0.256 Angle : 0.672 10.689 29488 Z= 0.343 Chirality : 0.047 0.304 3402 Planarity : 0.005 0.055 3706 Dihedral : 5.157 56.438 3460 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.05 % Favored : 93.92 % Rotamer: Outliers : 2.61 % Allowed : 13.26 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.16), residues: 2696 helix: 1.29 (0.18), residues: 766 sheet: 0.67 (0.21), residues: 660 loop : -0.97 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP D1039 HIS 0.010 0.002 HIS R 405 PHE 0.022 0.002 PHE R 74 TYR 0.020 0.002 TYR A 144 ARG 0.006 0.001 ARG B 162 Details of bonding type rmsd link_NAG-ASN : bond 0.00257 ( 2) link_NAG-ASN : angle 0.93914 ( 6) link_BETA1-4 : bond 0.00579 ( 2) link_BETA1-4 : angle 2.50796 ( 6) hydrogen bonds : bond 0.04135 ( 942) hydrogen bonds : angle 4.99165 ( 2754) SS BOND : bond 0.00444 ( 2) SS BOND : angle 1.06104 ( 4) covalent geometry : bond 0.00586 (21612) covalent geometry : angle 0.67099 (29472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 359 time to evaluate : 2.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 307 GLU cc_start: 0.6789 (mm-30) cc_final: 0.6450 (mm-30) REVERT: R 400 MET cc_start: 0.7270 (tpp) cc_final: 0.7021 (tpp) REVERT: R 491 SER cc_start: 0.7999 (m) cc_final: 0.7788 (p) REVERT: R 622 VAL cc_start: 0.7579 (t) cc_final: 0.7269 (p) REVERT: R 726 VAL cc_start: 0.8223 (t) cc_final: 0.7117 (t) REVERT: R 758 THR cc_start: 0.8503 (p) cc_final: 0.8203 (t) REVERT: S 1113 TRP cc_start: 0.8056 (m100) cc_final: 0.7178 (m100) REVERT: B 307 GLU cc_start: 0.6777 (mm-30) cc_final: 0.6469 (mm-30) REVERT: B 491 SER cc_start: 0.8073 (m) cc_final: 0.7865 (p) REVERT: B 622 VAL cc_start: 0.7577 (t) cc_final: 0.7263 (p) REVERT: B 726 VAL cc_start: 0.8216 (t) cc_final: 0.7114 (t) REVERT: B 758 THR cc_start: 0.8517 (p) cc_final: 0.8227 (t) REVERT: D 1113 TRP cc_start: 0.8008 (m100) cc_final: 0.7175 (m100) outliers start: 56 outliers final: 43 residues processed: 395 average time/residue: 0.3573 time to fit residues: 215.2553 Evaluate side-chains 330 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 287 time to evaluate : 2.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 236 LEU Chi-restraints excluded: chain R residue 279 ASP Chi-restraints excluded: chain R residue 379 ILE Chi-restraints excluded: chain R residue 604 THR Chi-restraints excluded: chain R residue 786 LEU Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 245 ASN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 236 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 245 ASN Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 79 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 187 optimal weight: 10.0000 chunk 78 optimal weight: 0.9990 chunk 256 optimal weight: 10.0000 chunk 151 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 5 optimal weight: 0.1980 chunk 237 optimal weight: 10.0000 chunk 46 optimal weight: 0.4980 chunk 138 optimal weight: 0.7980 chunk 215 optimal weight: 0.3980 chunk 192 optimal weight: 4.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 508 GLN A 111 HIS A 198 HIS A 210 HIS B 344 ASN B 346 HIS ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 508 GLN C 111 HIS C 210 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.129410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.113255 restraints weight = 49173.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.112736 restraints weight = 68370.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.113213 restraints weight = 69762.532| |-----------------------------------------------------------------------------| r_work (final): 0.3785 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3786 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3786 r_free = 0.3786 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3785 r_free = 0.3785 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3785 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.3299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 21618 Z= 0.129 Angle : 0.558 8.168 29488 Z= 0.284 Chirality : 0.043 0.288 3402 Planarity : 0.004 0.063 3706 Dihedral : 4.841 54.639 3460 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.71 % Favored : 95.22 % Rotamer: Outliers : 2.15 % Allowed : 16.48 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.16), residues: 2696 helix: 1.43 (0.18), residues: 768 sheet: 0.81 (0.22), residues: 628 loop : -0.95 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S1039 HIS 0.005 0.001 HIS B 405 PHE 0.017 0.002 PHE B 74 TYR 0.015 0.001 TYR S 50 ARG 0.005 0.001 ARG R 797 Details of bonding type rmsd link_NAG-ASN : bond 0.00024 ( 2) link_NAG-ASN : angle 1.07416 ( 6) link_BETA1-4 : bond 0.00312 ( 2) link_BETA1-4 : angle 1.79808 ( 6) hydrogen bonds : bond 0.03624 ( 942) hydrogen bonds : angle 4.78523 ( 2754) SS BOND : bond 0.00216 ( 2) SS BOND : angle 0.58734 ( 4) covalent geometry : bond 0.00289 (21612) covalent geometry : angle 0.55709 (29472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 307 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 307 GLU cc_start: 0.6758 (mm-30) cc_final: 0.6510 (mm-30) REVERT: R 387 GLU cc_start: 0.5241 (tt0) cc_final: 0.4919 (tt0) REVERT: R 491 SER cc_start: 0.8026 (m) cc_final: 0.7708 (p) REVERT: R 622 VAL cc_start: 0.7526 (t) cc_final: 0.7230 (p) REVERT: R 726 VAL cc_start: 0.8379 (t) cc_final: 0.8097 (t) REVERT: S 22 ILE cc_start: 0.8770 (mm) cc_final: 0.8556 (mm) REVERT: S 1113 TRP cc_start: 0.7939 (m100) cc_final: 0.7164 (m100) REVERT: B 307 GLU cc_start: 0.6745 (mm-30) cc_final: 0.6501 (mm-30) REVERT: B 387 GLU cc_start: 0.5218 (tt0) cc_final: 0.4905 (tt0) REVERT: B 400 MET cc_start: 0.7338 (tpp) cc_final: 0.6978 (tpp) REVERT: B 491 SER cc_start: 0.8050 (m) cc_final: 0.7578 (t) REVERT: B 622 VAL cc_start: 0.7531 (t) cc_final: 0.7233 (p) REVERT: B 726 VAL cc_start: 0.8376 (t) cc_final: 0.8094 (t) REVERT: D 1113 TRP cc_start: 0.7883 (m100) cc_final: 0.7570 (m-10) outliers start: 46 outliers final: 29 residues processed: 339 average time/residue: 0.3435 time to fit residues: 178.6474 Evaluate side-chains 301 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 272 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 279 ASP Chi-restraints excluded: chain R residue 344 ASN Chi-restraints excluded: chain R residue 506 THR Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain D residue 76 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 40 optimal weight: 0.9980 chunk 114 optimal weight: 0.6980 chunk 4 optimal weight: 0.0070 chunk 134 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 224 optimal weight: 0.0980 chunk 126 optimal weight: 7.9990 chunk 169 optimal weight: 0.0270 chunk 170 optimal weight: 0.9990 chunk 99 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS B 344 ASN B 383 ASN C 198 HIS D 38 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.129802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.113736 restraints weight = 49768.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.113792 restraints weight = 65301.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.114238 restraints weight = 64409.417| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3812 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3812 r_free = 0.3812 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3812 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 21618 Z= 0.112 Angle : 0.526 7.252 29488 Z= 0.270 Chirality : 0.043 0.354 3402 Planarity : 0.004 0.070 3706 Dihedral : 4.729 54.494 3460 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.82 % Favored : 95.10 % Rotamer: Outliers : 2.15 % Allowed : 16.90 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.16), residues: 2696 helix: 1.50 (0.18), residues: 768 sheet: 0.83 (0.22), residues: 628 loop : -0.94 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP R 355 HIS 0.006 0.001 HIS R 405 PHE 0.014 0.001 PHE D1071 TYR 0.013 0.001 TYR B 398 ARG 0.012 0.000 ARG B 797 Details of bonding type rmsd link_NAG-ASN : bond 0.00003 ( 2) link_NAG-ASN : angle 1.00409 ( 6) link_BETA1-4 : bond 0.00418 ( 2) link_BETA1-4 : angle 1.62695 ( 6) hydrogen bonds : bond 0.03447 ( 942) hydrogen bonds : angle 4.62663 ( 2754) SS BOND : bond 0.00291 ( 2) SS BOND : angle 0.54481 ( 4) covalent geometry : bond 0.00249 (21612) covalent geometry : angle 0.52497 (29472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 292 time to evaluate : 2.177 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 307 GLU cc_start: 0.6730 (mm-30) cc_final: 0.6491 (mm-30) REVERT: R 360 GLN cc_start: 0.6891 (mm-40) cc_final: 0.6579 (mm-40) REVERT: R 400 MET cc_start: 0.7282 (tpp) cc_final: 0.7023 (tpp) REVERT: R 491 SER cc_start: 0.8014 (m) cc_final: 0.7707 (p) REVERT: R 614 LEU cc_start: 0.7411 (OUTLIER) cc_final: 0.7203 (tp) REVERT: R 622 VAL cc_start: 0.7470 (t) cc_final: 0.7197 (p) REVERT: R 726 VAL cc_start: 0.8226 (t) cc_final: 0.7939 (t) REVERT: S 1113 TRP cc_start: 0.7892 (m100) cc_final: 0.7129 (m100) REVERT: B 307 GLU cc_start: 0.6716 (mm-30) cc_final: 0.6481 (mm-30) REVERT: B 360 GLN cc_start: 0.6862 (mm-40) cc_final: 0.6542 (mm-40) REVERT: B 400 MET cc_start: 0.7320 (tpp) cc_final: 0.7058 (tpp) REVERT: B 491 SER cc_start: 0.8060 (m) cc_final: 0.7741 (p) REVERT: B 614 LEU cc_start: 0.7388 (OUTLIER) cc_final: 0.7178 (tp) REVERT: B 622 VAL cc_start: 0.7480 (t) cc_final: 0.7209 (p) REVERT: B 726 VAL cc_start: 0.8220 (t) cc_final: 0.7930 (t) REVERT: D 1113 TRP cc_start: 0.7827 (m100) cc_final: 0.7113 (m100) outliers start: 46 outliers final: 35 residues processed: 325 average time/residue: 0.3477 time to fit residues: 173.6308 Evaluate side-chains 297 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 260 time to evaluate : 2.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 279 ASP Chi-restraints excluded: chain R residue 344 ASN Chi-restraints excluded: chain R residue 614 LEU Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 207 ILE Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 1023 LEU Chi-restraints excluded: chain S residue 1072 THR Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 1072 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 6 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 118 optimal weight: 4.9990 chunk 215 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 219 optimal weight: 9.9990 chunk 58 optimal weight: 0.8980 chunk 178 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 91 GLN B 344 ASN B 405 HIS D 38 GLN D 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.126544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.111261 restraints weight = 49474.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.111205 restraints weight = 82370.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.111706 restraints weight = 71929.991| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3763 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3763 r_free = 0.3763 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3763 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6713 moved from start: 0.3878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 21618 Z= 0.215 Angle : 0.595 8.592 29488 Z= 0.305 Chirality : 0.045 0.372 3402 Planarity : 0.004 0.055 3706 Dihedral : 4.910 53.789 3460 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.90 % Favored : 94.03 % Rotamer: Outliers : 3.36 % Allowed : 17.37 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.16), residues: 2696 helix: 1.10 (0.18), residues: 780 sheet: 0.76 (0.22), residues: 610 loop : -1.04 (0.16), residues: 1306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 297 HIS 0.007 0.001 HIS B 405 PHE 0.019 0.002 PHE R 74 TYR 0.024 0.002 TYR B 398 ARG 0.005 0.001 ARG A 165 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 2) link_NAG-ASN : angle 0.96874 ( 6) link_BETA1-4 : bond 0.00508 ( 2) link_BETA1-4 : angle 2.10282 ( 6) hydrogen bonds : bond 0.03969 ( 942) hydrogen bonds : angle 4.76249 ( 2754) SS BOND : bond 0.00333 ( 2) SS BOND : angle 0.60455 ( 4) covalent geometry : bond 0.00497 (21612) covalent geometry : angle 0.59396 (29472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 293 time to evaluate : 2.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: R 95 ILE cc_start: 0.8483 (OUTLIER) cc_final: 0.8232 (mm) REVERT: R 307 GLU cc_start: 0.6850 (mm-30) cc_final: 0.6570 (mm-30) REVERT: R 360 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6864 (mm-40) REVERT: R 472 GLN cc_start: 0.7905 (OUTLIER) cc_final: 0.7058 (pm20) REVERT: R 491 SER cc_start: 0.8115 (m) cc_final: 0.7779 (p) REVERT: R 726 VAL cc_start: 0.8211 (t) cc_final: 0.7915 (t) REVERT: S 91 GLN cc_start: 0.6974 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: S 1113 TRP cc_start: 0.8011 (m100) cc_final: 0.7127 (m100) REVERT: B 95 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8368 (mm) REVERT: B 307 GLU cc_start: 0.6849 (mm-30) cc_final: 0.6577 (mm-30) REVERT: B 360 GLN cc_start: 0.7169 (mm-40) cc_final: 0.6822 (mm-40) REVERT: B 400 MET cc_start: 0.7328 (tpp) cc_final: 0.7100 (tpp) REVERT: B 472 GLN cc_start: 0.7928 (OUTLIER) cc_final: 0.7100 (pm20) REVERT: B 491 SER cc_start: 0.8362 (m) cc_final: 0.8037 (p) REVERT: B 614 LEU cc_start: 0.7638 (OUTLIER) cc_final: 0.7426 (tp) REVERT: B 726 VAL cc_start: 0.8176 (t) cc_final: 0.7866 (t) REVERT: D 1113 TRP cc_start: 0.7906 (m100) cc_final: 0.7076 (m100) outliers start: 72 outliers final: 46 residues processed: 346 average time/residue: 0.3339 time to fit residues: 178.6060 Evaluate side-chains 322 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 270 time to evaluate : 2.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 279 ASP Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 344 ASN Chi-restraints excluded: chain R residue 472 GLN Chi-restraints excluded: chain R residue 506 THR Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 1023 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 614 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 42 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 1023 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 34 optimal weight: 0.6980 chunk 237 optimal weight: 7.9990 chunk 187 optimal weight: 6.9990 chunk 232 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 265 optimal weight: 4.9990 chunk 90 optimal weight: 9.9990 chunk 245 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 100 optimal weight: 4.9990 chunk 180 optimal weight: 1.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 ASN B 405 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.125820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.106357 restraints weight = 47188.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.104359 restraints weight = 57362.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.102478 restraints weight = 46974.043| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3576 r_free = 0.3576 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3575 r_free = 0.3575 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| r_final: 0.3575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 21618 Z= 0.299 Angle : 0.677 12.900 29488 Z= 0.344 Chirality : 0.047 0.163 3402 Planarity : 0.005 0.056 3706 Dihedral : 5.215 52.600 3460 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.16 % Favored : 93.77 % Rotamer: Outliers : 3.50 % Allowed : 18.35 % Favored : 78.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.16), residues: 2696 helix: 0.67 (0.18), residues: 778 sheet: 0.65 (0.22), residues: 610 loop : -1.24 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S1106 HIS 0.007 0.001 HIS B 405 PHE 0.020 0.002 PHE B 74 TYR 0.026 0.002 TYR B 398 ARG 0.005 0.001 ARG B 571 Details of bonding type rmsd link_NAG-ASN : bond 0.00088 ( 2) link_NAG-ASN : angle 1.05987 ( 6) link_BETA1-4 : bond 0.00542 ( 2) link_BETA1-4 : angle 2.28272 ( 6) hydrogen bonds : bond 0.04443 ( 942) hydrogen bonds : angle 5.05071 ( 2754) SS BOND : bond 0.00560 ( 2) SS BOND : angle 0.77653 ( 4) covalent geometry : bond 0.00693 (21612) covalent geometry : angle 0.67648 (29472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 295 time to evaluate : 2.442 Fit side-chains REVERT: R 95 ILE cc_start: 0.8703 (OUTLIER) cc_final: 0.8426 (mm) REVERT: R 231 GLU cc_start: 0.7639 (mt-10) cc_final: 0.7337 (mt-10) REVERT: R 307 GLU cc_start: 0.6912 (mm-30) cc_final: 0.6568 (mm-30) REVERT: R 324 GLU cc_start: 0.7120 (OUTLIER) cc_final: 0.6823 (tt0) REVERT: R 387 GLU cc_start: 0.5757 (tt0) cc_final: 0.5327 (tt0) REVERT: R 472 GLN cc_start: 0.8057 (OUTLIER) cc_final: 0.7073 (pm20) REVERT: R 491 SER cc_start: 0.8190 (m) cc_final: 0.7977 (p) REVERT: R 726 VAL cc_start: 0.8475 (t) cc_final: 0.8155 (t) REVERT: S 5 MET cc_start: 0.7633 (ptp) cc_final: 0.7078 (pmm) REVERT: S 91 GLN cc_start: 0.7053 (OUTLIER) cc_final: 0.6378 (tm-30) REVERT: S 1113 TRP cc_start: 0.8051 (m100) cc_final: 0.7136 (m100) REVERT: B 95 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8571 (mm) REVERT: B 307 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6545 (mm-30) REVERT: B 324 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6920 (tt0) REVERT: B 387 GLU cc_start: 0.5726 (tt0) cc_final: 0.5281 (tt0) REVERT: B 472 GLN cc_start: 0.8099 (OUTLIER) cc_final: 0.7196 (pm20) REVERT: B 726 VAL cc_start: 0.8465 (t) cc_final: 0.8139 (t) REVERT: D 1113 TRP cc_start: 0.7996 (m100) cc_final: 0.7086 (m100) outliers start: 75 outliers final: 55 residues processed: 348 average time/residue: 0.3344 time to fit residues: 181.9007 Evaluate side-chains 334 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 272 time to evaluate : 2.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 LEU Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 324 GLU Chi-restraints excluded: chain R residue 344 ASN Chi-restraints excluded: chain R residue 345 ASN Chi-restraints excluded: chain R residue 472 GLN Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 506 THR Chi-restraints excluded: chain R residue 629 THR Chi-restraints excluded: chain R residue 746 ILE Chi-restraints excluded: chain R residue 786 LEU Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain R residue 813 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 1023 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 629 THR Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 207 ILE Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1073 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 195 optimal weight: 0.9980 chunk 215 optimal weight: 10.0000 chunk 178 optimal weight: 0.8980 chunk 228 optimal weight: 0.0870 chunk 210 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 chunk 236 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 405 HIS R 498 HIS S 91 GLN B 405 HIS D 38 GLN D 91 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.127997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.109560 restraints weight = 47360.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.106407 restraints weight = 54232.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.105933 restraints weight = 56368.410| |-----------------------------------------------------------------------------| r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3646 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 14 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3646 r_free = 0.3646 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3646 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6944 moved from start: 0.4332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 21618 Z= 0.137 Angle : 0.580 13.949 29488 Z= 0.293 Chirality : 0.043 0.161 3402 Planarity : 0.004 0.054 3706 Dihedral : 4.937 52.508 3460 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.04 % Favored : 94.88 % Rotamer: Outliers : 2.94 % Allowed : 19.19 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 2696 helix: 0.90 (0.18), residues: 784 sheet: 0.63 (0.22), residues: 612 loop : -1.22 (0.16), residues: 1300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 355 HIS 0.007 0.001 HIS R 405 PHE 0.014 0.001 PHE B 74 TYR 0.025 0.001 TYR B 384 ARG 0.005 0.000 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00028 ( 2) link_NAG-ASN : angle 1.38797 ( 6) link_BETA1-4 : bond 0.00498 ( 2) link_BETA1-4 : angle 1.74970 ( 6) hydrogen bonds : bond 0.03829 ( 942) hydrogen bonds : angle 4.84004 ( 2754) SS BOND : bond 0.00185 ( 2) SS BOND : angle 0.52882 ( 4) covalent geometry : bond 0.00313 (21612) covalent geometry : angle 0.57959 (29472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 294 time to evaluate : 2.286 Fit side-chains revert: symmetry clash REVERT: R 307 GLU cc_start: 0.6794 (mm-30) cc_final: 0.6511 (mm-30) REVERT: R 324 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6805 (tt0) REVERT: R 624 LEU cc_start: 0.7294 (tt) cc_final: 0.6789 (tp) REVERT: R 726 VAL cc_start: 0.8390 (t) cc_final: 0.8071 (t) REVERT: S 5 MET cc_start: 0.7410 (ptp) cc_final: 0.7017 (pmm) REVERT: S 91 GLN cc_start: 0.6919 (OUTLIER) cc_final: 0.6484 (tm-30) REVERT: S 1113 TRP cc_start: 0.7991 (m100) cc_final: 0.7122 (m100) REVERT: B 307 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6522 (mm-30) REVERT: B 324 GLU cc_start: 0.7204 (OUTLIER) cc_final: 0.6935 (tt0) REVERT: B 624 LEU cc_start: 0.7131 (tt) cc_final: 0.6776 (tp) REVERT: B 726 VAL cc_start: 0.8387 (t) cc_final: 0.8084 (t) REVERT: D 1113 TRP cc_start: 0.7922 (m100) cc_final: 0.7151 (m100) outliers start: 63 outliers final: 46 residues processed: 341 average time/residue: 0.3404 time to fit residues: 178.4446 Evaluate side-chains 318 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 2.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 279 ASP Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 324 GLU Chi-restraints excluded: chain R residue 344 ASN Chi-restraints excluded: chain R residue 409 ARG Chi-restraints excluded: chain R residue 528 CYS Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain R residue 813 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 1023 LEU Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 409 ARG Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1089 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 236 optimal weight: 5.9990 chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 69 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 166 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 124 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 405 HIS S 91 GLN B 405 HIS D 38 GLN D 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.125916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.109231 restraints weight = 48947.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.110287 restraints weight = 87189.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.111039 restraints weight = 62363.354| |-----------------------------------------------------------------------------| r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3755 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3755 r_free = 0.3755 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3755 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 21618 Z= 0.180 Angle : 0.592 11.334 29488 Z= 0.299 Chirality : 0.044 0.160 3402 Planarity : 0.004 0.056 3706 Dihedral : 4.974 53.500 3460 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.71 % Favored : 94.21 % Rotamer: Outliers : 3.41 % Allowed : 19.47 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.16), residues: 2696 helix: 0.86 (0.18), residues: 786 sheet: 0.60 (0.22), residues: 614 loop : -1.24 (0.16), residues: 1296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 572 HIS 0.006 0.001 HIS R 405 PHE 0.021 0.002 PHE C 277 TYR 0.033 0.002 TYR D1033 ARG 0.006 0.000 ARG C 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00056 ( 2) link_NAG-ASN : angle 1.21246 ( 6) link_BETA1-4 : bond 0.00463 ( 2) link_BETA1-4 : angle 1.89765 ( 6) hydrogen bonds : bond 0.03866 ( 942) hydrogen bonds : angle 4.84853 ( 2754) SS BOND : bond 0.00202 ( 2) SS BOND : angle 0.56339 ( 4) covalent geometry : bond 0.00419 (21612) covalent geometry : angle 0.59099 (29472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 272 time to evaluate : 2.188 Fit side-chains REVERT: R 221 ASP cc_start: 0.6422 (OUTLIER) cc_final: 0.5797 (m-30) REVERT: R 307 GLU cc_start: 0.6914 (mm-30) cc_final: 0.6588 (mm-30) REVERT: R 324 GLU cc_start: 0.7229 (OUTLIER) cc_final: 0.6836 (tt0) REVERT: R 400 MET cc_start: 0.7208 (tpp) cc_final: 0.6876 (mpp) REVERT: R 624 LEU cc_start: 0.6886 (tt) cc_final: 0.6582 (tp) REVERT: R 726 VAL cc_start: 0.8204 (t) cc_final: 0.7904 (t) REVERT: S 5 MET cc_start: 0.7385 (ptp) cc_final: 0.7047 (pmm) REVERT: S 1113 TRP cc_start: 0.7938 (m100) cc_final: 0.7118 (m100) REVERT: B 307 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6572 (mm-30) REVERT: B 324 GLU cc_start: 0.7230 (OUTLIER) cc_final: 0.6820 (tt0) REVERT: B 400 MET cc_start: 0.7118 (tpp) cc_final: 0.6853 (mpp) REVERT: B 624 LEU cc_start: 0.7208 (tt) cc_final: 0.6815 (tp) REVERT: B 726 VAL cc_start: 0.8200 (t) cc_final: 0.7899 (t) REVERT: D 1113 TRP cc_start: 0.7814 (m100) cc_final: 0.7052 (m100) outliers start: 73 outliers final: 53 residues processed: 324 average time/residue: 0.3316 time to fit residues: 165.0727 Evaluate side-chains 322 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 266 time to evaluate : 2.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 221 ASP Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 324 GLU Chi-restraints excluded: chain R residue 344 ASN Chi-restraints excluded: chain R residue 409 ARG Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 528 CYS Chi-restraints excluded: chain R residue 758 THR Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain R residue 813 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 1023 LEU Chi-restraints excluded: chain S residue 1111 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1025 CYS Chi-restraints excluded: chain D residue 1099 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 127 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 206 optimal weight: 3.9990 chunk 260 optimal weight: 0.5980 chunk 229 optimal weight: 3.9990 chunk 194 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 405 HIS S 91 GLN B 405 HIS D 38 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.126542 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.109835 restraints weight = 48732.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.110145 restraints weight = 80272.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.111053 restraints weight = 77692.157| |-----------------------------------------------------------------------------| r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3746 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3746 r_free = 0.3746 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3746 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 21618 Z= 0.145 Angle : 0.582 13.073 29488 Z= 0.292 Chirality : 0.043 0.175 3402 Planarity : 0.004 0.055 3706 Dihedral : 4.948 53.629 3460 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.27 % Favored : 94.66 % Rotamer: Outliers : 3.27 % Allowed : 19.33 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.16), residues: 2696 helix: 0.94 (0.18), residues: 784 sheet: 0.59 (0.22), residues: 604 loop : -1.21 (0.16), residues: 1308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 355 HIS 0.007 0.001 HIS B 405 PHE 0.016 0.001 PHE B 630 TYR 0.025 0.002 TYR R 717 ARG 0.005 0.000 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00005 ( 2) link_NAG-ASN : angle 1.27174 ( 6) link_BETA1-4 : bond 0.00539 ( 2) link_BETA1-4 : angle 1.75429 ( 6) hydrogen bonds : bond 0.03755 ( 942) hydrogen bonds : angle 4.80049 ( 2754) SS BOND : bond 0.00235 ( 2) SS BOND : angle 0.52351 ( 4) covalent geometry : bond 0.00334 (21612) covalent geometry : angle 0.58087 (29472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 277 time to evaluate : 2.195 Fit side-chains revert: symmetry clash REVERT: R 95 ILE cc_start: 0.8469 (OUTLIER) cc_final: 0.8207 (mm) REVERT: R 307 GLU cc_start: 0.6877 (mm-30) cc_final: 0.6553 (mm-30) REVERT: R 324 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6630 (tt0) REVERT: R 360 GLN cc_start: 0.7219 (mm-40) cc_final: 0.7002 (mm-40) REVERT: R 624 LEU cc_start: 0.7035 (tt) cc_final: 0.6769 (tp) REVERT: R 726 VAL cc_start: 0.8264 (t) cc_final: 0.7960 (t) REVERT: S 5 MET cc_start: 0.7335 (ptp) cc_final: 0.7005 (pmm) REVERT: S 91 GLN cc_start: 0.6993 (OUTLIER) cc_final: 0.6634 (tm-30) REVERT: S 1113 TRP cc_start: 0.7911 (m100) cc_final: 0.7098 (m100) REVERT: B 95 ILE cc_start: 0.8532 (OUTLIER) cc_final: 0.8249 (mm) REVERT: B 307 GLU cc_start: 0.6882 (mm-30) cc_final: 0.6563 (mm-30) REVERT: B 324 GLU cc_start: 0.7170 (OUTLIER) cc_final: 0.6607 (tt0) REVERT: B 360 GLN cc_start: 0.7215 (mm-40) cc_final: 0.7004 (mm-40) REVERT: B 726 VAL cc_start: 0.8264 (t) cc_final: 0.7949 (t) REVERT: D 1113 TRP cc_start: 0.7768 (m100) cc_final: 0.7091 (m100) outliers start: 70 outliers final: 57 residues processed: 327 average time/residue: 0.3252 time to fit residues: 164.8404 Evaluate side-chains 331 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 269 time to evaluate : 2.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 279 ASP Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 324 GLU Chi-restraints excluded: chain R residue 344 ASN Chi-restraints excluded: chain R residue 409 ARG Chi-restraints excluded: chain R residue 490 LEU Chi-restraints excluded: chain R residue 528 CYS Chi-restraints excluded: chain R residue 758 THR Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain R residue 813 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 1023 LEU Chi-restraints excluded: chain S residue 1111 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 409 ARG Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 67 ASP Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1025 CYS Chi-restraints excluded: chain D residue 1089 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 80 optimal weight: 10.0000 chunk 184 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 193 optimal weight: 6.9990 chunk 160 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 150 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 405 HIS ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 91 GLN B 338 GLN B 405 HIS B 498 HIS C 198 HIS ** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 38 GLN D 91 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.125038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.106421 restraints weight = 47345.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.104117 restraints weight = 59922.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.102468 restraints weight = 50009.919| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3581 r_free = 0.3581 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7036 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 21618 Z= 0.288 Angle : 0.685 16.201 29488 Z= 0.348 Chirality : 0.047 0.160 3402 Planarity : 0.005 0.057 3706 Dihedral : 5.237 54.503 3460 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.97 % Favored : 92.95 % Rotamer: Outliers : 3.45 % Allowed : 19.42 % Favored : 77.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.16), residues: 2696 helix: 0.52 (0.18), residues: 784 sheet: 0.55 (0.22), residues: 600 loop : -1.32 (0.16), residues: 1312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 782 HIS 0.007 0.001 HIS B 405 PHE 0.020 0.002 PHE R 74 TYR 0.035 0.003 TYR R 398 ARG 0.006 0.001 ARG A 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00108 ( 2) link_NAG-ASN : angle 1.09859 ( 6) link_BETA1-4 : bond 0.00599 ( 2) link_BETA1-4 : angle 2.25417 ( 6) hydrogen bonds : bond 0.04398 ( 942) hydrogen bonds : angle 5.08014 ( 2754) SS BOND : bond 0.00402 ( 2) SS BOND : angle 0.87099 ( 4) covalent geometry : bond 0.00669 (21612) covalent geometry : angle 0.68461 (29472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5392 Ramachandran restraints generated. 2696 Oldfield, 0 Emsley, 2696 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 298 time to evaluate : 2.241 Fit side-chains REVERT: R 95 ILE cc_start: 0.8758 (OUTLIER) cc_final: 0.8500 (mm) REVERT: R 307 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6721 (mm-30) REVERT: R 324 GLU cc_start: 0.7311 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: R 400 MET cc_start: 0.7070 (tpp) cc_final: 0.6669 (mpp) REVERT: R 624 LEU cc_start: 0.7248 (tt) cc_final: 0.6841 (tp) REVERT: R 726 VAL cc_start: 0.8472 (t) cc_final: 0.8121 (t) REVERT: S 5 MET cc_start: 0.7628 (ptp) cc_final: 0.7117 (pmm) REVERT: S 91 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6343 (pp30) REVERT: S 1113 TRP cc_start: 0.8035 (m100) cc_final: 0.7081 (m100) REVERT: B 95 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8482 (mm) REVERT: B 307 GLU cc_start: 0.7104 (mm-30) cc_final: 0.6718 (mm-30) REVERT: B 324 GLU cc_start: 0.7294 (OUTLIER) cc_final: 0.6946 (tt0) REVERT: B 400 MET cc_start: 0.7049 (tpp) cc_final: 0.6635 (mpp) REVERT: B 624 LEU cc_start: 0.7328 (tt) cc_final: 0.7050 (tp) REVERT: B 726 VAL cc_start: 0.8464 (t) cc_final: 0.8132 (t) REVERT: D 1113 TRP cc_start: 0.7949 (m100) cc_final: 0.7081 (m100) outliers start: 74 outliers final: 60 residues processed: 348 average time/residue: 0.3329 time to fit residues: 179.9838 Evaluate side-chains 345 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 280 time to evaluate : 2.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 95 ILE Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 324 GLU Chi-restraints excluded: chain R residue 344 ASN Chi-restraints excluded: chain R residue 409 ARG Chi-restraints excluded: chain R residue 481 LEU Chi-restraints excluded: chain R residue 506 THR Chi-restraints excluded: chain R residue 528 CYS Chi-restraints excluded: chain R residue 758 THR Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain R residue 813 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 43 VAL Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 149 PHE Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 176 GLU Chi-restraints excluded: chain A residue 187 THR Chi-restraints excluded: chain A residue 223 ASN Chi-restraints excluded: chain A residue 275 THR Chi-restraints excluded: chain A residue 347 LEU Chi-restraints excluded: chain S residue 59 VAL Chi-restraints excluded: chain S residue 75 THR Chi-restraints excluded: chain S residue 76 ILE Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 1023 LEU Chi-restraints excluded: chain S residue 1111 ASP Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 481 LEU Chi-restraints excluded: chain B residue 506 THR Chi-restraints excluded: chain B residue 528 CYS Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain C residue 38 ASP Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 149 PHE Chi-restraints excluded: chain C residue 167 VAL Chi-restraints excluded: chain C residue 176 GLU Chi-restraints excluded: chain C residue 187 THR Chi-restraints excluded: chain C residue 223 ASN Chi-restraints excluded: chain C residue 275 THR Chi-restraints excluded: chain C residue 347 LEU Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 86 THR Chi-restraints excluded: chain D residue 91 GLN Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1025 CYS Chi-restraints excluded: chain D residue 1099 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 9 optimal weight: 0.0970 chunk 259 optimal weight: 0.3980 chunk 91 optimal weight: 0.0050 chunk 92 optimal weight: 0.6980 chunk 104 optimal weight: 0.0040 chunk 199 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 193 optimal weight: 0.8980 chunk 96 optimal weight: 0.0020 chunk 77 optimal weight: 0.9980 overall best weight: 0.1012 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 405 HIS ** S 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 38 GLN S 91 GLN B 338 GLN B 405 HIS D 38 GLN ** D 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.127499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.111340 restraints weight = 48977.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.111421 restraints weight = 74089.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.111908 restraints weight = 68380.569| |-----------------------------------------------------------------------------| r_work (final): 0.3769 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3768 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3768 r_free = 0.3768 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3768 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.4705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 21618 Z= 0.119 Angle : 0.596 11.796 29488 Z= 0.301 Chirality : 0.043 0.160 3402 Planarity : 0.004 0.054 3706 Dihedral : 4.912 54.009 3460 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 11.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.19 % Favored : 95.73 % Rotamer: Outliers : 2.24 % Allowed : 21.10 % Favored : 76.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.16), residues: 2696 helix: 0.94 (0.18), residues: 784 sheet: 0.48 (0.22), residues: 610 loop : -1.18 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP R 355 HIS 0.008 0.001 HIS B 405 PHE 0.028 0.002 PHE C 115 TYR 0.030 0.001 TYR S 92 ARG 0.006 0.001 ARG C 188 Details of bonding type rmsd link_NAG-ASN : bond 0.00043 ( 2) link_NAG-ASN : angle 1.55505 ( 6) link_BETA1-4 : bond 0.00244 ( 2) link_BETA1-4 : angle 1.25458 ( 6) hydrogen bonds : bond 0.03653 ( 942) hydrogen bonds : angle 4.83795 ( 2754) SS BOND : bond 0.00132 ( 2) SS BOND : angle 0.38373 ( 4) covalent geometry : bond 0.00259 (21612) covalent geometry : angle 0.59552 (29472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7381.47 seconds wall clock time: 128 minutes 43.94 seconds (7723.94 seconds total)