Starting phenix.real_space_refine on Thu Sep 18 23:07:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ii2_60588/09_2025/9ii2_60588.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ii2_60588/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9ii2_60588/09_2025/9ii2_60588.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ii2_60588/09_2025/9ii2_60588.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ii2_60588/09_2025/9ii2_60588.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ii2_60588/09_2025/9ii2_60588.map" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.008 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21112 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" 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: {'ARG:plan': 7, 'ASP:plan': 8, 'TYR:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 1, 'ASN:plan1': 7, 'HIS:plan': 3, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 117 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: {'ASN:plan1': 2, 'ASP:plan': 4, 'GLU:plan': 8, 'ARG:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 80 Chain: "S" 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: {'ASP:plan': 4, 'GLN:plan1': 6, 'ARG:plan': 2, 'GLU:plan': 3, 'ASN:plan1': 1} 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: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Classifications: {'peptide': 1} Chain: "R" 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: B, C, D, F 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: 8.75, per 1000 atoms: 0.41 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=18, symmetry=0 Simple disulfide: pdb=" SG CYS R 57 " - pdb=" SG CYS R 99 " distance=2.03 Simple disulfide: pdb=" SG CYS R 361 " - pdb=" SG CYS R 373 " distance=2.03 Simple disulfide: pdb=" SG CYS R 412 " - pdb=" SG CYS R 419 " distance=2.03 Simple disulfide: pdb=" SG CYS R 509 " - pdb=" SG CYS R 528 " distance=2.03 Simple disulfide: pdb=" SG CYS R 513 " - pdb=" SG CYS R 531 " distance=2.03 Simple disulfide: pdb=" SG CYS R 549 " - pdb=" SG CYS R 562 " distance=2.03 Simple disulfide: pdb=" SG CYS R 641 " - pdb=" SG CYS R 730 " distance=2.03 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 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 99 " distance=2.03 Simple disulfide: pdb=" SG CYS B 361 " - pdb=" SG CYS B 373 " distance=2.03 Simple disulfide: pdb=" SG CYS B 412 " - pdb=" SG CYS B 419 " distance=2.03 Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 528 " distance=2.03 Simple disulfide: pdb=" SG CYS B 513 " - pdb=" SG CYS B 531 " distance=2.03 Simple disulfide: pdb=" SG CYS B 549 " - pdb=" SG CYS B 562 " distance=2.03 Simple disulfide: pdb=" SG CYS B 641 " - pdb=" SG CYS B 730 " distance=2.03 Simple disulfide: pdb=" SG CYS D 24 " - pdb=" SG CYS D 89 " distance=2.03 Simple disulfide: pdb=" SG CYS D1025 " - pdb=" SG CYS D1099 " 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: 2.08 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.86 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: 5.19 Time building geometry restraints manager: 2.71 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: 12057 17.89 - 35.78: 979 35.78 - 53.67: 144 53.67 - 71.56: 18 71.56 - 89.46: 16 Dihedral angle restraints: 13214 sinusoidal: 5176 harmonic: 8038 Sorted by residual: dihedral pdb=" CB CYS R 412 " pdb=" SG CYS R 412 " pdb=" SG CYS R 419 " pdb=" CB CYS R 419 " ideal model delta sinusoidal sigma weight residual 93.00 175.41 -82.41 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS B 412 " pdb=" SG CYS B 412 " pdb=" SG CYS B 419 " pdb=" CB CYS B 419 " ideal model delta sinusoidal sigma weight residual 93.00 175.41 -82.41 1 1.00e+01 1.00e-02 8.33e+01 dihedral pdb=" CB CYS R 513 " pdb=" SG CYS R 513 " pdb=" SG CYS R 531 " pdb=" CB CYS R 531 " ideal model delta sinusoidal sigma weight residual 93.00 152.32 -59.32 1 1.00e+01 1.00e-02 4.70e+01 ... (remaining 13211 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: 2.16 - 2.71: 524 2.71 - 3.26: 20205 3.26 - 3.80: 34038 3.80 - 4.35: 41427 4.35 - 4.90: 71649 Nonbonded interactions: 167843 Sorted by model distance: nonbonded pdb=" O GLY B 148 " pdb=" OG SER B 154 " model vdw 2.161 3.040 nonbonded pdb=" O GLY R 148 " pdb=" OG SER R 154 " model vdw 2.162 3.040 nonbonded pdb=" O TYR B 212 " pdb=" OG SER B 507 " model vdw 2.193 3.040 nonbonded pdb=" O TYR R 212 " pdb=" OG SER R 507 " model vdw 2.194 3.040 nonbonded pdb=" O TYR B 626 " pdb=" OG1 THR B 629 " model vdw 2.242 3.040 ... (remaining 167838 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: 0.04 Found NCS groups: ncs_group { reference = chain 'R' selection = chain 'B' } ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'S' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'F' } 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: 5.610 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: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 26.450 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.690 ------------------------------------------------------------------------------- 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 21634 Z= 0.185 Angle : 0.515 12.668 29520 Z= 0.254 Chirality : 0.042 0.160 3402 Planarity : 0.003 0.051 3706 Dihedral : 12.872 89.455 7980 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 8.88 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 68 TYR 0.006 0.001 TYR B 656 PHE 0.012 0.001 PHE R 275 TRP 0.007 0.001 TRP R 355 HIS 0.002 0.000 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00370 (21612) covalent geometry : angle 0.51416 (29472) SS BOND : bond 0.00112 ( 18) SS BOND : angle 1.04325 ( 36) hydrogen bonds : bond 0.10607 ( 942) hydrogen bonds : angle 5.40727 ( 2754) link_BETA1-4 : bond 0.00433 ( 2) link_BETA1-4 : angle 0.94815 ( 6) link_NAG-ASN : bond 0.00014 ( 2) link_NAG-ASN : angle 0.85214 ( 6) *********************** 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 : 0.835 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: 0.1850 time to fit residues: 159.3135 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 : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 5.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 111 HIS A 223 ASN B 159 ASN B 292 ASN B 344 ASN ** B 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 383 ASN ** B 472 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN C 111 HIS C 223 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.126205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 90)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.105672 restraints weight = 47395.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.105715 restraints weight = 58577.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.105139 restraints weight = 40771.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.104534 restraints weight = 46885.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.104982 restraints weight = 40086.381| |-----------------------------------------------------------------------------| r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3630 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3630 r_free = 0.3630 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3629 r_free = 0.3629 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.103 21634 Z= 0.421 Angle : 0.830 11.664 29520 Z= 0.429 Chirality : 0.053 0.328 3402 Planarity : 0.006 0.057 3706 Dihedral : 5.690 56.207 3460 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.45 % Favored : 93.47 % Rotamer: Outliers : 3.08 % Allowed : 14.89 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.16), residues: 2696 helix: 0.62 (0.18), residues: 766 sheet: 0.44 (0.21), residues: 660 loop : -1.09 (0.17), residues: 1270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 68 TYR 0.024 0.003 TYR B 398 PHE 0.034 0.003 PHE D1105 TRP 0.016 0.003 TRP B 576 HIS 0.011 0.002 HIS C 353 Details of bonding type rmsd covalent geometry : bond 0.00966 (21612) covalent geometry : angle 0.82660 (29472) SS BOND : bond 0.00638 ( 18) SS BOND : angle 1.73187 ( 36) hydrogen bonds : bond 0.05140 ( 942) hydrogen bonds : angle 5.41141 ( 2754) link_BETA1-4 : bond 0.00274 ( 2) link_BETA1-4 : angle 3.26038 ( 6) link_NAG-ASN : bond 0.00559 ( 2) link_NAG-ASN : angle 0.84095 ( 6) *********************** 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 421 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 355 time to evaluate : 0.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 ILE cc_start: 0.8871 (OUTLIER) cc_final: 0.8380 (mm) REVERT: R 307 GLU cc_start: 0.6951 (mm-30) cc_final: 0.6576 (mm-30) REVERT: R 726 VAL cc_start: 0.8457 (t) cc_final: 0.7466 (t) REVERT: S 1113 TRP cc_start: 0.8091 (m100) cc_final: 0.7130 (m100) REVERT: B 95 ILE cc_start: 0.8876 (OUTLIER) cc_final: 0.8388 (mm) REVERT: B 307 GLU cc_start: 0.6960 (mm-30) cc_final: 0.6600 (mm-30) REVERT: B 726 VAL cc_start: 0.8455 (t) cc_final: 0.7482 (t) REVERT: D 1113 TRP cc_start: 0.8090 (m100) cc_final: 0.7095 (m100) outliers start: 66 outliers final: 48 residues processed: 401 average time/residue: 0.1483 time to fit residues: 91.8042 Evaluate side-chains 353 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 303 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 69 LEU 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 236 LEU Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 344 ASN 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 42 LEU 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 319 VAL 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 69 LEU 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 236 LEU Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 344 ASN 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 42 LEU 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 319 VAL 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 244 optimal weight: 4.9990 chunk 167 optimal weight: 0.8980 chunk 255 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 184 optimal weight: 2.9990 chunk 268 optimal weight: 9.9990 chunk 188 optimal weight: 10.0000 chunk 224 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 203 optimal weight: 6.9990 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 344 ASN R 346 HIS R 472 GLN R 508 GLN A 111 HIS B 344 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 GLN B 508 GLN C 111 HIS C 198 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.127738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.108121 restraints weight = 47340.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106304 restraints weight = 53829.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.105911 restraints weight = 45959.699| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.105911 restraints weight = 41609.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.105950 restraints weight = 37358.793| |-----------------------------------------------------------------------------| r_work (final): 0.3643 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3643 r_free = 0.3643 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.3821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 21634 Z= 0.187 Angle : 0.607 8.204 29520 Z= 0.309 Chirality : 0.045 0.326 3402 Planarity : 0.005 0.058 3706 Dihedral : 5.169 53.967 3460 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.56 % Favored : 94.36 % Rotamer: Outliers : 2.57 % Allowed : 17.41 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.20 (0.16), residues: 2696 helix: 0.90 (0.18), residues: 766 sheet: 0.54 (0.22), residues: 614 loop : -1.09 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 797 TYR 0.015 0.002 TYR D 92 PHE 0.016 0.002 PHE S1071 TRP 0.010 0.002 TRP S1039 HIS 0.005 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00432 (21612) covalent geometry : angle 0.60502 (29472) SS BOND : bond 0.00316 ( 18) SS BOND : angle 1.05246 ( 36) hydrogen bonds : bond 0.04073 ( 942) hydrogen bonds : angle 5.11319 ( 2754) link_BETA1-4 : bond 0.00453 ( 2) link_BETA1-4 : angle 2.22774 ( 6) link_NAG-ASN : bond 0.00102 ( 2) link_NAG-ASN : angle 1.32556 ( 6) *********************** 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 379 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 324 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 274 LEU cc_start: 0.7245 (OUTLIER) cc_final: 0.7035 (mp) REVERT: R 307 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6520 (mm-30) REVERT: R 726 VAL cc_start: 0.8457 (t) cc_final: 0.8215 (t) REVERT: A 229 LYS cc_start: 0.7107 (mtmt) cc_final: 0.6889 (mttp) REVERT: S 1072 THR cc_start: 0.7418 (p) cc_final: 0.7208 (t) REVERT: S 1113 TRP cc_start: 0.8040 (m100) cc_final: 0.7184 (m100) REVERT: B 307 GLU cc_start: 0.6820 (mm-30) cc_final: 0.6517 (mm-30) REVERT: B 726 VAL cc_start: 0.8444 (t) cc_final: 0.8207 (t) REVERT: D 1072 THR cc_start: 0.7388 (p) cc_final: 0.7184 (t) REVERT: D 1113 TRP cc_start: 0.8039 (m100) cc_final: 0.7159 (m100) outliers start: 55 outliers final: 40 residues processed: 359 average time/residue: 0.1503 time to fit residues: 83.5119 Evaluate side-chains 330 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 289 time to evaluate : 0.810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 85 LEU Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 279 ASP Chi-restraints excluded: chain R residue 344 ASN Chi-restraints excluded: chain R residue 604 THR Chi-restraints excluded: chain R residue 641 CYS Chi-restraints excluded: chain R residue 730 CYS 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 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 75 THR 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 604 THR Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 730 CYS 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 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 75 THR 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 51 optimal weight: 7.9990 chunk 145 optimal weight: 0.5980 chunk 192 optimal weight: 5.9990 chunk 221 optimal weight: 7.9990 chunk 100 optimal weight: 0.9980 chunk 203 optimal weight: 3.9990 chunk 97 optimal weight: 3.9990 chunk 270 optimal weight: 3.9990 chunk 254 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 58 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 344 ASN R 498 HIS A 198 HIS S 91 GLN B 344 ASN ** B 383 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 498 HIS C 198 HIS D 38 GLN D 91 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.126283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.106107 restraints weight = 47733.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.106307 restraints weight = 57665.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105146 restraints weight = 38413.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.104857 restraints weight = 40806.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.105033 restraints weight = 37335.686| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3635 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3635 r_free = 0.3635 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3635 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 21634 Z= 0.238 Angle : 0.621 9.137 29520 Z= 0.318 Chirality : 0.046 0.387 3402 Planarity : 0.005 0.056 3706 Dihedral : 5.227 54.551 3460 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.60 % Favored : 93.32 % Rotamer: Outliers : 4.53 % Allowed : 17.37 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.16), residues: 2696 helix: 0.75 (0.18), residues: 778 sheet: 0.46 (0.22), residues: 614 loop : -1.20 (0.16), residues: 1304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 797 TYR 0.016 0.002 TYR B 398 PHE 0.021 0.002 PHE R 74 TRP 0.009 0.002 TRP B 529 HIS 0.006 0.001 HIS B 346 Details of bonding type rmsd covalent geometry : bond 0.00554 (21612) covalent geometry : angle 0.61909 (29472) SS BOND : bond 0.00394 ( 18) SS BOND : angle 1.19497 ( 36) hydrogen bonds : bond 0.04256 ( 942) hydrogen bonds : angle 5.07698 ( 2754) link_BETA1-4 : bond 0.00363 ( 2) link_BETA1-4 : angle 2.32376 ( 6) link_NAG-ASN : bond 0.00130 ( 2) link_NAG-ASN : angle 1.18493 ( 6) *********************** 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 407 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 310 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 274 LEU cc_start: 0.7353 (OUTLIER) cc_final: 0.7128 (mp) REVERT: R 307 GLU cc_start: 0.6831 (mm-30) cc_final: 0.6489 (mm-30) REVERT: R 324 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6986 (tt0) REVERT: R 400 MET cc_start: 0.7242 (tpp) cc_final: 0.6819 (mpp) REVERT: R 506 THR cc_start: 0.6691 (p) cc_final: 0.6345 (t) REVERT: R 726 VAL cc_start: 0.8336 (t) cc_final: 0.8061 (t) REVERT: S 5 MET cc_start: 0.7391 (ptp) cc_final: 0.6950 (pmm) REVERT: S 1113 TRP cc_start: 0.8049 (m100) cc_final: 0.7108 (m100) REVERT: B 274 LEU cc_start: 0.7296 (OUTLIER) cc_final: 0.7021 (mp) REVERT: B 307 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6518 (mm-30) REVERT: B 324 GLU cc_start: 0.7243 (OUTLIER) cc_final: 0.6955 (tt0) REVERT: B 400 MET cc_start: 0.7226 (tpp) cc_final: 0.6805 (mpp) REVERT: B 506 THR cc_start: 0.6739 (p) cc_final: 0.6385 (t) REVERT: B 726 VAL cc_start: 0.8334 (t) cc_final: 0.8058 (t) REVERT: D 5 MET cc_start: 0.7400 (ptp) cc_final: 0.6938 (pmm) REVERT: D 1113 TRP cc_start: 0.8052 (m100) cc_final: 0.7088 (m100) outliers start: 97 outliers final: 65 residues processed: 388 average time/residue: 0.1413 time to fit residues: 87.0347 Evaluate side-chains 354 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 285 time to evaluate : 0.742 ------------------------------------------------------------------------------- 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 152 SER Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 274 LEU 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 604 THR Chi-restraints excluded: chain R residue 617 ILE Chi-restraints excluded: chain R residue 641 CYS Chi-restraints excluded: chain R residue 730 CYS 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 42 LEU Chi-restraints excluded: chain A residue 75 PHE 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 207 ILE 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 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 152 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 274 LEU 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 604 THR Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 730 CYS 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 42 LEU Chi-restraints excluded: chain C residue 75 PHE 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 1023 LEU Chi-restraints excluded: chain D residue 1111 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 174 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 160 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 153 optimal weight: 0.7980 chunk 246 optimal weight: 0.9980 chunk 258 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 190 optimal weight: 8.9990 chunk 5 optimal weight: 0.0050 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 91 GLN B 383 ASN C 198 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 = 0.4046 r_free = 0.4046 target = 0.128250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.108439 restraints weight = 47355.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.108543 restraints weight = 57364.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.108403 restraints weight = 40141.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.107861 restraints weight = 41978.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.108196 restraints weight = 36730.580| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3689 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3689 r_free = 0.3689 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3689 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.4136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 21634 Z= 0.136 Angle : 0.561 8.417 29520 Z= 0.287 Chirality : 0.044 0.362 3402 Planarity : 0.004 0.054 3706 Dihedral : 4.997 53.875 3460 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.53 % Favored : 94.40 % Rotamer: Outliers : 3.27 % Allowed : 18.30 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.16), residues: 2696 helix: 0.99 (0.18), residues: 780 sheet: 0.44 (0.22), residues: 614 loop : -1.20 (0.16), residues: 1302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 797 TYR 0.019 0.001 TYR D 50 PHE 0.017 0.001 PHE R 630 TRP 0.009 0.001 TRP D1106 HIS 0.007 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00310 (21612) covalent geometry : angle 0.55867 (29472) SS BOND : bond 0.00289 ( 18) SS BOND : angle 1.14220 ( 36) hydrogen bonds : bond 0.03781 ( 942) hydrogen bonds : angle 4.88810 ( 2754) link_BETA1-4 : bond 0.00483 ( 2) link_BETA1-4 : angle 1.82429 ( 6) link_NAG-ASN : bond 0.00030 ( 2) link_NAG-ASN : angle 1.28340 ( 6) *********************** 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 375 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 305 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 ILE cc_start: 0.8478 (OUTLIER) cc_final: 0.8268 (mm) REVERT: R 307 GLU cc_start: 0.6798 (mm-30) cc_final: 0.6457 (mm-30) REVERT: R 324 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7073 (tt0) REVERT: R 334 ASP cc_start: 0.7378 (t0) cc_final: 0.7114 (t0) REVERT: R 338 GLN cc_start: 0.6016 (mt0) cc_final: 0.5722 (mt0) REVERT: R 400 MET cc_start: 0.7238 (tpp) cc_final: 0.6781 (mpp) REVERT: R 506 THR cc_start: 0.6701 (p) cc_final: 0.6347 (t) REVERT: R 726 VAL cc_start: 0.8334 (t) cc_final: 0.8082 (t) REVERT: A 229 LYS cc_start: 0.7088 (mtmt) cc_final: 0.6788 (mttm) REVERT: S 5 MET cc_start: 0.7283 (ptp) cc_final: 0.6953 (pmm) REVERT: S 1113 TRP cc_start: 0.8063 (m100) cc_final: 0.7194 (m100) REVERT: B 307 GLU cc_start: 0.6804 (mm-30) cc_final: 0.6464 (mm-30) REVERT: B 324 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6970 (tt0) REVERT: B 334 ASP cc_start: 0.7365 (t0) cc_final: 0.7095 (t0) REVERT: B 338 GLN cc_start: 0.6011 (mt0) cc_final: 0.5713 (mt0) REVERT: B 400 MET cc_start: 0.7199 (tpp) cc_final: 0.6717 (mpp) REVERT: B 506 THR cc_start: 0.6737 (p) cc_final: 0.6365 (t) REVERT: B 726 VAL cc_start: 0.8328 (t) cc_final: 0.8069 (t) REVERT: D 5 MET cc_start: 0.7282 (ptp) cc_final: 0.6964 (pmm) REVERT: D 1113 TRP cc_start: 0.8057 (m100) cc_final: 0.7151 (m100) outliers start: 70 outliers final: 48 residues processed: 358 average time/residue: 0.1498 time to fit residues: 83.5705 Evaluate side-chains 318 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 267 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE 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 152 SER Chi-restraints excluded: chain R residue 279 ASP Chi-restraints excluded: chain R residue 324 GLU Chi-restraints excluded: chain R residue 641 CYS Chi-restraints excluded: chain R residue 730 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 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 207 ILE Chi-restraints excluded: chain A residue 223 ASN 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 60 ILE 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 152 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 279 ASP Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 730 CYS 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 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 275 THR Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1072 THR Chi-restraints excluded: chain D residue 1111 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 232 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 178 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 247 optimal weight: 3.9990 chunk 155 optimal weight: 0.0770 chunk 59 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 overall best weight: 1.1342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 345 ASN S 91 GLN B 345 ASN C 198 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 = 0.4032 r_free = 0.4032 target = 0.127371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 89)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.107639 restraints weight = 47604.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.107743 restraints weight = 57321.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.108099 restraints weight = 42532.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.107550 restraints weight = 40320.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.107943 restraints weight = 36682.635| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 21634 Z= 0.167 Angle : 0.572 8.602 29520 Z= 0.291 Chirality : 0.045 0.393 3402 Planarity : 0.004 0.056 3706 Dihedral : 5.004 54.349 3460 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.01 % Favored : 93.92 % Rotamer: Outliers : 4.15 % Allowed : 18.81 % Favored : 77.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.30 (0.16), residues: 2696 helix: 0.95 (0.18), residues: 782 sheet: 0.47 (0.22), residues: 604 loop : -1.25 (0.16), residues: 1310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 99 TYR 0.028 0.002 TYR D1033 PHE 0.017 0.002 PHE A 244 TRP 0.009 0.001 TRP R 572 HIS 0.006 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00386 (21612) covalent geometry : angle 0.56968 (29472) SS BOND : bond 0.00325 ( 18) SS BOND : angle 1.17830 ( 36) hydrogen bonds : bond 0.03861 ( 942) hydrogen bonds : angle 4.85899 ( 2754) link_BETA1-4 : bond 0.00571 ( 2) link_BETA1-4 : angle 1.94560 ( 6) link_NAG-ASN : bond 0.00035 ( 2) link_NAG-ASN : angle 1.17072 ( 6) *********************** 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 375 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 286 time to evaluate : 0.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 ILE cc_start: 0.8557 (OUTLIER) cc_final: 0.8320 (mm) REVERT: R 307 GLU cc_start: 0.6756 (mm-30) cc_final: 0.6457 (mm-30) REVERT: R 324 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6864 (tt0) REVERT: R 334 ASP cc_start: 0.7444 (t0) cc_final: 0.7175 (t0) REVERT: R 338 GLN cc_start: 0.6053 (mt0) cc_final: 0.5705 (mt0) REVERT: R 387 GLU cc_start: 0.5726 (tt0) cc_final: 0.5446 (tt0) REVERT: R 506 THR cc_start: 0.6699 (p) cc_final: 0.6359 (t) REVERT: R 523 PRO cc_start: 0.7253 (Cg_endo) cc_final: 0.6913 (Cg_exo) REVERT: R 726 VAL cc_start: 0.8233 (t) cc_final: 0.7967 (t) REVERT: A 229 LYS cc_start: 0.7046 (mtmt) cc_final: 0.6790 (mttm) REVERT: S 5 MET cc_start: 0.7311 (ptp) cc_final: 0.7060 (pmm) REVERT: S 38 GLN cc_start: 0.7937 (pp30) cc_final: 0.7726 (tt0) REVERT: S 1113 TRP cc_start: 0.8031 (m100) cc_final: 0.7170 (m100) REVERT: B 95 ILE cc_start: 0.8558 (OUTLIER) cc_final: 0.8326 (mm) REVERT: B 307 GLU cc_start: 0.6759 (mm-30) cc_final: 0.6469 (mm-30) REVERT: B 324 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6809 (tt0) REVERT: B 334 ASP cc_start: 0.7396 (t0) cc_final: 0.7113 (t0) REVERT: B 338 GLN cc_start: 0.6035 (mt0) cc_final: 0.5679 (mt0) REVERT: B 506 THR cc_start: 0.6727 (p) cc_final: 0.6374 (t) REVERT: B 726 VAL cc_start: 0.8189 (t) cc_final: 0.7926 (t) REVERT: D 5 MET cc_start: 0.7338 (ptp) cc_final: 0.7029 (pmm) REVERT: D 1113 TRP cc_start: 0.8071 (m100) cc_final: 0.7188 (m100) outliers start: 89 outliers final: 72 residues processed: 357 average time/residue: 0.1377 time to fit residues: 77.8832 Evaluate side-chains 342 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 266 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE 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 152 SER Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 274 LEU 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 490 LEU Chi-restraints excluded: chain R residue 617 ILE Chi-restraints excluded: chain R residue 641 CYS Chi-restraints excluded: chain R residue 730 CYS Chi-restraints excluded: chain R residue 786 LEU Chi-restraints excluded: chain R residue 788 ILE Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain R residue 813 VAL Chi-restraints excluded: chain R residue 835 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 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 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 60 ILE 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 152 SER Chi-restraints excluded: chain B residue 154 SER Chi-restraints excluded: chain B residue 182 SER Chi-restraints excluded: chain B residue 274 LEU 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 343 TYR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 835 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 168 ILE 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 1072 THR Chi-restraints excluded: chain D residue 1111 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 10 optimal weight: 2.9990 chunk 83 optimal weight: 10.0000 chunk 113 optimal weight: 0.9980 chunk 184 optimal weight: 6.9990 chunk 230 optimal weight: 30.0000 chunk 257 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 183 optimal weight: 9.9990 chunk 219 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 171 optimal weight: 0.6980 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 386 GLN A 198 HIS A 281 ASN S 39 GLN S 91 GLN C 198 HIS C 281 ASN D 38 GLN D 91 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.125324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.105252 restraints weight = 47754.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.105122 restraints weight = 59370.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.105240 restraints weight = 43895.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.104767 restraints weight = 40649.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.105127 restraints weight = 36800.376| |-----------------------------------------------------------------------------| r_work (final): 0.3638 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3638 r_free = 0.3638 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6939 moved from start: 0.4628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 21634 Z= 0.274 Angle : 0.649 9.937 29520 Z= 0.330 Chirality : 0.046 0.180 3402 Planarity : 0.005 0.056 3706 Dihedral : 5.287 54.167 3460 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.20 % Favored : 92.73 % Rotamer: Outliers : 4.86 % Allowed : 19.56 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.53 (0.16), residues: 2696 helix: 0.62 (0.18), residues: 780 sheet: 0.38 (0.22), residues: 594 loop : -1.30 (0.16), residues: 1322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 188 TYR 0.024 0.002 TYR B 398 PHE 0.020 0.002 PHE S1105 TRP 0.009 0.002 TRP D1106 HIS 0.007 0.001 HIS R 94 Details of bonding type rmsd covalent geometry : bond 0.00635 (21612) covalent geometry : angle 0.64663 (29472) SS BOND : bond 0.00414 ( 18) SS BOND : angle 1.34458 ( 36) hydrogen bonds : bond 0.04374 ( 942) hydrogen bonds : angle 5.08676 ( 2754) link_BETA1-4 : bond 0.00551 ( 2) link_BETA1-4 : angle 2.25598 ( 6) link_NAG-ASN : bond 0.00139 ( 2) link_NAG-ASN : angle 1.13900 ( 6) *********************** 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 407 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 303 time to evaluate : 0.822 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 95 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8505 (mm) REVERT: R 114 ARG cc_start: 0.7527 (ttp-170) cc_final: 0.7162 (ttm170) REVERT: R 307 GLU cc_start: 0.6852 (mm-30) cc_final: 0.6524 (mm-30) REVERT: R 472 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7229 (pm20) REVERT: R 506 THR cc_start: 0.6819 (p) cc_final: 0.6476 (t) REVERT: R 523 PRO cc_start: 0.7385 (Cg_endo) cc_final: 0.7013 (Cg_exo) REVERT: R 726 VAL cc_start: 0.8359 (t) cc_final: 0.8073 (t) REVERT: S 5 MET cc_start: 0.7354 (ptp) cc_final: 0.6833 (ptt) REVERT: S 1113 TRP cc_start: 0.8049 (m100) cc_final: 0.7155 (m100) REVERT: B 95 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8484 (mm) REVERT: B 114 ARG cc_start: 0.7543 (ttp-170) cc_final: 0.7217 (ttm170) REVERT: B 307 GLU cc_start: 0.6855 (mm-30) cc_final: 0.6530 (mm-30) REVERT: B 391 MET cc_start: 0.7573 (ppp) cc_final: 0.7230 (ppp) REVERT: B 472 GLN cc_start: 0.8323 (OUTLIER) cc_final: 0.7232 (pm20) REVERT: B 506 THR cc_start: 0.6878 (p) cc_final: 0.6522 (t) REVERT: B 726 VAL cc_start: 0.8362 (t) cc_final: 0.8072 (t) REVERT: D 1113 TRP cc_start: 0.8113 (m100) cc_final: 0.7108 (m100) outliers start: 104 outliers final: 78 residues processed: 386 average time/residue: 0.1329 time to fit residues: 81.3029 Evaluate side-chains 371 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 289 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE 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 152 SER Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 324 GLU Chi-restraints excluded: chain R residue 386 GLN Chi-restraints excluded: chain R residue 472 GLN Chi-restraints excluded: chain R residue 604 THR Chi-restraints excluded: chain R residue 617 ILE Chi-restraints excluded: chain R residue 641 CYS Chi-restraints excluded: chain R residue 730 CYS Chi-restraints excluded: chain R residue 746 ILE Chi-restraints excluded: chain R residue 786 LEU Chi-restraints excluded: chain R residue 788 ILE Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain R residue 813 VAL Chi-restraints excluded: chain R residue 834 VAL Chi-restraints excluded: chain R residue 835 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 98 THR 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 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 60 ILE 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 152 SER Chi-restraints excluded: chain B residue 154 SER 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 343 TYR Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 490 LEU Chi-restraints excluded: chain B residue 604 THR Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 746 ILE Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 835 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 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 1072 THR Chi-restraints excluded: chain D residue 1111 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 95 optimal weight: 9.9990 chunk 91 optimal weight: 5.9990 chunk 100 optimal weight: 3.9990 chunk 159 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 188 optimal weight: 9.9990 chunk 166 optimal weight: 0.8980 chunk 192 optimal weight: 4.9990 chunk 234 optimal weight: 7.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS S 91 GLN C 198 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 = 0.4023 r_free = 0.4023 target = 0.126780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.106483 restraints weight = 47301.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.106607 restraints weight = 54024.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.106555 restraints weight = 40682.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.106213 restraints weight = 38604.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.106597 restraints weight = 36167.380| |-----------------------------------------------------------------------------| r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3662 r_free = 0.3662 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6908 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 21634 Z= 0.162 Angle : 0.579 9.009 29520 Z= 0.296 Chirality : 0.044 0.173 3402 Planarity : 0.004 0.056 3706 Dihedral : 5.112 54.188 3460 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.27 % Favored : 93.66 % Rotamer: Outliers : 4.39 % Allowed : 19.84 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.45 (0.16), residues: 2696 helix: 0.74 (0.18), residues: 782 sheet: 0.39 (0.22), residues: 594 loop : -1.27 (0.16), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 188 TYR 0.020 0.001 TYR R 569 PHE 0.030 0.002 PHE A 115 TRP 0.009 0.001 TRP B 572 HIS 0.008 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00375 (21612) covalent geometry : angle 0.57651 (29472) SS BOND : bond 0.00319 ( 18) SS BOND : angle 1.26351 ( 36) hydrogen bonds : bond 0.03982 ( 942) hydrogen bonds : angle 4.97405 ( 2754) link_BETA1-4 : bond 0.00451 ( 2) link_BETA1-4 : angle 1.83815 ( 6) link_NAG-ASN : bond 0.00007 ( 2) link_NAG-ASN : angle 1.31280 ( 6) *********************** 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 390 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 296 time to evaluate : 0.811 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 64 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7922 (mtt-85) REVERT: R 95 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8275 (mm) REVERT: R 307 GLU cc_start: 0.6808 (mm-30) cc_final: 0.6510 (mm-30) REVERT: R 391 MET cc_start: 0.7605 (ppp) cc_final: 0.7223 (ppp) REVERT: R 472 GLN cc_start: 0.8251 (OUTLIER) cc_final: 0.7080 (pm20) REVERT: R 506 THR cc_start: 0.6802 (p) cc_final: 0.6468 (t) REVERT: R 726 VAL cc_start: 0.8375 (t) cc_final: 0.8084 (t) REVERT: S 1113 TRP cc_start: 0.8012 (m100) cc_final: 0.7174 (m100) REVERT: B 64 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7798 (mtt-85) REVERT: B 95 ILE cc_start: 0.8582 (OUTLIER) cc_final: 0.8246 (mm) REVERT: B 114 ARG cc_start: 0.7477 (ttp-170) cc_final: 0.7113 (ttm170) REVERT: B 307 GLU cc_start: 0.6797 (mm-30) cc_final: 0.6490 (mm-30) REVERT: B 387 GLU cc_start: 0.5554 (tt0) cc_final: 0.5282 (tt0) REVERT: B 391 MET cc_start: 0.7572 (ppp) cc_final: 0.7233 (ppp) REVERT: B 400 MET cc_start: 0.7065 (tpp) cc_final: 0.6621 (mmp) REVERT: B 472 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7098 (pm20) REVERT: B 506 THR cc_start: 0.6856 (p) cc_final: 0.6496 (t) REVERT: B 726 VAL cc_start: 0.8383 (t) cc_final: 0.8092 (t) REVERT: D 22 ILE cc_start: 0.8898 (mm) cc_final: 0.8662 (mm) REVERT: D 1113 TRP cc_start: 0.8046 (m100) cc_final: 0.7192 (m100) outliers start: 94 outliers final: 74 residues processed: 374 average time/residue: 0.1320 time to fit residues: 78.1915 Evaluate side-chains 358 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 278 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 64 ARG 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 152 SER Chi-restraints excluded: chain R residue 182 SER Chi-restraints excluded: chain R residue 194 ASP Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 274 LEU Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 324 GLU Chi-restraints excluded: chain R residue 472 GLN Chi-restraints excluded: chain R residue 617 ILE Chi-restraints excluded: chain R residue 641 CYS Chi-restraints excluded: chain R residue 730 CYS Chi-restraints excluded: chain R residue 749 ILE Chi-restraints excluded: chain R residue 786 LEU Chi-restraints excluded: chain R residue 788 ILE Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain R residue 813 VAL Chi-restraints excluded: chain R residue 835 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 98 THR 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 60 ILE Chi-restraints excluded: chain B residue 64 ARG 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 152 SER Chi-restraints excluded: chain B residue 154 SER 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 344 ASN Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 617 ILE Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 749 ILE Chi-restraints excluded: chain B residue 786 LEU Chi-restraints excluded: chain B residue 788 ILE Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 813 VAL Chi-restraints excluded: chain B residue 835 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 1023 LEU Chi-restraints excluded: chain D residue 1072 THR Chi-restraints excluded: chain D residue 1111 ASP Chi-restraints excluded: chain R residue 1001 GLU Chi-restraints excluded: chain B residue 1001 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 108 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 161 optimal weight: 0.9990 chunk 246 optimal weight: 3.9990 chunk 241 optimal weight: 0.0970 chunk 131 optimal weight: 7.9990 chunk 221 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 263 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 91 GLN C 198 HIS 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 = 0.4034 r_free = 0.4034 target = 0.127610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.108989 restraints weight = 47416.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 79)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.105036 restraints weight = 54962.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.104802 restraints weight = 57958.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.105111 restraints weight = 44591.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.105254 restraints weight = 38918.000| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3621 r_free = 0.3621 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| r_final: 0.3621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 21634 Z= 0.139 Angle : 0.576 9.201 29520 Z= 0.292 Chirality : 0.043 0.165 3402 Planarity : 0.004 0.055 3706 Dihedral : 4.998 55.177 3460 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.68 % Favored : 94.25 % Rotamer: Outliers : 3.27 % Allowed : 21.52 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.40 (0.16), residues: 2696 helix: 0.79 (0.18), residues: 782 sheet: 0.39 (0.22), residues: 598 loop : -1.24 (0.16), residues: 1316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 188 TYR 0.023 0.001 TYR B 398 PHE 0.016 0.002 PHE B 74 TRP 0.011 0.001 TRP B 350 HIS 0.009 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00315 (21612) covalent geometry : angle 0.57443 (29472) SS BOND : bond 0.00296 ( 18) SS BOND : angle 1.24569 ( 36) hydrogen bonds : bond 0.03832 ( 942) hydrogen bonds : angle 4.87554 ( 2754) link_BETA1-4 : bond 0.00494 ( 2) link_BETA1-4 : angle 1.65517 ( 6) link_NAG-ASN : bond 0.00035 ( 2) link_NAG-ASN : angle 1.26769 ( 6) *********************** 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 351 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 281 time to evaluate : 0.851 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 64 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7879 (mtt-85) REVERT: R 307 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6510 (mm-30) REVERT: R 324 GLU cc_start: 0.7278 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: R 384 TYR cc_start: 0.8135 (p90) cc_final: 0.7565 (p90) REVERT: R 391 MET cc_start: 0.7602 (ppp) cc_final: 0.7259 (ppp) REVERT: R 472 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.6888 (pm20) REVERT: R 506 THR cc_start: 0.6814 (p) cc_final: 0.6491 (t) REVERT: R 726 VAL cc_start: 0.8568 (t) cc_final: 0.8250 (t) REVERT: S 91 GLN cc_start: 0.7106 (tm130) cc_final: 0.6776 (tm-30) REVERT: S 1041 ARG cc_start: 0.6574 (ptp90) cc_final: 0.6175 (ptp-110) REVERT: S 1113 TRP cc_start: 0.8021 (m100) cc_final: 0.7118 (m100) REVERT: B 95 ILE cc_start: 0.8470 (OUTLIER) cc_final: 0.8245 (mm) REVERT: B 307 GLU cc_start: 0.6817 (mm-30) cc_final: 0.6547 (mm-30) REVERT: B 384 TYR cc_start: 0.8107 (p90) cc_final: 0.7426 (p90) REVERT: B 391 MET cc_start: 0.7639 (ppp) cc_final: 0.7279 (ppp) REVERT: B 400 MET cc_start: 0.7059 (tpp) cc_final: 0.6646 (mmp) REVERT: B 472 GLN cc_start: 0.8153 (OUTLIER) cc_final: 0.6958 (pm20) REVERT: B 506 THR cc_start: 0.6862 (p) cc_final: 0.6521 (t) REVERT: B 726 VAL cc_start: 0.8577 (t) cc_final: 0.8261 (t) REVERT: D 22 ILE cc_start: 0.8814 (mm) cc_final: 0.8545 (mm) REVERT: D 91 GLN cc_start: 0.7089 (tm130) cc_final: 0.6763 (tm-30) REVERT: D 1113 TRP cc_start: 0.8061 (m100) cc_final: 0.7187 (m100) outliers start: 70 outliers final: 58 residues processed: 341 average time/residue: 0.1517 time to fit residues: 80.7820 Evaluate side-chains 335 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 272 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain R residue 66 ILE Chi-restraints excluded: chain R residue 74 PHE Chi-restraints excluded: chain R residue 113 VAL Chi-restraints excluded: chain R residue 152 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 472 GLN Chi-restraints excluded: chain R residue 641 CYS Chi-restraints excluded: chain R residue 730 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 R residue 835 VAL Chi-restraints excluded: chain A residue 38 ASP 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 76 ILE Chi-restraints excluded: chain S residue 1023 LEU Chi-restraints excluded: chain S residue 1111 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 95 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 154 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 343 TYR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 730 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 B residue 835 VAL Chi-restraints excluded: chain C residue 38 ASP 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 76 ILE Chi-restraints excluded: chain D residue 1023 LEU Chi-restraints excluded: chain D residue 1072 THR Chi-restraints excluded: chain D residue 1111 ASP Chi-restraints excluded: chain R residue 1001 GLU Chi-restraints excluded: chain B residue 1001 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 68 optimal weight: 1.9990 chunk 199 optimal weight: 0.2980 chunk 178 optimal weight: 0.8980 chunk 247 optimal weight: 1.9990 chunk 123 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 164 optimal weight: 0.0270 chunk 193 optimal weight: 6.9990 chunk 130 optimal weight: 5.9990 chunk 141 optimal weight: 0.3980 chunk 244 optimal weight: 4.9990 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 699 GLN A 210 HIS B 699 GLN C 210 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 = 0.4047 r_free = 0.4047 target = 0.127191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.110788 restraints weight = 49060.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.111044 restraints weight = 68355.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.111756 restraints weight = 67864.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.112065 restraints weight = 38618.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.112461 restraints weight = 35537.316| |-----------------------------------------------------------------------------| r_work (final): 0.3773 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3773 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 10 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3773 r_free = 0.3773 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| r_final: 0.3773 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.4688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 21634 Z= 0.123 Angle : 0.573 12.512 29520 Z= 0.287 Chirality : 0.043 0.166 3402 Planarity : 0.004 0.055 3706 Dihedral : 4.871 55.582 3460 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.42 % Favored : 94.51 % Rotamer: Outliers : 3.17 % Allowed : 21.48 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.16), residues: 2696 helix: 0.91 (0.18), residues: 782 sheet: 0.66 (0.23), residues: 582 loop : -1.25 (0.16), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 188 TYR 0.023 0.001 TYR D 50 PHE 0.024 0.001 PHE A 115 TRP 0.011 0.001 TRP B 350 HIS 0.009 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00284 (21612) covalent geometry : angle 0.57070 (29472) SS BOND : bond 0.00264 ( 18) SS BOND : angle 1.22856 ( 36) hydrogen bonds : bond 0.03695 ( 942) hydrogen bonds : angle 4.76004 ( 2754) link_BETA1-4 : bond 0.00451 ( 2) link_BETA1-4 : angle 1.50586 ( 6) link_NAG-ASN : bond 0.00068 ( 2) link_NAG-ASN : angle 1.22632 ( 6) ********************** 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 340 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 272 time to evaluate : 0.725 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 64 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.7618 (mtt-85) REVERT: R 307 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6602 (mm-30) REVERT: R 384 TYR cc_start: 0.8061 (p90) cc_final: 0.7523 (p90) REVERT: R 472 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.6612 (pm20) REVERT: R 506 THR cc_start: 0.6793 (p) cc_final: 0.6452 (t) REVERT: R 726 VAL cc_start: 0.8390 (t) cc_final: 0.8110 (t) REVERT: A 275 THR cc_start: 0.7955 (OUTLIER) cc_final: 0.7492 (p) REVERT: S 1041 ARG cc_start: 0.6654 (ptp90) cc_final: 0.6358 (ptp-110) REVERT: S 1113 TRP cc_start: 0.7957 (m100) cc_final: 0.7135 (m100) REVERT: B 64 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7595 (mtt-85) REVERT: B 221 ASP cc_start: 0.6306 (t70) cc_final: 0.5683 (m-30) REVERT: B 307 GLU cc_start: 0.6920 (mm-30) cc_final: 0.6610 (mm-30) REVERT: B 338 GLN cc_start: 0.7468 (mm-40) cc_final: 0.7114 (mm-40) REVERT: B 384 TYR cc_start: 0.8083 (p90) cc_final: 0.7478 (p90) REVERT: B 391 MET cc_start: 0.7486 (ppp) cc_final: 0.7276 (ppp) REVERT: B 472 GLN cc_start: 0.8019 (OUTLIER) cc_final: 0.6637 (pm20) REVERT: B 506 THR cc_start: 0.6822 (p) cc_final: 0.6467 (t) REVERT: B 726 VAL cc_start: 0.8361 (t) cc_final: 0.8076 (t) REVERT: C 275 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7476 (p) REVERT: D 22 ILE cc_start: 0.8871 (mm) cc_final: 0.8633 (mm) REVERT: D 38 GLN cc_start: 0.7630 (tm130) cc_final: 0.7020 (tt0) REVERT: D 1113 TRP cc_start: 0.8023 (m100) cc_final: 0.7129 (m100) outliers start: 68 outliers final: 55 residues processed: 328 average time/residue: 0.1593 time to fit residues: 80.0578 Evaluate side-chains 322 residues out of total 2394 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 261 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 60 ILE Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain R residue 74 PHE 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 243 THR Chi-restraints excluded: chain R residue 279 ASP Chi-restraints excluded: chain R residue 316 VAL Chi-restraints excluded: chain R residue 472 GLN Chi-restraints excluded: chain R residue 641 CYS Chi-restraints excluded: chain R residue 730 CYS Chi-restraints excluded: chain R residue 758 THR Chi-restraints excluded: chain R residue 805 ILE Chi-restraints excluded: chain R residue 834 VAL Chi-restraints excluded: chain R residue 835 VAL Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 67 ASP Chi-restraints excluded: chain A residue 98 THR 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 76 ILE Chi-restraints excluded: chain S residue 1023 LEU Chi-restraints excluded: chain S residue 1111 ASP Chi-restraints excluded: chain B residue 60 ILE Chi-restraints excluded: chain B residue 64 ARG Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 194 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 316 VAL Chi-restraints excluded: chain B residue 343 TYR Chi-restraints excluded: chain B residue 344 ASN Chi-restraints excluded: chain B residue 472 GLN Chi-restraints excluded: chain B residue 641 CYS Chi-restraints excluded: chain B residue 730 CYS Chi-restraints excluded: chain B residue 758 THR Chi-restraints excluded: chain B residue 805 ILE Chi-restraints excluded: chain B residue 834 VAL Chi-restraints excluded: chain B residue 835 VAL Chi-restraints excluded: chain C residue 38 ASP 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 1023 LEU Chi-restraints excluded: chain D residue 1072 THR Chi-restraints excluded: chain D residue 1111 ASP Chi-restraints excluded: chain R residue 1001 GLU Chi-restraints excluded: chain B residue 1001 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 272 random chunks: chunk 183 optimal weight: 6.9990 chunk 66 optimal weight: 10.0000 chunk 2 optimal weight: 3.9990 chunk 123 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 203 optimal weight: 4.9990 chunk 194 optimal weight: 0.6980 chunk 260 optimal weight: 0.9990 chunk 198 optimal weight: 3.9990 chunk 103 optimal weight: 0.7980 chunk 217 optimal weight: 10.0000 overall best weight: 0.9082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 829 GLN A 223 ASN S 91 GLN C 210 HIS C 223 ASN D 91 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.127922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 105)---------------| | r_work = 0.3693 r_free = 0.3693 target = 0.107631 restraints weight = 47667.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.107530 restraints weight = 57715.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.107307 restraints weight = 42644.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.106989 restraints weight = 42184.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.107185 restraints weight = 40000.233| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3669 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 13 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3669 r_free = 0.3669 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 12 | |-----------------------------------------------------------------------------| r_final: 0.3669 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6888 moved from start: 0.4759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 21634 Z= 0.150 Angle : 0.602 18.464 29520 Z= 0.299 Chirality : 0.043 0.166 3402 Planarity : 0.004 0.055 3706 Dihedral : 4.916 56.030 3460 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.86 % Favored : 94.07 % Rotamer: Outliers : 3.27 % Allowed : 21.57 % Favored : 75.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.94 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.16), residues: 2696 helix: 0.93 (0.18), residues: 782 sheet: 0.52 (0.23), residues: 588 loop : -1.18 (0.16), residues: 1326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 188 TYR 0.022 0.001 TYR R 398 PHE 0.024 0.002 PHE A 115 TRP 0.012 0.001 TRP B 355 HIS 0.010 0.001 HIS B 405 Details of bonding type rmsd covalent geometry : bond 0.00349 (21612) covalent geometry : angle 0.60009 (29472) SS BOND : bond 0.00294 ( 18) SS BOND : angle 1.24991 ( 36) hydrogen bonds : bond 0.03861 ( 942) hydrogen bonds : angle 4.77156 ( 2754) link_BETA1-4 : bond 0.00470 ( 2) link_BETA1-4 : angle 1.64222 ( 6) link_NAG-ASN : bond 0.00017 ( 2) link_NAG-ASN : angle 1.17144 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3978.40 seconds wall clock time: 69 minutes 25.88 seconds (4165.88 seconds total)