Starting phenix.real_space_refine on Tue Aug 26 06:34:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xa1_38191/08_2025/8xa1_38191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xa1_38191/08_2025/8xa1_38191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xa1_38191/08_2025/8xa1_38191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xa1_38191/08_2025/8xa1_38191.map" model { file = "/net/cci-nas-00/data/ceres_data/8xa1_38191/08_2025/8xa1_38191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xa1_38191/08_2025/8xa1_38191.cif" } resolution = 4.8 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= 0.001 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 196 5.16 5 C 21575 2.51 5 N 5976 2.21 5 O 6234 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 61 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33981 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 10340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1345, 10340 Classifications: {'peptide': 1345} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 43} Link IDs: {'PCIS': 1, 'PTRANS': 81, 'TRANS': 1262} Chain breaks: 2 Unresolved non-hydrogen bonds: 187 Unresolved non-hydrogen angles: 231 Unresolved non-hydrogen dihedrals: 145 Unresolved non-hydrogen chiralities: 14 Planarities with less than four sites: {'ARG:plan': 14, 'ASP:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLN:plan1': 2, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 124 Chain: "C" Number of atoms: 10033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1297, 10033 Classifications: {'peptide': 1297} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 16} Link IDs: {'PCIS': 1, 'PTRANS': 82, 'TRANS': 1213} Chain breaks: 2 Unresolved non-hydrogen bonds: 104 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 86 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 12, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "G" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 8, 'PTRANS': 21, 'TRANS': 267} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 3, 'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "I" Number of atoms: 2124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2124 Classifications: {'peptide': 297} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'CIS': 8, 'PTRANS': 21, 'TRANS': 267} Chain breaks: 4 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 140 Unresolved non-hydrogen angles: 179 Unresolved non-hydrogen dihedrals: 108 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ASP:plan': 9, 'ARG:plan': 3, 'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 1, 'GLU:plan': 3, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "P" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2279 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 13, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 273} Chain breaks: 3 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 63 Chain: "R" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2279 Classifications: {'peptide': 307} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'CIS': 13, 'PCIS': 2, 'PTRANS': 18, 'TRANS': 273} Chain breaks: 3 Unresolved non-hydrogen bonds: 66 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 50 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 4, 'ARG:plan': 3, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 63 Chain: "Y" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2198 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'CIS': 22, 'PTRANS': 10, 'TRANS': 256} Chain breaks: 2 Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 119 Unresolved non-hydrogen dihedrals: 82 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 6, 'HIS:plan': 1, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 81 Chain: "d" Number of atoms: 2604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 357, 2604 Classifications: {'peptide': 357} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'CIS': 35, 'PCIS': 1, 'PTRANS': 12, 'TRANS': 308} Chain breaks: 4 Unresolved non-hydrogen bonds: 121 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 104 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ARG:plan': 7, 'ASN:plan1': 2, 'PHE:plan': 2, 'HIS:plan': 1, 'GLU:plan': 6, 'GLN:plan1': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 98 Time building chain proxies: 6.75, per 1000 atoms: 0.20 Number of scatterers: 33981 At special positions: 0 Unit cell: (193.05, 193.05, 180.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 196 16.00 O 6234 8.00 N 5976 7.00 C 21575 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 846 " - pdb=" SG CYS A 985 " distance=2.03 Simple disulfide: pdb=" SG CYS C 846 " - pdb=" SG CYS C 985 " 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 Time building additional restraints: 2.36 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 476.8 nanoseconds 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8404 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 49 sheets defined 29.3% alpha, 11.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.94 Creating SS restraints... Processing helix chain 'A' and resid 149 through 156 Processing helix chain 'A' and resid 163 through 202 removed outlier: 3.969A pdb=" N SER A 167 " --> pdb=" O THR A 163 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N SER A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N LEU A 169 " --> pdb=" O ILE A 165 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N PHE A 188 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLU A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ALA A 193 " --> pdb=" O GLU A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 217 Proline residue: A 212 - end of helix removed outlier: 3.844A pdb=" N LYS A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 241 removed outlier: 3.671A pdb=" N ASP A 241 " --> pdb=" O ARG A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 264 removed outlier: 3.971A pdb=" N SER A 256 " --> pdb=" O PRO A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 303 removed outlier: 3.887A pdb=" N GLY A 302 " --> pdb=" O GLN A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 338 removed outlier: 3.782A pdb=" N ASN A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N LEU A 331 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N LEU A 335 " --> pdb=" O LEU A 331 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 336 " --> pdb=" O VAL A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 Processing helix chain 'A' and resid 352 through 357 removed outlier: 3.988A pdb=" N GLU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 479 removed outlier: 3.611A pdb=" N CYS A 479 " --> pdb=" O MET A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.731A pdb=" N LEU A 483 " --> pdb=" O HIS A 480 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 484 " --> pdb=" O SER A 481 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ASP A 485 " --> pdb=" O SER A 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 480 through 485' Processing helix chain 'A' and resid 486 through 494 Processing helix chain 'A' and resid 517 through 528 Processing helix chain 'A' and resid 543 through 549 Processing helix chain 'A' and resid 552 through 556 removed outlier: 3.850A pdb=" N LEU A 555 " --> pdb=" O ASN A 552 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ARG A 556 " --> pdb=" O PRO A 553 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 552 through 556' Processing helix chain 'A' and resid 594 through 598 removed outlier: 3.613A pdb=" N ILE A 598 " --> pdb=" O ASN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 616 Processing helix chain 'A' and resid 623 through 634 removed outlier: 3.624A pdb=" N ILE A 627 " --> pdb=" O THR A 623 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 651 Processing helix chain 'A' and resid 653 through 659 removed outlier: 3.762A pdb=" N ALA A 659 " --> pdb=" O ARG A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 673 removed outlier: 3.914A pdb=" N LEU A 664 " --> pdb=" O LEU A 660 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLU A 673 " --> pdb=" O ARG A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 694 removed outlier: 4.601A pdb=" N LEU A 687 " --> pdb=" O ASN A 683 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N MET A 688 " --> pdb=" O PHE A 684 " (cutoff:3.500A) removed outlier: 5.693A pdb=" N TYR A 689 " --> pdb=" O HIS A 685 " (cutoff:3.500A) Processing helix chain 'A' and resid 700 through 724 removed outlier: 3.518A pdb=" N PHE A 724 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 735 through 741 Processing helix chain 'A' and resid 756 through 766 Processing helix chain 'A' and resid 822 through 835 removed outlier: 3.774A pdb=" N GLY A 826 " --> pdb=" O ASP A 822 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ILE A 827 " --> pdb=" O ARG A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 835 through 842 Processing helix chain 'A' and resid 851 through 860 removed outlier: 3.645A pdb=" N LEU A 855 " --> pdb=" O ARG A 851 " (cutoff:3.500A) Proline residue: A 857 - end of helix removed outlier: 3.979A pdb=" N GLN A 860 " --> pdb=" O TYR A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 885 through 889 Processing helix chain 'A' and resid 893 through 902 removed outlier: 3.775A pdb=" N TYR A 897 " --> pdb=" O SER A 893 " (cutoff:3.500A) Processing helix chain 'A' and resid 906 through 912 Processing helix chain 'A' and resid 912 through 917 Processing helix chain 'A' and resid 987 through 992 removed outlier: 3.790A pdb=" N ALA A 990 " --> pdb=" O GLU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 997 through 1004 Processing helix chain 'A' and resid 1010 through 1014 removed outlier: 3.501A pdb=" N GLY A1014 " --> pdb=" O PRO A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1022 through 1032 removed outlier: 3.678A pdb=" N ALA A1026 " --> pdb=" O ARG A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1035 through 1047 Processing helix chain 'A' and resid 1051 through 1062 Processing helix chain 'A' and resid 1147 through 1151 removed outlier: 3.863A pdb=" N PHE A1150 " --> pdb=" O ASN A1147 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1172 removed outlier: 3.686A pdb=" N THR A1163 " --> pdb=" O HIS A1159 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER A1172 " --> pdb=" O ARG A1168 " (cutoff:3.500A) Processing helix chain 'A' and resid 1214 through 1218 Processing helix chain 'A' and resid 1242 through 1247 Processing helix chain 'A' and resid 1270 through 1277 removed outlier: 3.619A pdb=" N ASN A1277 " --> pdb=" O ASP A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1278 through 1281 Processing helix chain 'A' and resid 1290 through 1294 removed outlier: 4.278A pdb=" N LYS A1294 " --> pdb=" O PRO A1291 " (cutoff:3.500A) Processing helix chain 'A' and resid 1306 through 1315 removed outlier: 3.779A pdb=" N ARG A1310 " --> pdb=" O ASN A1306 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 89 Processing helix chain 'C' and resid 98 through 102 removed outlier: 3.669A pdb=" N TYR C 101 " --> pdb=" O GLU C 98 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL C 102 " --> pdb=" O LEU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 102' Processing helix chain 'C' and resid 148 through 156 removed outlier: 3.543A pdb=" N LEU C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 166 through 202 removed outlier: 5.385A pdb=" N ARG C 172 " --> pdb=" O SER C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 217 Proline residue: C 212 - end of helix Processing helix chain 'C' and resid 223 through 241 removed outlier: 3.553A pdb=" N ASP C 241 " --> pdb=" O ARG C 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.801A pdb=" N HIS C 248 " --> pdb=" O PHE C 244 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 264 Processing helix chain 'C' and resid 292 through 301 Processing helix chain 'C' and resid 324 through 333 Processing helix chain 'C' and resid 472 through 477 removed outlier: 4.426A pdb=" N MET C 475 " --> pdb=" O ARG C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 480 through 485 removed outlier: 3.738A pdb=" N ASP C 485 " --> pdb=" O SER C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 486 through 494 removed outlier: 3.577A pdb=" N ARG C 494 " --> pdb=" O LEU C 490 " (cutoff:3.500A) Processing helix chain 'C' and resid 516 through 528 removed outlier: 3.597A pdb=" N MET C 520 " --> pdb=" O LEU C 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 549 Processing helix chain 'C' and resid 552 through 558 removed outlier: 3.719A pdb=" N LEU C 555 " --> pdb=" O ASN C 552 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG C 556 " --> pdb=" O PRO C 553 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N PHE C 557 " --> pdb=" O ARG C 554 " (cutoff:3.500A) Processing helix chain 'C' and resid 594 through 598 removed outlier: 3.869A pdb=" N ILE C 598 " --> pdb=" O ASN C 595 " (cutoff:3.500A) Processing helix chain 'C' and resid 604 through 616 removed outlier: 3.760A pdb=" N ARG C 608 " --> pdb=" O PRO C 604 " (cutoff:3.500A) Processing helix chain 'C' and resid 623 through 635 Processing helix chain 'C' and resid 640 through 651 removed outlier: 4.080A pdb=" N TYR C 644 " --> pdb=" O PRO C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 653 through 658 Processing helix chain 'C' and resid 660 through 676 removed outlier: 3.999A pdb=" N LEU C 664 " --> pdb=" O LEU C 660 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN C 674 " --> pdb=" O GLY C 670 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER C 675 " --> pdb=" O TYR C 671 " (cutoff:3.500A) Processing helix chain 'C' and resid 686 through 693 Processing helix chain 'C' and resid 700 through 724 removed outlier: 3.829A pdb=" N ILE C 704 " --> pdb=" O PRO C 700 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE C 724 " --> pdb=" O THR C 720 " (cutoff:3.500A) Processing helix chain 'C' and resid 756 through 764 Processing helix chain 'C' and resid 822 through 842 removed outlier: 3.623A pdb=" N GLY C 826 " --> pdb=" O ASP C 822 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE C 837 " --> pdb=" O TYR C 833 " (cutoff:3.500A) Proline residue: C 838 - end of helix Processing helix chain 'C' and resid 851 through 860 Proline residue: C 857 - end of helix Processing helix chain 'C' and resid 885 through 889 Processing helix chain 'C' and resid 893 through 901 removed outlier: 3.523A pdb=" N ALA C 901 " --> pdb=" O TYR C 897 " (cutoff:3.500A) Processing helix chain 'C' and resid 906 through 912 Processing helix chain 'C' and resid 912 through 917 Processing helix chain 'C' and resid 939 through 943 removed outlier: 3.563A pdb=" N ARG C 943 " --> pdb=" O ALA C 940 " (cutoff:3.500A) Processing helix chain 'C' and resid 987 through 992 removed outlier: 3.524A pdb=" N ALA C 990 " --> pdb=" O GLU C 987 " (cutoff:3.500A) Processing helix chain 'C' and resid 996 through 1006 Processing helix chain 'C' and resid 1010 through 1014 Processing helix chain 'C' and resid 1022 through 1031 removed outlier: 3.862A pdb=" N ALA C1026 " --> pdb=" O ARG C1022 " (cutoff:3.500A) Processing helix chain 'C' and resid 1036 through 1046 Processing helix chain 'C' and resid 1051 through 1061 Processing helix chain 'C' and resid 1147 through 1151 removed outlier: 3.841A pdb=" N PHE C1150 " --> pdb=" O ASN C1147 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER C1151 " --> pdb=" O LEU C1148 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 1147 through 1151' Processing helix chain 'C' and resid 1159 through 1172 removed outlier: 3.573A pdb=" N THR C1163 " --> pdb=" O HIS C1159 " (cutoff:3.500A) Processing helix chain 'C' and resid 1214 through 1220 removed outlier: 3.797A pdb=" N THR C1220 " --> pdb=" O TYR C1217 " (cutoff:3.500A) Processing helix chain 'C' and resid 1239 through 1244 removed outlier: 4.141A pdb=" N ALA C1243 " --> pdb=" O ALA C1239 " (cutoff:3.500A) Processing helix chain 'C' and resid 1270 through 1277 Processing helix chain 'C' and resid 1278 through 1281 Processing helix chain 'C' and resid 1292 through 1297 Processing helix chain 'C' and resid 1306 through 1315 removed outlier: 3.759A pdb=" N ARG C1310 " --> pdb=" O ASN C1306 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 26 removed outlier: 3.989A pdb=" N LEU G 24 " --> pdb=" O GLU G 20 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN G 25 " --> pdb=" O THR G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 52 removed outlier: 3.524A pdb=" N SER G 50 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 removed outlier: 4.007A pdb=" N LEU G 64 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N ALA G 66 " --> pdb=" O SER G 62 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ARG G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 153 through 159 removed outlier: 4.018A pdb=" N GLU G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 190 through 194 removed outlier: 4.108A pdb=" N LEU G 193 " --> pdb=" O VAL G 190 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA G 194 " --> pdb=" O GLN G 191 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 190 through 194' Processing helix chain 'G' and resid 198 through 208 removed outlier: 3.944A pdb=" N THR G 202 " --> pdb=" O ALA G 198 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LEU G 203 " --> pdb=" O ALA G 199 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 243 Processing helix chain 'G' and resid 246 through 256 Proline residue: G 254 - end of helix Processing helix chain 'G' and resid 266 through 273 removed outlier: 4.025A pdb=" N GLU G 271 " --> pdb=" O LEU G 267 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 286 Processing helix chain 'I' and resid 21 through 26 removed outlier: 4.060A pdb=" N GLN I 25 " --> pdb=" O THR I 21 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N LYS I 26 " --> pdb=" O SER I 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 21 through 26' Processing helix chain 'I' and resid 47 through 52 removed outlier: 3.504A pdb=" N TYR I 52 " --> pdb=" O SER I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 68 removed outlier: 3.800A pdb=" N LEU I 64 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ALA I 66 " --> pdb=" O SER I 62 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG I 68 " --> pdb=" O LEU I 64 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 162 removed outlier: 3.704A pdb=" N GLU I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 208 Processing helix chain 'I' and resid 234 through 243 Processing helix chain 'I' and resid 247 through 256 Proline residue: I 254 - end of helix Processing helix chain 'I' and resid 268 through 273 removed outlier: 4.007A pdb=" N THR I 272 " --> pdb=" O PRO I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 281 through 287 Processing helix chain 'P' and resid 17 through 27 removed outlier: 3.758A pdb=" N THR P 21 " --> pdb=" O SER P 17 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER P 22 " --> pdb=" O PRO P 18 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 69 removed outlier: 3.905A pdb=" N GLU P 65 " --> pdb=" O LEU P 61 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET P 69 " --> pdb=" O GLU P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 151 through 160 Processing helix chain 'P' and resid 198 through 207 Processing helix chain 'P' and resid 212 through 216 Processing helix chain 'P' and resid 222 through 231 removed outlier: 4.142A pdb=" N ALA P 230 " --> pdb=" O LEU P 226 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N HIS P 231 " --> pdb=" O VAL P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 282 through 288 Processing helix chain 'R' and resid 17 through 27 removed outlier: 3.511A pdb=" N SER R 22 " --> pdb=" O PRO R 18 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 69 Processing helix chain 'R' and resid 154 through 159 Processing helix chain 'R' and resid 198 through 206 Processing helix chain 'R' and resid 222 through 229 Processing helix chain 'R' and resid 271 through 276 Processing helix chain 'R' and resid 282 through 288 Processing helix chain 'Y' and resid 154 through 168 removed outlier: 3.913A pdb=" N ALA Y 158 " --> pdb=" O THR Y 154 " (cutoff:3.500A) Processing helix chain 'Y' and resid 188 through 194 Processing helix chain 'Y' and resid 201 through 207 removed outlier: 3.675A pdb=" N ASN Y 207 " --> pdb=" O ALA Y 203 " (cutoff:3.500A) Processing helix chain 'Y' and resid 209 through 216 Processing helix chain 'Y' and resid 224 through 237 Processing helix chain 'Y' and resid 339 through 345 Processing helix chain 'd' and resid 154 through 161 removed outlier: 3.508A pdb=" N ALA d 158 " --> pdb=" O THR d 154 " (cutoff:3.500A) Processing helix chain 'd' and resid 161 through 166 Processing helix chain 'd' and resid 188 through 194 Processing helix chain 'd' and resid 201 through 207 Processing helix chain 'd' and resid 209 through 216 removed outlier: 3.635A pdb=" N SER d 213 " --> pdb=" O THR d 209 " (cutoff:3.500A) Processing helix chain 'd' and resid 224 through 237 Processing helix chain 'd' and resid 339 through 345 removed outlier: 3.549A pdb=" N PHE d 345 " --> pdb=" O ARG d 341 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 105 through 107 Processing sheet with id=AA2, first strand: chain 'A' and resid 137 through 143 Processing sheet with id=AA3, first strand: chain 'A' and resid 146 through 148 Processing sheet with id=AA4, first strand: chain 'A' and resid 306 through 313 removed outlier: 6.833A pdb=" N LEU A 384 " --> pdb=" O ASP A 307 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR A 309 " --> pdb=" O ALA A 382 " (cutoff:3.500A) removed outlier: 10.326A pdb=" N ALA A 396 " --> pdb=" O PRO A 381 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N ASP A 383 " --> pdb=" O LEU A 394 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N LEU A 394 " --> pdb=" O ASP A 383 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N VAL A 387 " --> pdb=" O LYS A 390 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LYS A 390 " --> pdb=" O VAL A 387 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A1083 " --> pdb=" O VAL A 290 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N LEU A1082 " --> pdb=" O THR A1131 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N THR A1131 " --> pdb=" O LEU A1082 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N TYR A1084 " --> pdb=" O CYS A1129 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N CYS A1129 " --> pdb=" O TYR A1084 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 414 through 422 removed outlier: 4.131A pdb=" N GLN A1074 " --> pdb=" O VAL A1203 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL A1203 " --> pdb=" O GLN A1074 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N THR A1144 " --> pdb=" O CYS A1204 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N PHE A1206 " --> pdb=" O THR A1144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 563 through 568 Processing sheet with id=AA7, first strand: chain 'A' and resid 752 through 753 Processing sheet with id=AA8, first strand: chain 'A' and resid 956 through 958 removed outlier: 4.200A pdb=" N MET A 958 " --> pdb=" O CYS A 846 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N CYS A 846 " --> pdb=" O MET A 958 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1317 through 1319 Processing sheet with id=AB1, first strand: chain 'A' and resid 1355 through 1356 removed outlier: 3.514A pdb=" N CYS A1355 " --> pdb=" O ILE A1382 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 91 through 95 removed outlier: 6.222A pdb=" N ILE C 92 " --> pdb=" O TYR C1092 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL C1094 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR C 94 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 91 through 95 removed outlier: 6.222A pdb=" N ILE C 92 " --> pdb=" O TYR C1092 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N VAL C1094 " --> pdb=" O ILE C 92 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N THR C 94 " --> pdb=" O VAL C1094 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 106 through 112 Processing sheet with id=AB5, first strand: chain 'C' and resid 278 through 279 removed outlier: 6.548A pdb=" N ILE C 306 " --> pdb=" O ILE C 386 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ILE C 386 " --> pdb=" O ILE C 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ASP C 308 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ALA C 310 " --> pdb=" O ALA C 382 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N ALA C 382 " --> pdb=" O ALA C 310 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP C 312 " --> pdb=" O VAL C 380 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL C 380 " --> pdb=" O ASP C 312 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASP C 383 " --> pdb=" O LEU C 394 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU C 394 " --> pdb=" O ASP C 383 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N GLY C 287 " --> pdb=" O LEU C 391 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 414 through 422 removed outlier: 7.775A pdb=" N ARG C1076 " --> pdb=" O PRO C1137 " (cutoff:3.500A) removed outlier: 5.755A pdb=" N ALA C1078 " --> pdb=" O ARG C1135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 414 through 422 removed outlier: 4.400A pdb=" N GLN C1074 " --> pdb=" O VAL C1203 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N VAL C1203 " --> pdb=" O GLN C1074 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N THR C1144 " --> pdb=" O CYS C1204 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N PHE C1206 " --> pdb=" O THR C1144 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 466 through 470 removed outlier: 3.814A pdb=" N PHE C 459 " --> pdb=" O THR C 467 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 563 through 569 Processing sheet with id=AC1, first strand: chain 'C' and resid 752 through 753 Processing sheet with id=AC2, first strand: chain 'C' and resid 846 through 847 Processing sheet with id=AC3, first strand: chain 'C' and resid 1318 through 1319 Processing sheet with id=AC4, first strand: chain 'G' and resid 31 through 34 Processing sheet with id=AC5, first strand: chain 'G' and resid 99 through 100 removed outlier: 3.617A pdb=" N ILE G 99 " --> pdb=" O THR G 310 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N THR G 310 " --> pdb=" O ILE G 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'G' and resid 112 through 115 Processing sheet with id=AC7, first strand: chain 'G' and resid 127 through 128 Processing sheet with id=AC8, first strand: chain 'G' and resid 177 through 179 removed outlier: 3.807A pdb=" N TYR G 179 " --> pdb=" O ALA G 182 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALA G 182 " --> pdb=" O TYR G 179 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 31 through 34 Processing sheet with id=AD1, first strand: chain 'I' and resid 99 through 100 Processing sheet with id=AD2, first strand: chain 'I' and resid 127 through 128 removed outlier: 3.519A pdb=" N LEU I 128 " --> pdb=" O LEU I 133 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU I 133 " --> pdb=" O LEU I 128 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'I' and resid 177 through 179 Processing sheet with id=AD4, first strand: chain 'P' and resid 40 through 41 removed outlier: 6.285A pdb=" N GLU P 9 " --> pdb=" O ALA P 41 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 30 through 34 removed outlier: 3.777A pdb=" N LYS P 30 " --> pdb=" O ILE P 75 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'P' and resid 99 through 100 removed outlier: 4.790A pdb=" N ILE P 99 " --> pdb=" O THR P 310 " (cutoff:3.500A) removed outlier: 4.761A pdb=" N THR P 310 " --> pdb=" O ILE P 99 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'P' and resid 139 through 142 removed outlier: 3.972A pdb=" N LEU P 293 " --> pdb=" O ILE P 113 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 40 through 41 removed outlier: 6.458A pdb=" N GLU R 9 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ALA R 85 " --> pdb=" O ILE R 8 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL R 10 " --> pdb=" O LEU R 83 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 31 through 34 Processing sheet with id=AE1, first strand: chain 'R' and resid 99 through 100 Processing sheet with id=AE2, first strand: chain 'R' and resid 139 through 142 Processing sheet with id=AE3, first strand: chain 'Y' and resid 111 through 116 Processing sheet with id=AE4, first strand: chain 'Y' and resid 184 through 186 removed outlier: 4.588A pdb=" N ILE Y 133 " --> pdb=" O PHE Y 247 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N PHE Y 247 " --> pdb=" O ILE Y 133 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Y' and resid 269 through 270 removed outlier: 3.619A pdb=" N GLY Y 269 " --> pdb=" O TRP Y 457 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Y' and resid 288 through 289 removed outlier: 4.044A pdb=" N ILE Y 288 " --> pdb=" O LEU Y 452 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Y' and resid 327 through 332 removed outlier: 6.739A pdb=" N LEU Y 312 " --> pdb=" O LEU Y 424 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N LEU Y 424 " --> pdb=" O LEU Y 312 " (cutoff:3.500A) removed outlier: 7.666A pdb=" N PHE Y 314 " --> pdb=" O TYR Y 422 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N TYR Y 422 " --> pdb=" O PHE Y 314 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Y' and resid 439 through 440 removed outlier: 3.739A pdb=" N GLU Y 440 " --> pdb=" O VAL Y 447 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N VAL Y 447 " --> pdb=" O GLU Y 440 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE8 Processing sheet with id=AE9, first strand: chain 'd' and resid 111 through 116 Processing sheet with id=AF1, first strand: chain 'd' and resid 183 through 186 removed outlier: 6.841A pdb=" N VAL d 131 " --> pdb=" O PHE d 248 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'd' and resid 269 through 270 removed outlier: 4.230A pdb=" N GLY d 269 " --> pdb=" O TRP d 457 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'd' and resid 288 through 289 removed outlier: 4.608A pdb=" N ILE d 288 " --> pdb=" O LEU d 452 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LEU d 452 " --> pdb=" O ILE d 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'd' and resid 327 through 332 removed outlier: 6.807A pdb=" N LEU d 312 " --> pdb=" O LEU d 424 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N LEU d 424 " --> pdb=" O LEU d 312 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE d 314 " --> pdb=" O TYR d 422 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N TYR d 422 " --> pdb=" O PHE d 314 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N ALA d 420 " --> pdb=" O CYS d 466 " (cutoff:3.500A) 930 hydrogen bonds defined for protein. 2547 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: 6.62 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 10295 1.34 - 1.46: 8105 1.46 - 1.59: 16014 1.59 - 1.71: 2 1.71 - 1.84: 298 Bond restraints: 34714 Sorted by residual: bond pdb=" CA THR Y 108 " pdb=" C THR Y 108 " ideal model delta sigma weight residual 1.525 1.586 -0.061 2.10e-02 2.27e+03 8.32e+00 bond pdb=" N ILE P 292 " pdb=" CA ILE P 292 " ideal model delta sigma weight residual 1.458 1.510 -0.052 1.90e-02 2.77e+03 7.62e+00 bond pdb=" CA ALA d 22 " pdb=" C ALA d 22 " ideal model delta sigma weight residual 1.525 1.582 -0.057 2.10e-02 2.27e+03 7.24e+00 bond pdb=" CA ILE P 292 " pdb=" CB ILE P 292 " ideal model delta sigma weight residual 1.540 1.610 -0.070 2.70e-02 1.37e+03 6.70e+00 bond pdb=" N SER I 278 " pdb=" CA SER I 278 " ideal model delta sigma weight residual 1.458 1.506 -0.048 1.90e-02 2.77e+03 6.42e+00 ... (remaining 34709 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 46305 4.10 - 8.19: 857 8.19 - 12.29: 142 12.29 - 16.38: 31 16.38 - 20.48: 6 Bond angle restraints: 47341 Sorted by residual: angle pdb=" C ALA P 291 " pdb=" N ILE P 292 " pdb=" CA ILE P 292 " ideal model delta sigma weight residual 121.70 142.18 -20.48 1.80e+00 3.09e-01 1.29e+02 angle pdb=" C ILE G 277 " pdb=" N SER G 278 " pdb=" CA SER G 278 " ideal model delta sigma weight residual 121.70 140.20 -18.50 1.80e+00 3.09e-01 1.06e+02 angle pdb=" C ILE I 277 " pdb=" N SER I 278 " pdb=" CA SER I 278 " ideal model delta sigma weight residual 121.70 139.53 -17.83 1.80e+00 3.09e-01 9.82e+01 angle pdb=" C ILE Y 450 " pdb=" N TRP Y 451 " pdb=" CA TRP Y 451 " ideal model delta sigma weight residual 121.70 138.91 -17.21 1.80e+00 3.09e-01 9.15e+01 angle pdb=" C ILE d 450 " pdb=" N TRP d 451 " pdb=" CA TRP d 451 " ideal model delta sigma weight residual 121.70 138.54 -16.84 1.80e+00 3.09e-01 8.75e+01 ... (remaining 47336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 18732 17.68 - 35.37: 1743 35.37 - 53.05: 243 53.05 - 70.74: 42 70.74 - 88.42: 33 Dihedral angle restraints: 20793 sinusoidal: 7783 harmonic: 13010 Sorted by residual: dihedral pdb=" CA ILE R 218 " pdb=" C ILE R 218 " pdb=" N LEU R 219 " pdb=" CA LEU R 219 " ideal model delta harmonic sigma weight residual 180.00 138.12 41.88 0 5.00e+00 4.00e-02 7.02e+01 dihedral pdb=" CA ILE R 292 " pdb=" C ILE R 292 " pdb=" N LEU R 293 " pdb=" CA LEU R 293 " ideal model delta harmonic sigma weight residual 180.00 -138.20 -41.80 0 5.00e+00 4.00e-02 6.99e+01 dihedral pdb=" CB CYS C 846 " pdb=" SG CYS C 846 " pdb=" SG CYS C 985 " pdb=" CB CYS C 985 " ideal model delta sinusoidal sigma weight residual -86.00 -12.03 -73.97 1 1.00e+01 1.00e-02 6.95e+01 ... (remaining 20790 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.184: 5447 0.184 - 0.367: 98 0.367 - 0.551: 5 0.551 - 0.734: 2 0.734 - 0.918: 1 Chirality restraints: 5553 Sorted by residual: chirality pdb=" CB ILE P 292 " pdb=" CA ILE P 292 " pdb=" CG1 ILE P 292 " pdb=" CG2 ILE P 292 " both_signs ideal model delta sigma weight residual False 2.64 1.73 0.92 2.00e-01 2.50e+01 2.11e+01 chirality pdb=" CB VAL d 77 " pdb=" CA VAL d 77 " pdb=" CG1 VAL d 77 " pdb=" CG2 VAL d 77 " both_signs ideal model delta sigma weight residual False -2.63 -2.00 -0.62 2.00e-01 2.50e+01 9.76e+00 chirality pdb=" CB VAL G 190 " pdb=" CA VAL G 190 " pdb=" CG1 VAL G 190 " pdb=" CG2 VAL G 190 " both_signs ideal model delta sigma weight residual False -2.63 -2.02 -0.61 2.00e-01 2.50e+01 9.43e+00 ... (remaining 5550 not shown) Planarity restraints: 6151 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU d 140 " 0.081 5.00e-02 4.00e+02 1.23e-01 2.44e+01 pdb=" N PRO d 141 " -0.214 5.00e-02 4.00e+02 pdb=" CA PRO d 141 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO d 141 " 0.063 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU Y 140 " 0.073 5.00e-02 4.00e+02 1.11e-01 1.96e+01 pdb=" N PRO Y 141 " -0.192 5.00e-02 4.00e+02 pdb=" CA PRO Y 141 " 0.061 5.00e-02 4.00e+02 pdb=" CD PRO Y 141 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE Y 428 " 0.062 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO Y 429 " -0.164 5.00e-02 4.00e+02 pdb=" CA PRO Y 429 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO Y 429 " 0.051 5.00e-02 4.00e+02 ... (remaining 6148 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 4078 2.75 - 3.29: 33751 3.29 - 3.83: 57574 3.83 - 4.36: 63342 4.36 - 4.90: 104727 Nonbonded interactions: 263472 Sorted by model distance: nonbonded pdb=" OG SER A1323 " pdb=" O LYS A1331 " model vdw 2.216 3.040 nonbonded pdb=" OD1 ASP C 194 " pdb=" OH TYR C 402 " model vdw 2.233 3.040 nonbonded pdb=" OG SER G 17 " pdb=" OE1 GLU G 20 " model vdw 2.234 3.040 nonbonded pdb=" OG SER A1091 " pdb=" O VAL A1119 " model vdw 2.248 3.040 nonbonded pdb=" O GLU A 729 " pdb=" OG SER A 736 " model vdw 2.252 3.040 ... (remaining 263467 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 26 through 39 or (resid 40 and (name N or name CA or name \ C or name O or name CB )) or resid 41 through 42 or resid 47 through 48 or resid \ 79 or resid 81 through 181 or (resid 182 and (name N or name CA or name C or na \ me O or name CB or name CG or name CD )) or resid 183 through 184 or resid 186 t \ hrough 326 or resid 328 or resid 330 through 342 or resid 377 through 1231 or (r \ esid 1232 through 1234 and (name N or name CA or name C or name O or name CB )) \ or resid 1235 through 1394)) selection = (chain 'C' and (resid 26 through 184 or resid 186 through 316 or (resid 321 thro \ ugh 322 and (name N or name CA or name C or name O or name CB )) or resid 324 or \ (resid 326 through 333 and (name N or name CA or name C or name O or name CB )) \ or resid 334 or (resid 335 through 338 and (name N or name CA or name C or name \ O or name CB )) or resid 377 through 1394)) } ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.580 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: 0.030 Extract box with map and model: 0.450 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.600 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 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 : 0.005 0.079 34716 Z= 0.267 Angle : 1.353 20.478 47345 Z= 0.700 Chirality : 0.069 0.918 5553 Planarity : 0.009 0.123 6151 Dihedral : 14.095 88.421 12383 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 1.47 % Allowed : 11.94 % Favored : 86.60 % Rotamer: Outliers : 0.08 % Allowed : 0.93 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.48 % 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: -3.52 (0.11), residues: 4432 helix: -2.41 (0.12), residues: 1245 sheet: -1.31 (0.23), residues: 505 loop : -2.62 (0.11), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 718 TYR 0.043 0.002 TYR A 101 PHE 0.058 0.003 PHE C 634 TRP 0.025 0.002 TRP I 276 HIS 0.011 0.001 HIS A1269 Details of bonding type rmsd covalent geometry : bond 0.00537 (34714) covalent geometry : angle 1.35305 (47341) SS BOND : bond 0.00313 ( 2) SS BOND : angle 0.74406 ( 4) hydrogen bonds : bond 0.17421 ( 918) hydrogen bonds : angle 7.93265 ( 2547) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 777 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 774 time to evaluate : 1.209 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9652 (pp) cc_final: 0.9418 (pp) REVERT: A 87 LEU cc_start: 0.8497 (mm) cc_final: 0.8228 (tp) REVERT: A 115 MET cc_start: 0.2353 (mtm) cc_final: 0.1734 (ttt) REVERT: A 132 MET cc_start: 0.4285 (pmm) cc_final: 0.4002 (ptp) REVERT: A 145 PHE cc_start: 0.8034 (t80) cc_final: 0.7623 (t80) REVERT: A 234 LEU cc_start: 0.9662 (mm) cc_final: 0.9232 (mm) REVERT: A 242 MET cc_start: 0.8019 (tmm) cc_final: 0.7382 (tmm) REVERT: A 243 PHE cc_start: 0.8603 (m-80) cc_final: 0.7102 (m-80) REVERT: A 284 GLN cc_start: 0.8654 (pp30) cc_final: 0.7971 (pp30) REVERT: A 297 ARG cc_start: 0.9348 (ptt-90) cc_final: 0.8893 (ptt90) REVERT: A 301 GLN cc_start: 0.9114 (pp30) cc_final: 0.8668 (pp30) REVERT: A 400 ARG cc_start: 0.8900 (mtm110) cc_final: 0.8571 (mtm110) REVERT: A 441 PHE cc_start: 0.8267 (m-10) cc_final: 0.7960 (m-10) REVERT: A 461 ASN cc_start: 0.9345 (m110) cc_final: 0.9028 (m110) REVERT: A 496 GLN cc_start: 0.9315 (mp10) cc_final: 0.9059 (mp10) REVERT: A 520 MET cc_start: 0.8513 (tpp) cc_final: 0.7836 (tpp) REVERT: A 531 MET cc_start: 0.8684 (tpt) cc_final: 0.8424 (tpp) REVERT: A 541 HIS cc_start: 0.7844 (p-80) cc_final: 0.7454 (p-80) REVERT: A 632 ASP cc_start: 0.8811 (t0) cc_final: 0.8522 (t0) REVERT: A 645 MET cc_start: 0.8505 (mtt) cc_final: 0.8101 (mtp) REVERT: A 676 HIS cc_start: 0.9025 (m-70) cc_final: 0.8624 (m-70) REVERT: A 689 TYR cc_start: 0.8446 (m-10) cc_final: 0.8114 (m-80) REVERT: A 817 ILE cc_start: 0.8279 (mm) cc_final: 0.7647 (tt) REVERT: A 832 TYR cc_start: 0.9197 (t80) cc_final: 0.8651 (t80) REVERT: A 896 VAL cc_start: 0.6993 (p) cc_final: 0.6627 (t) REVERT: A 1055 LEU cc_start: 0.9309 (tt) cc_final: 0.8854 (tt) REVERT: A 1058 GLN cc_start: 0.8198 (pp30) cc_final: 0.7421 (pp30) REVERT: A 1069 PHE cc_start: 0.8917 (m-10) cc_final: 0.8079 (m-10) REVERT: A 1166 LEU cc_start: 0.9554 (mt) cc_final: 0.9302 (mt) REVERT: A 1227 ARG cc_start: 0.8404 (ttt180) cc_final: 0.8162 (ttt180) REVERT: A 1242 GLU cc_start: 0.8352 (pm20) cc_final: 0.8062 (pm20) REVERT: A 1245 MET cc_start: 0.8881 (ppp) cc_final: 0.8409 (ppp) REVERT: A 1256 THR cc_start: 0.8810 (p) cc_final: 0.8604 (p) REVERT: A 1261 LEU cc_start: 0.8756 (tp) cc_final: 0.8404 (tp) REVERT: A 1295 PHE cc_start: 0.8425 (m-10) cc_final: 0.8073 (m-80) REVERT: A 1344 CYS cc_start: 0.8393 (p) cc_final: 0.7382 (m) REVERT: A 1351 TYR cc_start: 0.9183 (m-10) cc_final: 0.8412 (m-10) REVERT: A 1358 ASP cc_start: 0.8517 (t70) cc_final: 0.8125 (t70) REVERT: A 1377 LEU cc_start: 0.9356 (tp) cc_final: 0.8954 (tt) REVERT: C 96 PHE cc_start: 0.9298 (t80) cc_final: 0.8948 (t80) REVERT: C 177 MET cc_start: 0.9451 (mmp) cc_final: 0.9238 (mmm) REVERT: C 284 GLN cc_start: 0.8556 (pp30) cc_final: 0.8350 (pp30) REVERT: C 301 GLN cc_start: 0.8792 (pp30) cc_final: 0.8435 (pp30) REVERT: C 400 ARG cc_start: 0.4345 (tpt170) cc_final: 0.4023 (tpt170) REVERT: C 473 ASP cc_start: 0.8799 (p0) cc_final: 0.8477 (p0) REVERT: C 520 MET cc_start: 0.8848 (tpp) cc_final: 0.8382 (tpp) REVERT: C 536 HIS cc_start: 0.7971 (m-70) cc_final: 0.7766 (m-70) REVERT: C 540 GLU cc_start: 0.7858 (pm20) cc_final: 0.7446 (mp0) REVERT: C 594 ILE cc_start: 0.8540 (mm) cc_final: 0.8120 (mt) REVERT: C 643 PHE cc_start: 0.9348 (m-10) cc_final: 0.8781 (m-80) REVERT: C 712 GLN cc_start: 0.9567 (tm-30) cc_final: 0.9253 (tm-30) REVERT: C 848 MET cc_start: 0.8213 (mmp) cc_final: 0.7132 (mmp) REVERT: C 917 MET cc_start: 0.8411 (mmp) cc_final: 0.7782 (mmm) REVERT: C 945 MET cc_start: 0.9019 (mtp) cc_final: 0.8699 (mtp) REVERT: C 1049 LYS cc_start: 0.7786 (pttm) cc_final: 0.7539 (pttm) REVERT: C 1071 VAL cc_start: 0.9322 (m) cc_final: 0.8987 (p) REVERT: C 1084 TYR cc_start: 0.8482 (t80) cc_final: 0.8165 (t80) REVERT: C 1231 MET cc_start: 0.7813 (ppp) cc_final: 0.7541 (ppp) REVERT: C 1295 PHE cc_start: 0.8676 (m-10) cc_final: 0.8136 (m-10) REVERT: C 1348 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8101 (mm-40) REVERT: C 1361 MET cc_start: 0.8475 (mpp) cc_final: 0.8184 (mpp) REVERT: G 106 ASP cc_start: 0.6747 (m-30) cc_final: 0.6319 (m-30) REVERT: G 136 VAL cc_start: 0.7743 (t) cc_final: 0.7093 (p) REVERT: G 146 MET cc_start: 0.8119 (pmm) cc_final: 0.7782 (pmm) REVERT: G 273 ILE cc_start: 0.7277 (tp) cc_final: 0.6716 (pt) REVERT: G 282 ARG cc_start: 0.9019 (pmt170) cc_final: 0.8557 (tmt170) REVERT: I 64 LEU cc_start: 0.9163 (pp) cc_final: 0.8879 (pp) REVERT: I 67 TYR cc_start: 0.8830 (m-10) cc_final: 0.8270 (m-80) REVERT: I 69 MET cc_start: 0.9128 (mmm) cc_final: 0.8725 (mmm) REVERT: I 112 TYR cc_start: 0.8891 (m-10) cc_final: 0.8604 (m-80) REVERT: I 114 CYS cc_start: 0.9269 (m) cc_final: 0.8917 (m) REVERT: I 134 GLU cc_start: 0.8630 (tp30) cc_final: 0.8240 (tp30) REVERT: I 135 ILE cc_start: 0.9144 (mt) cc_final: 0.8853 (pt) REVERT: I 137 PHE cc_start: 0.8895 (m-80) cc_final: 0.8546 (m-80) REVERT: I 146 MET cc_start: 0.6346 (mtt) cc_final: 0.6105 (mtt) REVERT: I 147 ARG cc_start: 0.8659 (ppt170) cc_final: 0.8309 (tmm160) REVERT: I 219 LEU cc_start: 0.7926 (mt) cc_final: 0.7315 (mp) REVERT: I 298 PHE cc_start: 0.8345 (t80) cc_final: 0.7923 (m-10) REVERT: P 143 GLN cc_start: 0.8715 (tp40) cc_final: 0.7588 (pm20) REVERT: P 144 THR cc_start: 0.8722 (p) cc_final: 0.8510 (p) REVERT: P 146 MET cc_start: 0.8316 (tpt) cc_final: 0.7978 (tpp) REVERT: P 150 ILE cc_start: 0.8909 (tt) cc_final: 0.8673 (tt) REVERT: P 218 ILE cc_start: 0.5914 (mm) cc_final: 0.5688 (pt) REVERT: P 290 ARG cc_start: 0.8054 (ptm-80) cc_final: 0.7685 (ttp80) REVERT: R 6 PHE cc_start: 0.8258 (t80) cc_final: 0.7856 (t80) REVERT: R 113 ILE cc_start: 0.9328 (mp) cc_final: 0.8992 (mp) REVERT: R 146 MET cc_start: 0.9381 (tpt) cc_final: 0.9137 (tpp) REVERT: R 220 THR cc_start: 0.4919 (p) cc_final: 0.4621 (p) REVERT: R 276 TRP cc_start: 0.8693 (t60) cc_final: 0.8328 (t60) REVERT: R 293 LEU cc_start: 0.8630 (tp) cc_final: 0.8394 (tp) REVERT: Y 116 LEU cc_start: 0.8919 (mp) cc_final: 0.8373 (tp) REVERT: d 134 LEU cc_start: 0.9039 (tp) cc_final: 0.8684 (tp) REVERT: d 142 HIS cc_start: 0.4208 (m-70) cc_final: 0.4005 (m-70) REVERT: d 253 GLU cc_start: 0.9281 (tt0) cc_final: 0.8885 (tt0) REVERT: d 335 ASN cc_start: 0.8830 (m-40) cc_final: 0.8452 (m-40) REVERT: d 439 MET cc_start: 0.6400 (tpt) cc_final: 0.6179 (tpt) outliers start: 3 outliers final: 1 residues processed: 777 average time/residue: 0.1718 time to fit residues: 220.7465 Evaluate side-chains 612 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 611 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 432 optimal weight: 20.0000 chunk 197 optimal weight: 8.9990 chunk 388 optimal weight: 40.0000 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 40.0000 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 20.0000 chunk 207 optimal weight: 5.9990 chunk 401 optimal weight: 7.9990 chunk 424 optimal weight: 40.0000 overall best weight: 7.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 195 GLN A 217 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 427 GLN A 451 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 HIS A 685 HIS A1031 HIS ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 437 HIS C 451 GLN ** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN G 206 ASN I 162 ASN P 143 GLN R 86 HIS Y 136 HIS Y 328 HIS ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 461 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.109034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.082720 restraints weight = 151785.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.085141 restraints weight = 94858.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.086824 restraints weight = 67066.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.088033 restraints weight = 51756.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.088891 restraints weight = 42526.879| |-----------------------------------------------------------------------------| r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 34716 Z= 0.184 Angle : 0.848 15.191 47345 Z= 0.441 Chirality : 0.049 0.494 5553 Planarity : 0.006 0.124 6151 Dihedral : 6.385 36.851 4880 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 1.33 % Allowed : 11.26 % Favored : 87.41 % Rotamer: Outliers : 0.11 % Allowed : 6.59 % Favored : 93.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.01 (0.12), residues: 4432 helix: -1.48 (0.13), residues: 1282 sheet: -1.31 (0.22), residues: 531 loop : -2.52 (0.11), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 179 TYR 0.020 0.002 TYR A 73 PHE 0.029 0.002 PHE C 458 TRP 0.017 0.002 TRP A 672 HIS 0.006 0.001 HIS C 685 Details of bonding type rmsd covalent geometry : bond 0.00383 (34714) covalent geometry : angle 0.84790 (47341) SS BOND : bond 0.00495 ( 2) SS BOND : angle 1.01124 ( 4) hydrogen bonds : bond 0.03777 ( 918) hydrogen bonds : angle 6.01883 ( 2547) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 727 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 723 time to evaluate : 1.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9562 (pp) cc_final: 0.9283 (pp) REVERT: A 115 MET cc_start: 0.4115 (mtm) cc_final: 0.3364 (ttt) REVERT: A 132 MET cc_start: 0.4738 (pmm) cc_final: 0.4252 (ptp) REVERT: A 145 PHE cc_start: 0.8106 (t80) cc_final: 0.7501 (t80) REVERT: A 195 GLN cc_start: 0.9375 (OUTLIER) cc_final: 0.9145 (pp30) REVERT: A 221 HIS cc_start: 0.8642 (m-70) cc_final: 0.8420 (m90) REVERT: A 234 LEU cc_start: 0.9678 (mm) cc_final: 0.9249 (mm) REVERT: A 259 LEU cc_start: 0.9554 (mp) cc_final: 0.9319 (mp) REVERT: A 284 GLN cc_start: 0.8712 (pp30) cc_final: 0.8177 (pp30) REVERT: A 297 ARG cc_start: 0.9364 (ptt-90) cc_final: 0.8756 (ptt90) REVERT: A 301 GLN cc_start: 0.9098 (pp30) cc_final: 0.8720 (pp30) REVERT: A 390 LYS cc_start: 0.8559 (ptpp) cc_final: 0.8255 (ptpp) REVERT: A 400 ARG cc_start: 0.8869 (mtm110) cc_final: 0.8574 (mtm110) REVERT: A 441 PHE cc_start: 0.8245 (m-10) cc_final: 0.7855 (m-10) REVERT: A 475 MET cc_start: 0.8311 (mmp) cc_final: 0.8099 (mmm) REVERT: A 520 MET cc_start: 0.8512 (tpp) cc_final: 0.7880 (tpp) REVERT: A 531 MET cc_start: 0.8845 (tpt) cc_final: 0.8555 (tpt) REVERT: A 558 GLU cc_start: 0.8846 (tp30) cc_final: 0.8426 (tp30) REVERT: A 632 ASP cc_start: 0.8864 (t0) cc_final: 0.8543 (t0) REVERT: A 645 MET cc_start: 0.8589 (mtt) cc_final: 0.8163 (mtp) REVERT: A 676 HIS cc_start: 0.8923 (m-70) cc_final: 0.8509 (m-70) REVERT: A 753 LEU cc_start: 0.9335 (tp) cc_final: 0.9110 (tp) REVERT: A 817 ILE cc_start: 0.8163 (mm) cc_final: 0.7658 (tt) REVERT: A 832 TYR cc_start: 0.9128 (t80) cc_final: 0.8521 (t80) REVERT: A 1057 HIS cc_start: 0.8403 (m90) cc_final: 0.8184 (m-70) REVERT: A 1069 PHE cc_start: 0.9106 (m-80) cc_final: 0.8459 (m-10) REVERT: A 1141 MET cc_start: 0.8469 (mmp) cc_final: 0.8268 (mmm) REVERT: A 1166 LEU cc_start: 0.9609 (mt) cc_final: 0.9364 (mt) REVERT: A 1227 ARG cc_start: 0.8184 (ttt180) cc_final: 0.7939 (ttt180) REVERT: A 1261 LEU cc_start: 0.8817 (tp) cc_final: 0.8450 (tp) REVERT: A 1344 CYS cc_start: 0.8476 (p) cc_final: 0.8085 (p) REVERT: A 1358 ASP cc_start: 0.8423 (t70) cc_final: 0.8093 (t70) REVERT: A 1361 MET cc_start: 0.8852 (ppp) cc_final: 0.8589 (ppp) REVERT: A 1377 LEU cc_start: 0.9368 (tp) cc_final: 0.8953 (tp) REVERT: C 96 PHE cc_start: 0.9273 (t80) cc_final: 0.8927 (t80) REVERT: C 177 MET cc_start: 0.9441 (mmp) cc_final: 0.9217 (mmm) REVERT: C 301 GLN cc_start: 0.8830 (pp30) cc_final: 0.8600 (pp30) REVERT: C 400 ARG cc_start: 0.4502 (tpt170) cc_final: 0.4091 (tpt170) REVERT: C 473 ASP cc_start: 0.8915 (p0) cc_final: 0.8618 (p0) REVERT: C 520 MET cc_start: 0.8736 (tpp) cc_final: 0.8304 (tpp) REVERT: C 536 HIS cc_start: 0.8075 (m-70) cc_final: 0.7773 (m-70) REVERT: C 643 PHE cc_start: 0.9315 (m-10) cc_final: 0.8361 (m-10) REVERT: C 724 PHE cc_start: 0.9370 (m-80) cc_final: 0.9005 (m-80) REVERT: C 848 MET cc_start: 0.8364 (mmp) cc_final: 0.7444 (mmp) REVERT: C 917 MET cc_start: 0.8470 (mmp) cc_final: 0.7883 (mmm) REVERT: C 945 MET cc_start: 0.9021 (mtp) cc_final: 0.8648 (mtp) REVERT: C 1049 LYS cc_start: 0.8125 (pttm) cc_final: 0.7702 (pttt) REVERT: C 1084 TYR cc_start: 0.8817 (t80) cc_final: 0.8536 (t80) REVERT: C 1231 MET cc_start: 0.8052 (ppp) cc_final: 0.7796 (ppp) REVERT: C 1348 GLN cc_start: 0.9421 (mm-40) cc_final: 0.8285 (mm-40) REVERT: C 1361 MET cc_start: 0.8720 (mpp) cc_final: 0.8469 (mpp) REVERT: G 128 LEU cc_start: 0.7403 (mp) cc_final: 0.7183 (mp) REVERT: G 273 ILE cc_start: 0.7372 (tp) cc_final: 0.6978 (pt) REVERT: I 67 TYR cc_start: 0.8698 (m-10) cc_final: 0.8294 (m-80) REVERT: I 69 MET cc_start: 0.9227 (mmm) cc_final: 0.8857 (mmm) REVERT: I 114 CYS cc_start: 0.9329 (m) cc_final: 0.9017 (m) REVERT: I 135 ILE cc_start: 0.9072 (mt) cc_final: 0.8682 (tp) REVERT: I 137 PHE cc_start: 0.8886 (m-80) cc_final: 0.8361 (m-80) REVERT: I 146 MET cc_start: 0.7177 (mtt) cc_final: 0.6275 (mtt) REVERT: I 147 ARG cc_start: 0.9167 (ppt170) cc_final: 0.8603 (tmm160) REVERT: I 148 GLU cc_start: 0.9331 (pm20) cc_final: 0.9070 (pm20) REVERT: I 298 PHE cc_start: 0.8420 (t80) cc_final: 0.7951 (m-10) REVERT: P 290 ARG cc_start: 0.8123 (ptm-80) cc_final: 0.7687 (ttp80) REVERT: R 6 PHE cc_start: 0.8228 (t80) cc_final: 0.7743 (t80) REVERT: R 27 CYS cc_start: 0.9090 (m) cc_final: 0.8756 (m) REVERT: R 97 LEU cc_start: 0.8139 (mt) cc_final: 0.7869 (mm) REVERT: R 146 MET cc_start: 0.9419 (tpt) cc_final: 0.9218 (tpp) REVERT: R 189 ASN cc_start: 0.8116 (m-40) cc_final: 0.7833 (m110) REVERT: R 270 TYR cc_start: 0.8899 (t80) cc_final: 0.8697 (t80) REVERT: Y 418 MET cc_start: 0.4987 (mmp) cc_final: 0.4326 (mmp) REVERT: d 110 LEU cc_start: 0.8876 (mt) cc_final: 0.8478 (mt) REVERT: d 134 LEU cc_start: 0.9102 (tp) cc_final: 0.8818 (tp) REVERT: d 142 HIS cc_start: 0.4173 (m-70) cc_final: 0.3953 (m-70) REVERT: d 253 GLU cc_start: 0.9169 (tt0) cc_final: 0.8706 (mt-10) REVERT: d 335 ASN cc_start: 0.8940 (m-40) cc_final: 0.8531 (m-40) outliers start: 4 outliers final: 2 residues processed: 726 average time/residue: 0.1691 time to fit residues: 204.6157 Evaluate side-chains 572 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 569 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 146 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 5.9990 chunk 318 optimal weight: 30.0000 chunk 393 optimal weight: 40.0000 chunk 32 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 chunk 292 optimal weight: 6.9990 chunk 179 optimal weight: 20.0000 chunk 236 optimal weight: 7.9990 overall best weight: 4.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A 595 ASN A 902 HIS ** A 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1098 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN C 451 GLN C 536 HIS ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS Y 136 HIS ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 318 GLN d 461 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.109546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.083258 restraints weight = 150730.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.085691 restraints weight = 93889.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.087428 restraints weight = 66252.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.088667 restraints weight = 50890.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.089560 restraints weight = 41664.208| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34716 Z= 0.152 Angle : 0.834 15.121 47345 Z= 0.426 Chirality : 0.049 0.550 5553 Planarity : 0.006 0.123 6151 Dihedral : 6.127 34.795 4880 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 1.22 % Allowed : 11.21 % Favored : 87.57 % Rotamer: Outliers : 0.11 % Allowed : 4.98 % Favored : 94.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.78 (0.12), residues: 4432 helix: -1.08 (0.14), residues: 1286 sheet: -1.16 (0.22), residues: 524 loop : -2.50 (0.11), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 139 TYR 0.020 0.001 TYR G 112 PHE 0.026 0.001 PHE C 458 TRP 0.012 0.001 TRP A 672 HIS 0.004 0.001 HIS C 685 Details of bonding type rmsd covalent geometry : bond 0.00322 (34714) covalent geometry : angle 0.83412 (47341) SS BOND : bond 0.00314 ( 2) SS BOND : angle 0.46628 ( 4) hydrogen bonds : bond 0.03456 ( 918) hydrogen bonds : angle 5.65972 ( 2547) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 735 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 LEU cc_start: 0.9574 (pp) cc_final: 0.9352 (pp) REVERT: A 115 MET cc_start: 0.3603 (mtt) cc_final: 0.3176 (ttt) REVERT: A 132 MET cc_start: 0.4742 (pmm) cc_final: 0.4406 (ptp) REVERT: A 145 PHE cc_start: 0.8158 (t80) cc_final: 0.7708 (t80) REVERT: A 234 LEU cc_start: 0.9757 (mm) cc_final: 0.9337 (mm) REVERT: A 259 LEU cc_start: 0.9573 (mp) cc_final: 0.9337 (mp) REVERT: A 297 ARG cc_start: 0.9335 (ptt-90) cc_final: 0.8828 (ptt90) REVERT: A 298 GLN cc_start: 0.9428 (tp40) cc_final: 0.8804 (tp40) REVERT: A 301 GLN cc_start: 0.9139 (pp30) cc_final: 0.8648 (pp30) REVERT: A 441 PHE cc_start: 0.8208 (m-10) cc_final: 0.7777 (m-10) REVERT: A 520 MET cc_start: 0.8463 (tpp) cc_final: 0.7857 (tpp) REVERT: A 531 MET cc_start: 0.8806 (tpt) cc_final: 0.8518 (tpt) REVERT: A 558 GLU cc_start: 0.8675 (tp30) cc_final: 0.8213 (tp30) REVERT: A 632 ASP cc_start: 0.8802 (t0) cc_final: 0.8513 (t0) REVERT: A 645 MET cc_start: 0.8579 (mtt) cc_final: 0.8138 (mtp) REVERT: A 676 HIS cc_start: 0.8887 (m-70) cc_final: 0.8511 (m-70) REVERT: A 753 LEU cc_start: 0.9331 (tp) cc_final: 0.9089 (tp) REVERT: A 817 ILE cc_start: 0.8188 (mm) cc_final: 0.7662 (tt) REVERT: A 832 TYR cc_start: 0.9121 (t80) cc_final: 0.8585 (t80) REVERT: A 928 LEU cc_start: 0.9435 (tt) cc_final: 0.8914 (mm) REVERT: A 1058 GLN cc_start: 0.8409 (pp30) cc_final: 0.8140 (pp30) REVERT: A 1141 MET cc_start: 0.8525 (mmp) cc_final: 0.8269 (mmm) REVERT: A 1166 LEU cc_start: 0.9634 (mt) cc_final: 0.9372 (mt) REVERT: A 1242 GLU cc_start: 0.8819 (pm20) cc_final: 0.8553 (pm20) REVERT: A 1245 MET cc_start: 0.9222 (ppp) cc_final: 0.8858 (ppp) REVERT: A 1261 LEU cc_start: 0.8705 (tp) cc_final: 0.8171 (tp) REVERT: A 1269 HIS cc_start: 0.8366 (m-70) cc_final: 0.7957 (m90) REVERT: A 1295 PHE cc_start: 0.8713 (m-10) cc_final: 0.8407 (m-80) REVERT: A 1358 ASP cc_start: 0.8418 (t70) cc_final: 0.8081 (t70) REVERT: A 1361 MET cc_start: 0.8759 (ppp) cc_final: 0.8411 (ppp) REVERT: A 1377 LEU cc_start: 0.9305 (tp) cc_final: 0.8920 (tt) REVERT: C 96 PHE cc_start: 0.9250 (t80) cc_final: 0.8895 (t80) REVERT: C 177 MET cc_start: 0.9442 (mmp) cc_final: 0.9210 (mmm) REVERT: C 301 GLN cc_start: 0.9013 (pp30) cc_final: 0.8800 (pp30) REVERT: C 400 ARG cc_start: 0.4344 (tpt170) cc_final: 0.3966 (tpt170) REVERT: C 473 ASP cc_start: 0.8904 (p0) cc_final: 0.8557 (p0) REVERT: C 520 MET cc_start: 0.8743 (tpp) cc_final: 0.8321 (tpp) REVERT: C 536 HIS cc_start: 0.7935 (m90) cc_final: 0.7660 (m-70) REVERT: C 537 TRP cc_start: 0.7708 (p-90) cc_final: 0.7118 (p-90) REVERT: C 643 PHE cc_start: 0.9362 (m-10) cc_final: 0.8311 (m-80) REVERT: C 724 PHE cc_start: 0.9341 (m-80) cc_final: 0.9002 (m-80) REVERT: C 742 ILE cc_start: 0.9152 (mp) cc_final: 0.8621 (mm) REVERT: C 762 ARG cc_start: 0.9034 (tmt-80) cc_final: 0.8553 (tmm160) REVERT: C 848 MET cc_start: 0.8308 (mmp) cc_final: 0.7387 (mmp) REVERT: C 917 MET cc_start: 0.8530 (mmp) cc_final: 0.7735 (mmm) REVERT: C 945 MET cc_start: 0.9062 (mtp) cc_final: 0.8698 (mtp) REVERT: C 1348 GLN cc_start: 0.9405 (mm-40) cc_final: 0.8428 (mm-40) REVERT: C 1361 MET cc_start: 0.8742 (mpp) cc_final: 0.8433 (mpp) REVERT: G 128 LEU cc_start: 0.7392 (mp) cc_final: 0.7184 (mp) REVERT: G 146 MET cc_start: 0.7888 (pmm) cc_final: 0.7569 (pmm) REVERT: G 273 ILE cc_start: 0.7328 (tp) cc_final: 0.6665 (pt) REVERT: I 67 TYR cc_start: 0.8696 (m-10) cc_final: 0.8324 (m-80) REVERT: I 69 MET cc_start: 0.9283 (mmm) cc_final: 0.8954 (mmm) REVERT: I 114 CYS cc_start: 0.9361 (m) cc_final: 0.9047 (m) REVERT: I 135 ILE cc_start: 0.9071 (mt) cc_final: 0.8630 (tp) REVERT: I 137 PHE cc_start: 0.8847 (m-80) cc_final: 0.8354 (m-80) REVERT: I 146 MET cc_start: 0.7311 (mtt) cc_final: 0.6257 (mtt) REVERT: I 147 ARG cc_start: 0.8985 (ppt170) cc_final: 0.8359 (tmm160) REVERT: I 148 GLU cc_start: 0.9325 (pm20) cc_final: 0.9036 (pm20) REVERT: I 293 LEU cc_start: 0.9538 (tp) cc_final: 0.9311 (tp) REVERT: I 298 PHE cc_start: 0.8479 (t80) cc_final: 0.8056 (m-10) REVERT: P 52 TYR cc_start: 0.7918 (m-80) cc_final: 0.7207 (m-80) REVERT: P 57 PRO cc_start: 0.6475 (Cg_endo) cc_final: 0.5936 (Cg_exo) REVERT: P 146 MET cc_start: 0.8570 (tpt) cc_final: 0.8083 (tpp) REVERT: P 150 ILE cc_start: 0.8844 (tt) cc_final: 0.8538 (tt) REVERT: R 6 PHE cc_start: 0.8163 (t80) cc_final: 0.7659 (t80) REVERT: R 27 CYS cc_start: 0.9118 (m) cc_final: 0.8763 (m) REVERT: R 97 LEU cc_start: 0.8185 (mt) cc_final: 0.7939 (mm) REVERT: R 189 ASN cc_start: 0.8128 (m-40) cc_final: 0.7841 (m110) REVERT: R 220 THR cc_start: 0.6556 (t) cc_final: 0.6279 (t) REVERT: R 270 TYR cc_start: 0.8870 (t80) cc_final: 0.8662 (t80) REVERT: Y 335 ASN cc_start: 0.9233 (t0) cc_final: 0.8851 (t0) REVERT: Y 418 MET cc_start: 0.5094 (mmp) cc_final: 0.4648 (mmp) REVERT: d 110 LEU cc_start: 0.8849 (mt) cc_final: 0.8488 (mt) REVERT: d 134 LEU cc_start: 0.9113 (tp) cc_final: 0.8841 (tp) REVERT: d 142 HIS cc_start: 0.4068 (m-70) cc_final: 0.3847 (m-70) REVERT: d 253 GLU cc_start: 0.9184 (tt0) cc_final: 0.8718 (mt-10) REVERT: d 335 ASN cc_start: 0.8997 (m-40) cc_final: 0.8482 (m-40) outliers start: 4 outliers final: 0 residues processed: 737 average time/residue: 0.1652 time to fit residues: 203.7732 Evaluate side-chains 556 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 1.017 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 337 optimal weight: 0.0370 chunk 142 optimal weight: 5.9990 chunk 112 optimal weight: 0.6980 chunk 25 optimal weight: 40.0000 chunk 93 optimal weight: 20.0000 chunk 196 optimal weight: 0.9980 chunk 275 optimal weight: 50.0000 chunk 285 optimal weight: 10.0000 chunk 2 optimal weight: 8.9990 chunk 341 optimal weight: 0.5980 chunk 64 optimal weight: 20.0000 overall best weight: 1.6660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN A 217 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN C 468 GLN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN I 162 ASN R 86 HIS Y 136 HIS Y 238 HIS ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 309 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.111272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.084860 restraints weight = 147012.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087350 restraints weight = 91254.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.089118 restraints weight = 64162.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.090372 restraints weight = 49113.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.091325 restraints weight = 40107.614| |-----------------------------------------------------------------------------| r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34716 Z= 0.135 Angle : 0.821 15.445 47345 Z= 0.416 Chirality : 0.049 0.439 5553 Planarity : 0.005 0.120 6151 Dihedral : 5.866 34.317 4880 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 12.99 Ramachandran Plot: Outliers : 1.26 % Allowed : 10.97 % Favored : 87.77 % Rotamer: Outliers : 0.08 % Allowed : 4.19 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.64 (0.12), residues: 4432 helix: -0.88 (0.14), residues: 1282 sheet: -1.05 (0.22), residues: 524 loop : -2.46 (0.11), residues: 2626 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG R 282 TYR 0.016 0.001 TYR G 112 PHE 0.024 0.001 PHE A1246 TRP 0.015 0.001 TRP A 672 HIS 0.006 0.001 HIS A 820 Details of bonding type rmsd covalent geometry : bond 0.00285 (34714) covalent geometry : angle 0.82127 (47341) SS BOND : bond 0.00204 ( 2) SS BOND : angle 0.36674 ( 4) hydrogen bonds : bond 0.03167 ( 918) hydrogen bonds : angle 5.39818 ( 2547) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 749 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 746 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.2585 (t80) cc_final: 0.2091 (t80) REVERT: A 81 ARG cc_start: 0.9185 (ttm110) cc_final: 0.8977 (ttp-110) REVERT: A 115 MET cc_start: 0.3837 (mtt) cc_final: 0.3314 (ttt) REVERT: A 132 MET cc_start: 0.4430 (pmm) cc_final: 0.3989 (ptp) REVERT: A 145 PHE cc_start: 0.8025 (t80) cc_final: 0.7592 (t80) REVERT: A 195 GLN cc_start: 0.9253 (OUTLIER) cc_final: 0.9021 (pp30) REVERT: A 202 GLU cc_start: 0.9105 (mp0) cc_final: 0.8873 (mp0) REVERT: A 217 GLN cc_start: 0.8707 (tm130) cc_final: 0.8491 (tm-30) REVERT: A 221 HIS cc_start: 0.8608 (m-70) cc_final: 0.7823 (m90) REVERT: A 234 LEU cc_start: 0.9630 (mm) cc_final: 0.9154 (mm) REVERT: A 242 MET cc_start: 0.8325 (tmm) cc_final: 0.7415 (tmm) REVERT: A 243 PHE cc_start: 0.8621 (m-80) cc_final: 0.6920 (m-80) REVERT: A 259 LEU cc_start: 0.9566 (mp) cc_final: 0.9309 (mp) REVERT: A 297 ARG cc_start: 0.9268 (ptt-90) cc_final: 0.8723 (ptt90) REVERT: A 298 GLN cc_start: 0.9323 (tp40) cc_final: 0.8626 (tp40) REVERT: A 301 GLN cc_start: 0.9116 (pp30) cc_final: 0.8586 (pp30) REVERT: A 386 ILE cc_start: 0.9323 (tt) cc_final: 0.8985 (mt) REVERT: A 398 GLU cc_start: 0.9069 (mm-30) cc_final: 0.8805 (mm-30) REVERT: A 441 PHE cc_start: 0.8148 (m-10) cc_final: 0.7846 (m-10) REVERT: A 459 PHE cc_start: 0.9217 (p90) cc_final: 0.8828 (p90) REVERT: A 520 MET cc_start: 0.8490 (tpp) cc_final: 0.7895 (tpp) REVERT: A 531 MET cc_start: 0.8751 (tpt) cc_final: 0.8438 (tpt) REVERT: A 541 HIS cc_start: 0.7722 (p-80) cc_final: 0.7396 (p-80) REVERT: A 632 ASP cc_start: 0.8872 (t0) cc_final: 0.8541 (t0) REVERT: A 676 HIS cc_start: 0.8847 (m-70) cc_final: 0.8494 (m-70) REVERT: A 753 LEU cc_start: 0.9356 (tp) cc_final: 0.9147 (mt) REVERT: A 817 ILE cc_start: 0.8370 (mm) cc_final: 0.7780 (tt) REVERT: A 832 TYR cc_start: 0.9119 (t80) cc_final: 0.8625 (t80) REVERT: A 928 LEU cc_start: 0.9397 (tt) cc_final: 0.8874 (mm) REVERT: A 1057 HIS cc_start: 0.8440 (m90) cc_final: 0.8172 (m-70) REVERT: A 1069 PHE cc_start: 0.8970 (m-10) cc_final: 0.8474 (m-10) REVERT: A 1093 PHE cc_start: 0.8516 (m-80) cc_final: 0.7839 (m-80) REVERT: A 1141 MET cc_start: 0.8487 (mmp) cc_final: 0.8216 (mmm) REVERT: A 1166 LEU cc_start: 0.9584 (mt) cc_final: 0.9371 (mt) REVERT: A 1227 ARG cc_start: 0.8442 (ttt180) cc_final: 0.8117 (ttt180) REVERT: A 1234 MET cc_start: 0.3995 (ptt) cc_final: 0.2859 (tmm) REVERT: A 1242 GLU cc_start: 0.8838 (pm20) cc_final: 0.8595 (pm20) REVERT: A 1245 MET cc_start: 0.8917 (ppp) cc_final: 0.8488 (ppp) REVERT: A 1261 LEU cc_start: 0.8665 (tp) cc_final: 0.8118 (tp) REVERT: A 1269 HIS cc_start: 0.8342 (m-70) cc_final: 0.7857 (m90) REVERT: A 1295 PHE cc_start: 0.8606 (m-10) cc_final: 0.8307 (m-80) REVERT: A 1344 CYS cc_start: 0.8568 (p) cc_final: 0.7069 (m) REVERT: A 1358 ASP cc_start: 0.8466 (t70) cc_final: 0.8210 (t70) REVERT: A 1377 LEU cc_start: 0.9303 (tp) cc_final: 0.8927 (tt) REVERT: C 96 PHE cc_start: 0.9236 (t80) cc_final: 0.8858 (t80) REVERT: C 177 MET cc_start: 0.9470 (mmp) cc_final: 0.9232 (mmm) REVERT: C 236 ARG cc_start: 0.9169 (tpp-160) cc_final: 0.8675 (tpp-160) REVERT: C 400 ARG cc_start: 0.4285 (tpt170) cc_final: 0.4014 (tpt170) REVERT: C 473 ASP cc_start: 0.8780 (p0) cc_final: 0.8475 (p0) REVERT: C 520 MET cc_start: 0.8675 (tpp) cc_final: 0.8300 (tpp) REVERT: C 536 HIS cc_start: 0.8015 (m90) cc_final: 0.7752 (m-70) REVERT: C 537 TRP cc_start: 0.7616 (p-90) cc_final: 0.6908 (p-90) REVERT: C 643 PHE cc_start: 0.9379 (m-10) cc_final: 0.8311 (m-80) REVERT: C 712 GLN cc_start: 0.9421 (tm-30) cc_final: 0.9193 (tm-30) REVERT: C 724 PHE cc_start: 0.9353 (m-80) cc_final: 0.8987 (m-80) REVERT: C 742 ILE cc_start: 0.9081 (mp) cc_final: 0.8540 (mm) REVERT: C 762 ARG cc_start: 0.9113 (tmt-80) cc_final: 0.8615 (tmm160) REVERT: C 840 PHE cc_start: 0.8729 (m-80) cc_final: 0.8276 (m-10) REVERT: C 848 MET cc_start: 0.8226 (mmp) cc_final: 0.7297 (mmp) REVERT: C 917 MET cc_start: 0.8273 (mmp) cc_final: 0.7610 (mmm) REVERT: C 945 MET cc_start: 0.9148 (mtp) cc_final: 0.8740 (mtp) REVERT: C 1231 MET cc_start: 0.8163 (ppp) cc_final: 0.7953 (ppp) REVERT: C 1348 GLN cc_start: 0.9407 (mm-40) cc_final: 0.8409 (mm-40) REVERT: C 1361 MET cc_start: 0.8742 (mpp) cc_final: 0.8402 (mpp) REVERT: G 148 GLU cc_start: 0.8841 (pm20) cc_final: 0.8488 (mp0) REVERT: G 273 ILE cc_start: 0.7228 (tp) cc_final: 0.6592 (pt) REVERT: I 67 TYR cc_start: 0.8591 (m-10) cc_final: 0.8226 (m-80) REVERT: I 69 MET cc_start: 0.9260 (mmm) cc_final: 0.8989 (mmm) REVERT: I 114 CYS cc_start: 0.9320 (m) cc_final: 0.9039 (m) REVERT: I 135 ILE cc_start: 0.9093 (mt) cc_final: 0.8804 (pt) REVERT: I 137 PHE cc_start: 0.8815 (m-80) cc_final: 0.8293 (m-80) REVERT: I 146 MET cc_start: 0.7341 (mtt) cc_final: 0.6912 (mtt) REVERT: I 147 ARG cc_start: 0.9113 (ppt170) cc_final: 0.8475 (tmm160) REVERT: I 298 PHE cc_start: 0.8489 (t80) cc_final: 0.7975 (m-10) REVERT: P 52 TYR cc_start: 0.8026 (m-80) cc_final: 0.7364 (m-80) REVERT: P 57 PRO cc_start: 0.6375 (Cg_endo) cc_final: 0.5859 (Cg_exo) REVERT: P 146 MET cc_start: 0.8537 (tpt) cc_final: 0.8037 (tpp) REVERT: P 150 ILE cc_start: 0.8851 (tt) cc_final: 0.8491 (tt) REVERT: P 197 ASP cc_start: 0.6816 (t0) cc_final: 0.6484 (m-30) REVERT: P 257 MET cc_start: 0.1183 (ptt) cc_final: 0.0926 (ptp) REVERT: R 6 PHE cc_start: 0.8117 (t80) cc_final: 0.7634 (t80) REVERT: R 45 ASP cc_start: 0.6512 (t70) cc_final: 0.6186 (t0) REVERT: R 97 LEU cc_start: 0.8132 (mt) cc_final: 0.7897 (mm) REVERT: R 189 ASN cc_start: 0.8073 (m-40) cc_final: 0.7800 (m110) REVERT: R 270 TYR cc_start: 0.8846 (t80) cc_final: 0.8612 (t80) REVERT: Y 335 ASN cc_start: 0.9148 (t0) cc_final: 0.8858 (t0) REVERT: Y 418 MET cc_start: 0.5105 (mmp) cc_final: 0.4589 (mmp) REVERT: d 110 LEU cc_start: 0.8771 (mt) cc_final: 0.8393 (mt) REVERT: d 134 LEU cc_start: 0.9214 (tp) cc_final: 0.8937 (tp) REVERT: d 253 GLU cc_start: 0.9169 (tt0) cc_final: 0.8689 (mt-10) REVERT: d 291 CYS cc_start: 0.8493 (m) cc_final: 0.8188 (m) REVERT: d 335 ASN cc_start: 0.8844 (m-40) cc_final: 0.8452 (m-40) outliers start: 3 outliers final: 1 residues processed: 748 average time/residue: 0.1711 time to fit residues: 212.9415 Evaluate side-chains 567 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 565 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 138 optimal weight: 7.9990 chunk 235 optimal weight: 50.0000 chunk 275 optimal weight: 5.9990 chunk 195 optimal weight: 30.0000 chunk 83 optimal weight: 0.2980 chunk 418 optimal weight: 3.9990 chunk 39 optimal weight: 20.0000 chunk 246 optimal weight: 10.0000 chunk 294 optimal weight: 40.0000 chunk 216 optimal weight: 40.0000 chunk 111 optimal weight: 6.9990 overall best weight: 5.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN C 451 GLN C 468 GLN ** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 136 HIS Y 301 HIS ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 461 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.109464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.083094 restraints weight = 150627.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.085532 restraints weight = 93733.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.087271 restraints weight = 66109.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.088486 restraints weight = 50787.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.089392 restraints weight = 41634.663| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 34716 Z= 0.151 Angle : 0.821 15.254 47345 Z= 0.418 Chirality : 0.049 0.640 5553 Planarity : 0.006 0.119 6151 Dihedral : 5.782 33.932 4880 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 1.22 % Allowed : 11.71 % Favored : 87.07 % Rotamer: Outliers : 0.03 % Allowed : 3.00 % Favored : 96.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.52 (0.12), residues: 4432 helix: -0.73 (0.14), residues: 1294 sheet: -1.03 (0.22), residues: 522 loop : -2.41 (0.12), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 283 TYR 0.023 0.001 TYR A 258 PHE 0.023 0.001 PHE C 458 TRP 0.021 0.002 TRP C 672 HIS 0.010 0.001 HIS d 242 Details of bonding type rmsd covalent geometry : bond 0.00321 (34714) covalent geometry : angle 0.82140 (47341) SS BOND : bond 0.00398 ( 2) SS BOND : angle 0.42207 ( 4) hydrogen bonds : bond 0.03141 ( 918) hydrogen bonds : angle 5.30063 ( 2547) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 715 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 714 time to evaluate : 1.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.9237 (ttm110) cc_final: 0.9035 (ttp-110) REVERT: A 115 MET cc_start: 0.4069 (mtt) cc_final: 0.3484 (ttt) REVERT: A 132 MET cc_start: 0.4560 (pmm) cc_final: 0.4195 (ptt) REVERT: A 145 PHE cc_start: 0.8122 (t80) cc_final: 0.7668 (t80) REVERT: A 202 GLU cc_start: 0.9137 (mm-30) cc_final: 0.8888 (pp20) REVERT: A 242 MET cc_start: 0.8362 (tmm) cc_final: 0.7678 (tmm) REVERT: A 243 PHE cc_start: 0.8502 (m-80) cc_final: 0.6724 (m-80) REVERT: A 259 LEU cc_start: 0.9548 (mp) cc_final: 0.9334 (mp) REVERT: A 297 ARG cc_start: 0.9263 (ptt-90) cc_final: 0.8739 (ptt90) REVERT: A 298 GLN cc_start: 0.9343 (tp40) cc_final: 0.8671 (tp40) REVERT: A 301 GLN cc_start: 0.9125 (pp30) cc_final: 0.8603 (pp30) REVERT: A 386 ILE cc_start: 0.9287 (tt) cc_final: 0.8985 (mt) REVERT: A 441 PHE cc_start: 0.8164 (m-10) cc_final: 0.7879 (m-10) REVERT: A 475 MET cc_start: 0.8502 (mmp) cc_final: 0.8282 (mmm) REVERT: A 520 MET cc_start: 0.8297 (tpp) cc_final: 0.7787 (tpp) REVERT: A 524 MET cc_start: 0.9017 (ppp) cc_final: 0.8764 (ppp) REVERT: A 531 MET cc_start: 0.8737 (tpt) cc_final: 0.8435 (tpt) REVERT: A 558 GLU cc_start: 0.8738 (tp30) cc_final: 0.8153 (tp30) REVERT: A 632 ASP cc_start: 0.8890 (t0) cc_final: 0.8565 (t0) REVERT: A 676 HIS cc_start: 0.8914 (m-70) cc_final: 0.8485 (m-70) REVERT: A 753 LEU cc_start: 0.9367 (tp) cc_final: 0.9163 (tp) REVERT: A 817 ILE cc_start: 0.8437 (mm) cc_final: 0.7879 (tt) REVERT: A 832 TYR cc_start: 0.9126 (t80) cc_final: 0.8604 (t80) REVERT: A 928 LEU cc_start: 0.9380 (tt) cc_final: 0.8902 (mm) REVERT: A 1058 GLN cc_start: 0.8278 (pp30) cc_final: 0.7898 (pp30) REVERT: A 1069 PHE cc_start: 0.9017 (m-10) cc_final: 0.8521 (m-10) REVERT: A 1141 MET cc_start: 0.8550 (mmp) cc_final: 0.8322 (mmm) REVERT: A 1164 GLU cc_start: 0.9023 (tp30) cc_final: 0.8285 (tp30) REVERT: A 1166 LEU cc_start: 0.9581 (mt) cc_final: 0.9305 (mt) REVERT: A 1242 GLU cc_start: 0.8858 (pm20) cc_final: 0.8520 (pm20) REVERT: A 1245 MET cc_start: 0.8964 (ppp) cc_final: 0.8642 (ppp) REVERT: A 1261 LEU cc_start: 0.8670 (tp) cc_final: 0.8093 (tp) REVERT: A 1269 HIS cc_start: 0.8288 (m-70) cc_final: 0.7819 (m90) REVERT: A 1295 PHE cc_start: 0.8730 (m-10) cc_final: 0.8426 (m-80) REVERT: A 1344 CYS cc_start: 0.8645 (p) cc_final: 0.8218 (p) REVERT: A 1358 ASP cc_start: 0.8408 (t70) cc_final: 0.8100 (t70) REVERT: A 1377 LEU cc_start: 0.9278 (tp) cc_final: 0.8915 (tt) REVERT: C 96 PHE cc_start: 0.9245 (t80) cc_final: 0.8862 (t80) REVERT: C 177 MET cc_start: 0.9479 (mmp) cc_final: 0.9200 (mmm) REVERT: C 296 LYS cc_start: 0.9687 (tttt) cc_final: 0.9485 (ttmt) REVERT: C 400 ARG cc_start: 0.4396 (tpt170) cc_final: 0.4087 (tpt170) REVERT: C 473 ASP cc_start: 0.8800 (p0) cc_final: 0.8509 (p0) REVERT: C 520 MET cc_start: 0.8724 (tpp) cc_final: 0.8362 (tpp) REVERT: C 536 HIS cc_start: 0.8060 (m90) cc_final: 0.7797 (m-70) REVERT: C 537 TRP cc_start: 0.7794 (p-90) cc_final: 0.6853 (p-90) REVERT: C 643 PHE cc_start: 0.9390 (m-10) cc_final: 0.8328 (m-10) REVERT: C 724 PHE cc_start: 0.9397 (m-80) cc_final: 0.8989 (m-80) REVERT: C 742 ILE cc_start: 0.9190 (mp) cc_final: 0.8665 (mm) REVERT: C 840 PHE cc_start: 0.8935 (m-80) cc_final: 0.8540 (m-80) REVERT: C 848 MET cc_start: 0.8255 (mmp) cc_final: 0.7239 (mmp) REVERT: C 917 MET cc_start: 0.8453 (mmp) cc_final: 0.7719 (mmm) REVERT: C 945 MET cc_start: 0.9142 (mtp) cc_final: 0.8776 (mtp) REVERT: C 1168 ARG cc_start: 0.8937 (mmp80) cc_final: 0.8731 (mmp80) REVERT: C 1348 GLN cc_start: 0.9390 (mm-40) cc_final: 0.8439 (mm-40) REVERT: C 1361 MET cc_start: 0.8798 (mpp) cc_final: 0.8484 (mpp) REVERT: G 128 LEU cc_start: 0.7386 (mp) cc_final: 0.7177 (mp) REVERT: G 146 MET cc_start: 0.8097 (pmm) cc_final: 0.7835 (pmm) REVERT: I 67 TYR cc_start: 0.8603 (m-10) cc_final: 0.8244 (m-80) REVERT: I 69 MET cc_start: 0.9241 (mmm) cc_final: 0.9000 (mmm) REVERT: I 114 CYS cc_start: 0.9416 (m) cc_final: 0.9167 (m) REVERT: I 135 ILE cc_start: 0.9216 (mt) cc_final: 0.8840 (pt) REVERT: I 137 PHE cc_start: 0.8762 (m-80) cc_final: 0.8244 (m-80) REVERT: I 146 MET cc_start: 0.7213 (mtt) cc_final: 0.6761 (mtt) REVERT: I 147 ARG cc_start: 0.9063 (ppt170) cc_final: 0.8362 (ttp80) REVERT: P 52 TYR cc_start: 0.7941 (m-80) cc_final: 0.7321 (m-80) REVERT: P 57 PRO cc_start: 0.6436 (Cg_endo) cc_final: 0.5945 (Cg_exo) REVERT: P 146 MET cc_start: 0.8531 (tpt) cc_final: 0.8074 (tpp) REVERT: P 150 ILE cc_start: 0.8873 (tt) cc_final: 0.8549 (tt) REVERT: P 303 THR cc_start: 0.8899 (p) cc_final: 0.8626 (p) REVERT: R 6 PHE cc_start: 0.8080 (t80) cc_final: 0.7584 (t80) REVERT: R 97 LEU cc_start: 0.8226 (mt) cc_final: 0.7968 (mm) REVERT: R 189 ASN cc_start: 0.8216 (m-40) cc_final: 0.8003 (m110) REVERT: Y 335 ASN cc_start: 0.9217 (t0) cc_final: 0.8911 (t0) REVERT: Y 418 MET cc_start: 0.5283 (mmp) cc_final: 0.4697 (mmp) REVERT: d 253 GLU cc_start: 0.9133 (tt0) cc_final: 0.8636 (mt-10) REVERT: d 291 CYS cc_start: 0.8540 (m) cc_final: 0.8004 (m) REVERT: d 295 ASP cc_start: 0.7805 (m-30) cc_final: 0.7417 (m-30) REVERT: d 305 ASP cc_start: 0.8346 (m-30) cc_final: 0.8037 (t0) REVERT: d 335 ASN cc_start: 0.8702 (m-40) cc_final: 0.8315 (m-40) REVERT: d 439 MET cc_start: 0.5398 (tpt) cc_final: 0.5142 (tpt) outliers start: 1 outliers final: 0 residues processed: 714 average time/residue: 0.1750 time to fit residues: 207.8695 Evaluate side-chains 556 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 556 time to evaluate : 1.053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 213 optimal weight: 30.0000 chunk 132 optimal weight: 40.0000 chunk 174 optimal weight: 5.9990 chunk 265 optimal weight: 50.0000 chunk 11 optimal weight: 9.9990 chunk 439 optimal weight: 40.0000 chunk 98 optimal weight: 20.0000 chunk 196 optimal weight: 0.9990 chunk 134 optimal weight: 30.0000 chunk 31 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN C 451 GLN ** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 HIS G 162 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 461 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.109077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.082705 restraints weight = 149236.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.085142 restraints weight = 93161.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.086875 restraints weight = 65898.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.088096 restraints weight = 50685.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.088973 restraints weight = 41627.470| |-----------------------------------------------------------------------------| r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.2403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 34716 Z= 0.149 Angle : 0.825 15.333 47345 Z= 0.418 Chirality : 0.050 0.674 5553 Planarity : 0.005 0.119 6151 Dihedral : 5.731 33.343 4880 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 1.22 % Allowed : 11.57 % Favored : 87.21 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -2.41 (0.12), residues: 4432 helix: -0.60 (0.15), residues: 1287 sheet: -0.92 (0.23), residues: 503 loop : -2.37 (0.12), residues: 2642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 118 TYR 0.032 0.001 TYR A 707 PHE 0.023 0.001 PHE C 458 TRP 0.034 0.001 TRP Y 451 HIS 0.012 0.001 HIS C1057 Details of bonding type rmsd covalent geometry : bond 0.00317 (34714) covalent geometry : angle 0.82510 (47341) SS BOND : bond 0.00347 ( 2) SS BOND : angle 0.25759 ( 4) hydrogen bonds : bond 0.03078 ( 918) hydrogen bonds : angle 5.25195 ( 2547) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 721 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 TYR cc_start: 0.2966 (t80) cc_final: 0.2487 (t80) REVERT: A 81 ARG cc_start: 0.9219 (ttm110) cc_final: 0.9010 (ttp-110) REVERT: A 115 MET cc_start: 0.4611 (mtt) cc_final: 0.3834 (ttt) REVERT: A 145 PHE cc_start: 0.8333 (t80) cc_final: 0.7769 (t80) REVERT: A 221 HIS cc_start: 0.8745 (m-70) cc_final: 0.7881 (m90) REVERT: A 259 LEU cc_start: 0.9570 (mp) cc_final: 0.9352 (mp) REVERT: A 297 ARG cc_start: 0.9295 (ptt-90) cc_final: 0.8758 (ptt90) REVERT: A 298 GLN cc_start: 0.9334 (tp40) cc_final: 0.8628 (tp40) REVERT: A 301 GLN cc_start: 0.9133 (pp30) cc_final: 0.8624 (pp30) REVERT: A 386 ILE cc_start: 0.9224 (tt) cc_final: 0.8871 (mt) REVERT: A 441 PHE cc_start: 0.8135 (m-10) cc_final: 0.7825 (m-10) REVERT: A 475 MET cc_start: 0.8563 (mmp) cc_final: 0.8330 (mmm) REVERT: A 531 MET cc_start: 0.8763 (tpt) cc_final: 0.8489 (tpt) REVERT: A 676 HIS cc_start: 0.8888 (m-70) cc_final: 0.8481 (m-70) REVERT: A 753 LEU cc_start: 0.9385 (tp) cc_final: 0.9164 (tp) REVERT: A 817 ILE cc_start: 0.8463 (mm) cc_final: 0.7902 (tt) REVERT: A 832 TYR cc_start: 0.9082 (t80) cc_final: 0.8494 (t80) REVERT: A 928 LEU cc_start: 0.9373 (tt) cc_final: 0.8863 (mm) REVERT: A 1057 HIS cc_start: 0.8466 (m90) cc_final: 0.8252 (m90) REVERT: A 1058 GLN cc_start: 0.8332 (pp30) cc_final: 0.7927 (pp30) REVERT: A 1069 PHE cc_start: 0.9012 (m-10) cc_final: 0.8436 (m-10) REVERT: A 1164 GLU cc_start: 0.8773 (tp30) cc_final: 0.8476 (tp30) REVERT: A 1166 LEU cc_start: 0.9537 (mt) cc_final: 0.9259 (mt) REVERT: A 1234 MET cc_start: 0.4250 (ptt) cc_final: 0.2917 (tmm) REVERT: A 1242 GLU cc_start: 0.8805 (pm20) cc_final: 0.8542 (pm20) REVERT: A 1245 MET cc_start: 0.9065 (ppp) cc_final: 0.8715 (ppp) REVERT: A 1261 LEU cc_start: 0.8709 (tp) cc_final: 0.8163 (tp) REVERT: A 1269 HIS cc_start: 0.8190 (m-70) cc_final: 0.7745 (m90) REVERT: A 1295 PHE cc_start: 0.8690 (m-10) cc_final: 0.8400 (m-80) REVERT: A 1344 CYS cc_start: 0.8810 (p) cc_final: 0.8214 (p) REVERT: A 1347 PHE cc_start: 0.8708 (m-80) cc_final: 0.8479 (m-80) REVERT: A 1358 ASP cc_start: 0.8303 (t70) cc_final: 0.8029 (t70) REVERT: A 1377 LEU cc_start: 0.9249 (tp) cc_final: 0.8854 (tt) REVERT: C 96 PHE cc_start: 0.9264 (t80) cc_final: 0.8867 (t80) REVERT: C 177 MET cc_start: 0.9490 (mmp) cc_final: 0.9204 (mmm) REVERT: C 333 MET cc_start: 0.5927 (mmt) cc_final: 0.5726 (mmt) REVERT: C 400 ARG cc_start: 0.4426 (tpt170) cc_final: 0.4129 (tpt170) REVERT: C 473 ASP cc_start: 0.8614 (p0) cc_final: 0.8300 (p0) REVERT: C 520 MET cc_start: 0.8703 (tpp) cc_final: 0.8362 (tpp) REVERT: C 536 HIS cc_start: 0.8026 (m90) cc_final: 0.7742 (m-70) REVERT: C 537 TRP cc_start: 0.7590 (p-90) cc_final: 0.6702 (p-90) REVERT: C 643 PHE cc_start: 0.9391 (m-10) cc_final: 0.8302 (m-10) REVERT: C 724 PHE cc_start: 0.9403 (m-80) cc_final: 0.8992 (m-80) REVERT: C 742 ILE cc_start: 0.9151 (mp) cc_final: 0.8636 (mm) REVERT: C 832 TYR cc_start: 0.8876 (t80) cc_final: 0.8504 (t80) REVERT: C 840 PHE cc_start: 0.8951 (m-80) cc_final: 0.8572 (m-80) REVERT: C 848 MET cc_start: 0.8297 (mmp) cc_final: 0.7254 (mmp) REVERT: C 917 MET cc_start: 0.8451 (mmp) cc_final: 0.7769 (mmm) REVERT: C 945 MET cc_start: 0.9156 (mtp) cc_final: 0.8788 (mtp) REVERT: C 1168 ARG cc_start: 0.8969 (mmp80) cc_final: 0.8747 (mmp80) REVERT: C 1231 MET cc_start: 0.8206 (ppp) cc_final: 0.7964 (ppp) REVERT: C 1245 MET cc_start: 0.9269 (ppp) cc_final: 0.8810 (ppp) REVERT: C 1348 GLN cc_start: 0.9377 (mm-40) cc_final: 0.8520 (mm-40) REVERT: C 1361 MET cc_start: 0.8788 (mpp) cc_final: 0.8453 (mpp) REVERT: G 146 MET cc_start: 0.8059 (pmm) cc_final: 0.7697 (pmm) REVERT: G 282 ARG cc_start: 0.8980 (pmt170) cc_final: 0.8332 (tmt170) REVERT: I 67 TYR cc_start: 0.8608 (m-10) cc_final: 0.8251 (m-80) REVERT: I 69 MET cc_start: 0.9236 (mmm) cc_final: 0.9025 (mmm) REVERT: I 112 TYR cc_start: 0.8878 (m-80) cc_final: 0.8123 (m-80) REVERT: I 114 CYS cc_start: 0.9431 (m) cc_final: 0.9216 (m) REVERT: I 134 GLU cc_start: 0.8295 (tp30) cc_final: 0.7720 (tp30) REVERT: I 135 ILE cc_start: 0.9251 (mt) cc_final: 0.8937 (pt) REVERT: I 137 PHE cc_start: 0.8783 (m-80) cc_final: 0.8232 (m-80) REVERT: I 219 LEU cc_start: 0.7434 (mt) cc_final: 0.7169 (mp) REVERT: I 276 TRP cc_start: 0.6874 (m100) cc_final: 0.6674 (m100) REVERT: I 314 GLN cc_start: 0.8670 (tm-30) cc_final: 0.7958 (tm-30) REVERT: P 52 TYR cc_start: 0.7978 (m-80) cc_final: 0.7396 (m-80) REVERT: P 57 PRO cc_start: 0.5967 (Cg_endo) cc_final: 0.5422 (Cg_exo) REVERT: P 146 MET cc_start: 0.8539 (tpt) cc_final: 0.8064 (tpp) REVERT: P 150 ILE cc_start: 0.8776 (tt) cc_final: 0.8393 (tt) REVERT: R 6 PHE cc_start: 0.8092 (t80) cc_final: 0.7626 (t80) REVERT: R 97 LEU cc_start: 0.8095 (mt) cc_final: 0.7873 (mm) REVERT: R 189 ASN cc_start: 0.8216 (m-40) cc_final: 0.8010 (m110) REVERT: Y 131 VAL cc_start: 0.6451 (p) cc_final: 0.6170 (t) REVERT: Y 136 HIS cc_start: 0.5577 (m-70) cc_final: 0.5142 (m-70) REVERT: Y 335 ASN cc_start: 0.9219 (t0) cc_final: 0.8969 (t0) REVERT: Y 418 MET cc_start: 0.5551 (mmp) cc_final: 0.5001 (mmp) REVERT: d 253 GLU cc_start: 0.9178 (tt0) cc_final: 0.8718 (mt-10) REVERT: d 291 CYS cc_start: 0.8563 (m) cc_final: 0.7997 (m) REVERT: d 295 ASP cc_start: 0.7773 (m-30) cc_final: 0.7390 (m-30) REVERT: d 305 ASP cc_start: 0.8364 (m-30) cc_final: 0.8041 (t0) REVERT: d 335 ASN cc_start: 0.8953 (m-40) cc_final: 0.8578 (m-40) REVERT: d 439 MET cc_start: 0.5286 (tpt) cc_final: 0.4875 (tpt) outliers start: 0 outliers final: 0 residues processed: 721 average time/residue: 0.1664 time to fit residues: 200.8253 Evaluate side-chains 550 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 550 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 297 optimal weight: 0.2980 chunk 198 optimal weight: 30.0000 chunk 291 optimal weight: 3.9990 chunk 169 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 405 optimal weight: 5.9990 chunk 325 optimal weight: 2.9990 chunk 309 optimal weight: 50.0000 chunk 122 optimal weight: 10.0000 chunk 150 optimal weight: 7.9990 chunk 254 optimal weight: 7.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 HIS A 175 GLN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN C 451 GLN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 HIS G 162 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.108973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082616 restraints weight = 152265.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.085079 restraints weight = 94690.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.086816 restraints weight = 66826.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.088039 restraints weight = 51427.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.088950 restraints weight = 42201.950| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.2562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 34716 Z= 0.145 Angle : 0.830 15.215 47345 Z= 0.420 Chirality : 0.050 0.750 5553 Planarity : 0.005 0.117 6151 Dihedral : 5.680 33.242 4880 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 1.20 % Allowed : 11.42 % Favored : 87.39 % Rotamer: Outliers : 0.03 % Allowed : 2.43 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.39 (0.12), residues: 4432 helix: -0.59 (0.15), residues: 1286 sheet: -0.92 (0.23), residues: 518 loop : -2.35 (0.12), residues: 2628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 399 TYR 0.021 0.001 TYR A 258 PHE 0.023 0.001 PHE C 458 TRP 0.022 0.002 TRP Y 451 HIS 0.011 0.001 HIS C1057 Details of bonding type rmsd covalent geometry : bond 0.00309 (34714) covalent geometry : angle 0.83015 (47341) SS BOND : bond 0.00330 ( 2) SS BOND : angle 0.21690 ( 4) hydrogen bonds : bond 0.03040 ( 918) hydrogen bonds : angle 5.22149 ( 2547) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 715 time to evaluate : 0.758 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.9233 (ttm110) cc_final: 0.9008 (ttp-110) REVERT: A 115 MET cc_start: 0.4743 (mtt) cc_final: 0.4029 (ttt) REVERT: A 221 HIS cc_start: 0.8497 (m-70) cc_final: 0.7738 (m90) REVERT: A 223 ASN cc_start: 0.8273 (t0) cc_final: 0.8060 (t0) REVERT: A 259 LEU cc_start: 0.9574 (mp) cc_final: 0.9335 (mp) REVERT: A 297 ARG cc_start: 0.9291 (ptt-90) cc_final: 0.8842 (ptt90) REVERT: A 298 GLN cc_start: 0.9333 (tp40) cc_final: 0.8653 (tp40) REVERT: A 301 GLN cc_start: 0.9133 (pp30) cc_final: 0.8598 (pp30) REVERT: A 386 ILE cc_start: 0.9196 (tt) cc_final: 0.8830 (mt) REVERT: A 441 PHE cc_start: 0.8138 (m-10) cc_final: 0.7839 (m-10) REVERT: A 531 MET cc_start: 0.8755 (tpt) cc_final: 0.8471 (tpt) REVERT: A 676 HIS cc_start: 0.8932 (m-70) cc_final: 0.8513 (m-70) REVERT: A 817 ILE cc_start: 0.8352 (mm) cc_final: 0.7798 (tt) REVERT: A 832 TYR cc_start: 0.9085 (t80) cc_final: 0.8468 (t80) REVERT: A 928 LEU cc_start: 0.9352 (tt) cc_final: 0.8854 (mm) REVERT: A 1058 GLN cc_start: 0.8368 (pp30) cc_final: 0.7939 (pp30) REVERT: A 1069 PHE cc_start: 0.9077 (m-10) cc_final: 0.8456 (m-10) REVERT: A 1164 GLU cc_start: 0.8768 (tp30) cc_final: 0.8384 (tp30) REVERT: A 1166 LEU cc_start: 0.9547 (mt) cc_final: 0.9277 (mt) REVERT: A 1227 ARG cc_start: 0.8430 (ttt180) cc_final: 0.8186 (ttt180) REVERT: A 1234 MET cc_start: 0.4144 (ptt) cc_final: 0.2857 (tmm) REVERT: A 1242 GLU cc_start: 0.8887 (pm20) cc_final: 0.8423 (pm20) REVERT: A 1245 MET cc_start: 0.8990 (ppp) cc_final: 0.8723 (ppp) REVERT: A 1261 LEU cc_start: 0.8705 (tp) cc_final: 0.8149 (tp) REVERT: A 1295 PHE cc_start: 0.8683 (m-10) cc_final: 0.8355 (m-80) REVERT: A 1344 CYS cc_start: 0.8943 (p) cc_final: 0.8281 (p) REVERT: A 1358 ASP cc_start: 0.8359 (t70) cc_final: 0.8086 (t70) REVERT: A 1377 LEU cc_start: 0.9218 (tp) cc_final: 0.8826 (tt) REVERT: C 96 PHE cc_start: 0.9257 (t80) cc_final: 0.8841 (t80) REVERT: C 177 MET cc_start: 0.9500 (mmp) cc_final: 0.9235 (mmm) REVERT: C 400 ARG cc_start: 0.4460 (tpt170) cc_final: 0.4127 (tpt170) REVERT: C 473 ASP cc_start: 0.8684 (p0) cc_final: 0.8435 (p0) REVERT: C 520 MET cc_start: 0.8697 (tpp) cc_final: 0.8379 (tpp) REVERT: C 536 HIS cc_start: 0.8087 (m90) cc_final: 0.7813 (m-70) REVERT: C 537 TRP cc_start: 0.7699 (p-90) cc_final: 0.7387 (p-90) REVERT: C 643 PHE cc_start: 0.9407 (m-10) cc_final: 0.8301 (m-10) REVERT: C 724 PHE cc_start: 0.9420 (m-80) cc_final: 0.8930 (m-80) REVERT: C 832 TYR cc_start: 0.8887 (t80) cc_final: 0.8539 (t80) REVERT: C 848 MET cc_start: 0.8237 (mmp) cc_final: 0.7103 (mmp) REVERT: C 917 MET cc_start: 0.8479 (mmp) cc_final: 0.7693 (mmm) REVERT: C 945 MET cc_start: 0.9158 (mtp) cc_final: 0.8807 (mtp) REVERT: C 1126 THR cc_start: 0.9354 (p) cc_final: 0.8977 (p) REVERT: C 1231 MET cc_start: 0.8146 (ppp) cc_final: 0.7928 (ppp) REVERT: C 1245 MET cc_start: 0.9284 (ppp) cc_final: 0.8793 (ppp) REVERT: C 1348 GLN cc_start: 0.9376 (mm-40) cc_final: 0.8531 (mm-40) REVERT: C 1361 MET cc_start: 0.8800 (mpp) cc_final: 0.8442 (mpp) REVERT: G 128 LEU cc_start: 0.7430 (mp) cc_final: 0.7207 (mp) REVERT: I 67 TYR cc_start: 0.8486 (m-10) cc_final: 0.7994 (m-80) REVERT: I 69 MET cc_start: 0.9235 (mmm) cc_final: 0.9029 (mmm) REVERT: I 112 TYR cc_start: 0.8840 (m-80) cc_final: 0.8452 (m-80) REVERT: I 134 GLU cc_start: 0.8288 (tp30) cc_final: 0.8043 (tp30) REVERT: I 135 ILE cc_start: 0.9231 (mt) cc_final: 0.8898 (pt) REVERT: I 137 PHE cc_start: 0.8880 (m-80) cc_final: 0.8277 (m-80) REVERT: I 145 LEU cc_start: 0.9440 (mp) cc_final: 0.9225 (mp) REVERT: I 147 ARG cc_start: 0.9034 (ppt170) cc_final: 0.8250 (ttp80) REVERT: I 219 LEU cc_start: 0.7477 (mt) cc_final: 0.7039 (mp) REVERT: I 276 TRP cc_start: 0.6738 (m100) cc_final: 0.6344 (m100) REVERT: P 52 TYR cc_start: 0.7878 (m-80) cc_final: 0.7274 (m-80) REVERT: P 57 PRO cc_start: 0.6500 (Cg_endo) cc_final: 0.6068 (Cg_exo) REVERT: P 146 MET cc_start: 0.8531 (tpt) cc_final: 0.8091 (tpp) REVERT: P 150 ILE cc_start: 0.8737 (tt) cc_final: 0.8470 (tt) REVERT: P 303 THR cc_start: 0.8850 (p) cc_final: 0.8565 (p) REVERT: R 6 PHE cc_start: 0.8087 (t80) cc_final: 0.7622 (t80) REVERT: R 97 LEU cc_start: 0.8131 (mt) cc_final: 0.7908 (mm) REVERT: Y 131 VAL cc_start: 0.6431 (p) cc_final: 0.6111 (t) REVERT: Y 136 HIS cc_start: 0.5283 (m-70) cc_final: 0.4856 (m-70) REVERT: Y 335 ASN cc_start: 0.9196 (t0) cc_final: 0.8951 (t0) REVERT: Y 418 MET cc_start: 0.5704 (mmp) cc_final: 0.5087 (mmp) REVERT: d 220 MET cc_start: 0.8009 (tmm) cc_final: 0.7005 (mmt) REVERT: d 253 GLU cc_start: 0.9168 (tt0) cc_final: 0.8723 (mt-10) REVERT: d 291 CYS cc_start: 0.8639 (m) cc_final: 0.8101 (m) REVERT: d 295 ASP cc_start: 0.7797 (m-30) cc_final: 0.7277 (m-30) REVERT: d 335 ASN cc_start: 0.8934 (m-40) cc_final: 0.8547 (m-40) outliers start: 1 outliers final: 0 residues processed: 716 average time/residue: 0.1644 time to fit residues: 195.9283 Evaluate side-chains 569 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 569 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 214 optimal weight: 50.0000 chunk 139 optimal weight: 3.9990 chunk 272 optimal weight: 8.9990 chunk 374 optimal weight: 20.0000 chunk 360 optimal weight: 9.9990 chunk 175 optimal weight: 8.9990 chunk 396 optimal weight: 0.0980 chunk 400 optimal weight: 8.9990 chunk 442 optimal weight: 50.0000 chunk 104 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 overall best weight: 5.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN A 480 HIS ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN C 451 GLN ** C 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 HIS ** C1379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 ASN R 86 HIS R 192 HIS ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 461 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.108121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.081876 restraints weight = 152418.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.084274 restraints weight = 95042.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.085979 restraints weight = 67241.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.087195 restraints weight = 51797.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.088045 restraints weight = 42546.873| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 34716 Z= 0.160 Angle : 0.855 15.477 47345 Z= 0.431 Chirality : 0.050 0.776 5553 Planarity : 0.006 0.117 6151 Dihedral : 5.737 35.206 4880 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 16.40 Ramachandran Plot: Outliers : 1.17 % Allowed : 11.60 % Favored : 87.23 % Rotamer: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.31 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.35 (0.12), residues: 4432 helix: -0.52 (0.15), residues: 1280 sheet: -0.97 (0.22), residues: 512 loop : -2.33 (0.12), residues: 2640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 399 TYR 0.033 0.001 TYR A 707 PHE 0.024 0.002 PHE C 458 TRP 0.024 0.002 TRP Y 451 HIS 0.010 0.001 HIS C1057 Details of bonding type rmsd covalent geometry : bond 0.00341 (34714) covalent geometry : angle 0.85527 (47341) SS BOND : bond 0.00436 ( 2) SS BOND : angle 0.38022 ( 4) hydrogen bonds : bond 0.03121 ( 918) hydrogen bonds : angle 5.26025 ( 2547) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 705 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 ARG cc_start: 0.9329 (ttm110) cc_final: 0.9104 (ttp-110) REVERT: A 115 MET cc_start: 0.5341 (mtt) cc_final: 0.4624 (pmm) REVERT: A 221 HIS cc_start: 0.8573 (m-70) cc_final: 0.7831 (m90) REVERT: A 259 LEU cc_start: 0.9582 (mp) cc_final: 0.9355 (mp) REVERT: A 284 GLN cc_start: 0.7343 (pp30) cc_final: 0.7097 (pp30) REVERT: A 297 ARG cc_start: 0.9276 (ptt-90) cc_final: 0.8785 (ptt90) REVERT: A 298 GLN cc_start: 0.9377 (tp40) cc_final: 0.8737 (tp40) REVERT: A 301 GLN cc_start: 0.9084 (pp30) cc_final: 0.8652 (pp30) REVERT: A 441 PHE cc_start: 0.8041 (m-10) cc_final: 0.7760 (m-10) REVERT: A 475 MET cc_start: 0.8544 (mmp) cc_final: 0.8328 (mmm) REVERT: A 531 MET cc_start: 0.8761 (tpt) cc_final: 0.8454 (tpt) REVERT: A 676 HIS cc_start: 0.8980 (m-70) cc_final: 0.8664 (m-70) REVERT: A 753 LEU cc_start: 0.9363 (tp) cc_final: 0.9158 (tp) REVERT: A 817 ILE cc_start: 0.8367 (mm) cc_final: 0.7781 (tt) REVERT: A 832 TYR cc_start: 0.9109 (t80) cc_final: 0.8507 (t80) REVERT: A 928 LEU cc_start: 0.9354 (tt) cc_final: 0.8880 (mm) REVERT: A 1057 HIS cc_start: 0.8552 (m90) cc_final: 0.8350 (m90) REVERT: A 1069 PHE cc_start: 0.9095 (m-10) cc_final: 0.8477 (m-10) REVERT: A 1164 GLU cc_start: 0.8784 (tp30) cc_final: 0.8520 (tp30) REVERT: A 1166 LEU cc_start: 0.9543 (mt) cc_final: 0.9272 (mt) REVERT: A 1234 MET cc_start: 0.4393 (ptt) cc_final: 0.3080 (tmm) REVERT: A 1261 LEU cc_start: 0.8734 (tp) cc_final: 0.8174 (tp) REVERT: A 1295 PHE cc_start: 0.8793 (m-10) cc_final: 0.8479 (m-80) REVERT: A 1344 CYS cc_start: 0.8778 (p) cc_final: 0.8385 (p) REVERT: A 1358 ASP cc_start: 0.8311 (t70) cc_final: 0.8063 (t70) REVERT: A 1377 LEU cc_start: 0.9253 (tp) cc_final: 0.8875 (tt) REVERT: C 96 PHE cc_start: 0.9293 (t80) cc_final: 0.8857 (t80) REVERT: C 177 MET cc_start: 0.9504 (mmp) cc_final: 0.9204 (mmm) REVERT: C 296 LYS cc_start: 0.9627 (tttt) cc_final: 0.9404 (ttmt) REVERT: C 301 GLN cc_start: 0.9154 (pp30) cc_final: 0.8908 (pp30) REVERT: C 400 ARG cc_start: 0.4623 (tpt170) cc_final: 0.4274 (tpt170) REVERT: C 473 ASP cc_start: 0.8691 (p0) cc_final: 0.8442 (p0) REVERT: C 520 MET cc_start: 0.8693 (tpp) cc_final: 0.8390 (tpp) REVERT: C 530 MET cc_start: 0.8730 (ppp) cc_final: 0.8465 (ppp) REVERT: C 536 HIS cc_start: 0.8082 (m90) cc_final: 0.7767 (m-70) REVERT: C 537 TRP cc_start: 0.7739 (p-90) cc_final: 0.7394 (p-90) REVERT: C 559 LEU cc_start: 0.9226 (mp) cc_final: 0.9020 (mp) REVERT: C 643 PHE cc_start: 0.9431 (m-10) cc_final: 0.8307 (m-10) REVERT: C 724 PHE cc_start: 0.9443 (m-80) cc_final: 0.8940 (m-80) REVERT: C 756 CYS cc_start: 0.8937 (m) cc_final: 0.8338 (t) REVERT: C 832 TYR cc_start: 0.8905 (t80) cc_final: 0.8506 (t80) REVERT: C 840 PHE cc_start: 0.8975 (m-80) cc_final: 0.8659 (m-10) REVERT: C 848 MET cc_start: 0.8213 (mmp) cc_final: 0.6983 (mmp) REVERT: C 917 MET cc_start: 0.8445 (mmp) cc_final: 0.7576 (mmm) REVERT: C 945 MET cc_start: 0.9173 (mtp) cc_final: 0.8830 (mtp) REVERT: C 1049 LYS cc_start: 0.8229 (pttt) cc_final: 0.7861 (pttt) REVERT: C 1231 MET cc_start: 0.8189 (ppp) cc_final: 0.7967 (ppp) REVERT: C 1245 MET cc_start: 0.9341 (ppp) cc_final: 0.9109 (ppp) REVERT: C 1348 GLN cc_start: 0.9467 (mm-40) cc_final: 0.8089 (mm-40) REVERT: C 1361 MET cc_start: 0.8844 (mpp) cc_final: 0.8455 (mpp) REVERT: G 128 LEU cc_start: 0.7462 (mp) cc_final: 0.7246 (mp) REVERT: G 146 MET cc_start: 0.7915 (pmm) cc_final: 0.7440 (pmm) REVERT: I 67 TYR cc_start: 0.8552 (m-10) cc_final: 0.8034 (m-80) REVERT: I 112 TYR cc_start: 0.8698 (m-80) cc_final: 0.8361 (m-80) REVERT: I 135 ILE cc_start: 0.9224 (mt) cc_final: 0.9012 (pt) REVERT: I 145 LEU cc_start: 0.9461 (mp) cc_final: 0.9255 (mp) REVERT: I 147 ARG cc_start: 0.8996 (ppt170) cc_final: 0.8188 (ttp80) REVERT: I 219 LEU cc_start: 0.7359 (mt) cc_final: 0.7082 (mp) REVERT: I 276 TRP cc_start: 0.6659 (m100) cc_final: 0.6293 (m100) REVERT: I 314 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8057 (tm-30) REVERT: P 52 TYR cc_start: 0.7883 (m-80) cc_final: 0.7307 (m-80) REVERT: P 57 PRO cc_start: 0.6234 (Cg_endo) cc_final: 0.5754 (Cg_exo) REVERT: P 146 MET cc_start: 0.8327 (tpt) cc_final: 0.8007 (tpp) REVERT: P 150 ILE cc_start: 0.8973 (tt) cc_final: 0.8512 (tt) REVERT: P 303 THR cc_start: 0.8832 (p) cc_final: 0.8532 (p) REVERT: R 6 PHE cc_start: 0.8022 (t80) cc_final: 0.7566 (t80) REVERT: R 97 LEU cc_start: 0.8159 (mt) cc_final: 0.7932 (mm) REVERT: R 257 MET cc_start: 0.1241 (tpt) cc_final: 0.0894 (tpp) REVERT: Y 131 VAL cc_start: 0.6057 (p) cc_final: 0.5692 (t) REVERT: Y 136 HIS cc_start: 0.5370 (m-70) cc_final: 0.4864 (m-70) REVERT: Y 335 ASN cc_start: 0.9191 (t0) cc_final: 0.8941 (t0) REVERT: Y 418 MET cc_start: 0.5852 (mmp) cc_final: 0.5356 (mmp) REVERT: d 202 GLN cc_start: 0.8485 (tm-30) cc_final: 0.8254 (tm-30) REVERT: d 253 GLU cc_start: 0.9168 (tt0) cc_final: 0.8729 (mt-10) REVERT: d 291 CYS cc_start: 0.8639 (m) cc_final: 0.8061 (m) REVERT: d 295 ASP cc_start: 0.7841 (m-30) cc_final: 0.7289 (m-30) REVERT: d 335 ASN cc_start: 0.8889 (m-40) cc_final: 0.8526 (m-40) outliers start: 0 outliers final: 0 residues processed: 705 average time/residue: 0.1647 time to fit residues: 193.4522 Evaluate side-chains 560 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 5 optimal weight: 10.0000 chunk 279 optimal weight: 6.9990 chunk 160 optimal weight: 0.2980 chunk 394 optimal weight: 10.0000 chunk 266 optimal weight: 30.0000 chunk 276 optimal weight: 50.0000 chunk 156 optimal weight: 20.0000 chunk 174 optimal weight: 30.0000 chunk 349 optimal weight: 9.9990 chunk 114 optimal weight: 0.2980 chunk 73 optimal weight: 8.9990 overall best weight: 5.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN C 451 GLN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 HIS G 162 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.107959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.081688 restraints weight = 151724.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.084097 restraints weight = 94684.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.085788 restraints weight = 67010.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.086997 restraints weight = 51698.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.087870 restraints weight = 42497.350| |-----------------------------------------------------------------------------| r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 34716 Z= 0.156 Angle : 0.850 15.105 47345 Z= 0.429 Chirality : 0.050 0.675 5553 Planarity : 0.006 0.116 6151 Dihedral : 5.733 33.158 4880 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 16.65 Ramachandran Plot: Outliers : 1.20 % Allowed : 11.96 % Favored : 86.85 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.31 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.31 (0.12), residues: 4432 helix: -0.46 (0.15), residues: 1268 sheet: -0.97 (0.22), residues: 514 loop : -2.31 (0.12), residues: 2650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 147 TYR 0.022 0.001 TYR A 258 PHE 0.023 0.001 PHE C 458 TRP 0.022 0.002 TRP Y 451 HIS 0.010 0.001 HIS C1057 Details of bonding type rmsd covalent geometry : bond 0.00333 (34714) covalent geometry : angle 0.85003 (47341) SS BOND : bond 0.00233 ( 2) SS BOND : angle 0.25544 ( 4) hydrogen bonds : bond 0.03098 ( 918) hydrogen bonds : angle 5.25765 ( 2547) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 705 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 705 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.9224 (t80) cc_final: 0.8935 (t80) REVERT: A 81 ARG cc_start: 0.9336 (ttm110) cc_final: 0.9108 (ttp-110) REVERT: A 101 TYR cc_start: 0.8513 (t80) cc_final: 0.8274 (t80) REVERT: A 115 MET cc_start: 0.6134 (mtt) cc_final: 0.5592 (pmm) REVERT: A 221 HIS cc_start: 0.8581 (m-70) cc_final: 0.7800 (m90) REVERT: A 259 LEU cc_start: 0.9593 (mp) cc_final: 0.9358 (mp) REVERT: A 286 ASP cc_start: 0.8665 (t0) cc_final: 0.8315 (t0) REVERT: A 297 ARG cc_start: 0.9255 (ptt-90) cc_final: 0.8776 (ptt90) REVERT: A 298 GLN cc_start: 0.9357 (tp40) cc_final: 0.8707 (tp40) REVERT: A 301 GLN cc_start: 0.9081 (pp30) cc_final: 0.8643 (pp30) REVERT: A 441 PHE cc_start: 0.7972 (m-10) cc_final: 0.7734 (m-10) REVERT: A 531 MET cc_start: 0.8775 (tpt) cc_final: 0.8483 (tpt) REVERT: A 676 HIS cc_start: 0.9081 (m-70) cc_final: 0.8697 (m-70) REVERT: A 817 ILE cc_start: 0.8384 (mm) cc_final: 0.7795 (tt) REVERT: A 832 TYR cc_start: 0.9049 (t80) cc_final: 0.8479 (t80) REVERT: A 928 LEU cc_start: 0.9338 (tt) cc_final: 0.8868 (mm) REVERT: A 1069 PHE cc_start: 0.9105 (m-10) cc_final: 0.8479 (m-10) REVERT: A 1084 TYR cc_start: 0.8759 (t80) cc_final: 0.8353 (t80) REVERT: A 1164 GLU cc_start: 0.8807 (tp30) cc_final: 0.8302 (tp30) REVERT: A 1166 LEU cc_start: 0.9537 (mt) cc_final: 0.9273 (mt) REVERT: A 1218 PHE cc_start: 0.9647 (m-80) cc_final: 0.9292 (m-10) REVERT: A 1227 ARG cc_start: 0.8404 (ttt180) cc_final: 0.8072 (ttt180) REVERT: A 1234 MET cc_start: 0.4245 (ptt) cc_final: 0.3099 (tmm) REVERT: A 1242 GLU cc_start: 0.8919 (pm20) cc_final: 0.8457 (pm20) REVERT: A 1245 MET cc_start: 0.8870 (ppp) cc_final: 0.8559 (ppp) REVERT: A 1261 LEU cc_start: 0.8728 (tp) cc_final: 0.8160 (tp) REVERT: A 1281 ASN cc_start: 0.9400 (m110) cc_final: 0.9141 (m-40) REVERT: A 1295 PHE cc_start: 0.8718 (m-10) cc_final: 0.8374 (m-80) REVERT: A 1344 CYS cc_start: 0.8995 (p) cc_final: 0.8402 (p) REVERT: A 1358 ASP cc_start: 0.8335 (t70) cc_final: 0.8071 (t70) REVERT: C 96 PHE cc_start: 0.9301 (t80) cc_final: 0.8695 (t80) REVERT: C 177 MET cc_start: 0.9467 (mmp) cc_final: 0.9185 (mmm) REVERT: C 400 ARG cc_start: 0.4534 (tpt170) cc_final: 0.4323 (tpt170) REVERT: C 473 ASP cc_start: 0.8700 (p0) cc_final: 0.8456 (p0) REVERT: C 520 MET cc_start: 0.8683 (tpp) cc_final: 0.8389 (tpp) REVERT: C 530 MET cc_start: 0.8808 (ppp) cc_final: 0.8590 (ppp) REVERT: C 536 HIS cc_start: 0.8109 (m90) cc_final: 0.7803 (m-70) REVERT: C 537 TRP cc_start: 0.7718 (p-90) cc_final: 0.7416 (p-90) REVERT: C 559 LEU cc_start: 0.9215 (mp) cc_final: 0.8980 (mp) REVERT: C 643 PHE cc_start: 0.9431 (m-10) cc_final: 0.8318 (m-10) REVERT: C 712 GLN cc_start: 0.9418 (tm-30) cc_final: 0.9210 (tm-30) REVERT: C 724 PHE cc_start: 0.9439 (m-80) cc_final: 0.8933 (m-80) REVERT: C 832 TYR cc_start: 0.8854 (t80) cc_final: 0.8436 (t80) REVERT: C 848 MET cc_start: 0.8564 (mmp) cc_final: 0.7562 (mmp) REVERT: C 917 MET cc_start: 0.8489 (mmp) cc_final: 0.7699 (mmm) REVERT: C 945 MET cc_start: 0.9185 (mtp) cc_final: 0.8816 (mtp) REVERT: C 1231 MET cc_start: 0.8164 (ppp) cc_final: 0.7927 (ppp) REVERT: C 1245 MET cc_start: 0.9289 (ppp) cc_final: 0.9007 (ppp) REVERT: C 1294 LYS cc_start: 0.9485 (pptt) cc_final: 0.9108 (pptt) REVERT: C 1295 PHE cc_start: 0.8324 (m-80) cc_final: 0.7624 (m-80) REVERT: C 1348 GLN cc_start: 0.9282 (mm-40) cc_final: 0.8230 (mm110) REVERT: C 1361 MET cc_start: 0.8849 (mpp) cc_final: 0.8439 (mpp) REVERT: G 128 LEU cc_start: 0.7466 (mp) cc_final: 0.7258 (mp) REVERT: G 146 MET cc_start: 0.7927 (pmm) cc_final: 0.7563 (pmm) REVERT: I 67 TYR cc_start: 0.8556 (m-10) cc_final: 0.8074 (m-80) REVERT: I 112 TYR cc_start: 0.8656 (m-80) cc_final: 0.8316 (m-80) REVERT: I 135 ILE cc_start: 0.9227 (mt) cc_final: 0.8998 (pt) REVERT: I 146 MET cc_start: 0.7375 (mtt) cc_final: 0.6780 (mtm) REVERT: I 147 ARG cc_start: 0.8946 (ppt170) cc_final: 0.8260 (ttp80) REVERT: I 148 GLU cc_start: 0.9158 (pm20) cc_final: 0.8949 (pm20) REVERT: I 219 LEU cc_start: 0.7286 (mt) cc_final: 0.7002 (mp) REVERT: I 276 TRP cc_start: 0.6691 (m100) cc_final: 0.6247 (m100) REVERT: I 314 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8050 (tm-30) REVERT: P 52 TYR cc_start: 0.7861 (m-80) cc_final: 0.7340 (m-80) REVERT: P 57 PRO cc_start: 0.6265 (Cg_endo) cc_final: 0.5799 (Cg_exo) REVERT: P 146 MET cc_start: 0.8238 (tpt) cc_final: 0.7869 (tpp) REVERT: P 150 ILE cc_start: 0.8933 (tt) cc_final: 0.8498 (tt) REVERT: P 303 THR cc_start: 0.8777 (p) cc_final: 0.8555 (p) REVERT: R 6 PHE cc_start: 0.8067 (t80) cc_final: 0.7618 (t80) REVERT: R 45 ASP cc_start: 0.6587 (t70) cc_final: 0.6290 (t0) REVERT: R 97 LEU cc_start: 0.8166 (mt) cc_final: 0.7936 (mm) REVERT: R 257 MET cc_start: 0.1340 (tpt) cc_final: 0.0995 (tpp) REVERT: R 293 LEU cc_start: 0.8438 (tp) cc_final: 0.8222 (tp) REVERT: Y 308 LYS cc_start: 0.8138 (tptt) cc_final: 0.7843 (tppt) REVERT: Y 418 MET cc_start: 0.5876 (mmp) cc_final: 0.5370 (mmp) REVERT: d 202 GLN cc_start: 0.8472 (tm-30) cc_final: 0.8234 (tm-30) REVERT: d 220 MET cc_start: 0.7996 (tmm) cc_final: 0.7060 (mmt) REVERT: d 253 GLU cc_start: 0.9177 (tt0) cc_final: 0.8732 (mt-10) REVERT: d 291 CYS cc_start: 0.8654 (m) cc_final: 0.8065 (m) REVERT: d 295 ASP cc_start: 0.7845 (m-30) cc_final: 0.7282 (m-30) REVERT: d 305 ASP cc_start: 0.8136 (m-30) cc_final: 0.7892 (m-30) REVERT: d 335 ASN cc_start: 0.8954 (m-40) cc_final: 0.8492 (m-40) outliers start: 0 outliers final: 0 residues processed: 705 average time/residue: 0.1663 time to fit residues: 195.2506 Evaluate side-chains 577 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 577 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 40 optimal weight: 0.2980 chunk 250 optimal weight: 9.9990 chunk 210 optimal weight: 20.0000 chunk 205 optimal weight: 0.0470 chunk 290 optimal weight: 10.0000 chunk 304 optimal weight: 20.0000 chunk 80 optimal weight: 9.9990 chunk 246 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 395 optimal weight: 7.9990 chunk 439 optimal weight: 2.9990 overall best weight: 3.6684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 741 ASN ** A 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 HIS C1102 HIS G 162 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 461 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.108762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.082503 restraints weight = 151454.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.084926 restraints weight = 94213.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.086642 restraints weight = 66444.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.087875 restraints weight = 51123.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.088753 restraints weight = 41899.649| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.3024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 34716 Z= 0.147 Angle : 0.861 14.832 47345 Z= 0.432 Chirality : 0.050 0.660 5553 Planarity : 0.006 0.116 6151 Dihedral : 5.684 33.339 4880 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 1.22 % Allowed : 11.60 % Favored : 87.18 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.31 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.32 (0.12), residues: 4432 helix: -0.44 (0.15), residues: 1270 sheet: -1.01 (0.22), residues: 532 loop : -2.32 (0.12), residues: 2630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A1189 TYR 0.021 0.001 TYR C1084 PHE 0.032 0.001 PHE A 51 TRP 0.023 0.001 TRP Y 451 HIS 0.012 0.001 HIS C1057 Details of bonding type rmsd covalent geometry : bond 0.00316 (34714) covalent geometry : angle 0.86101 (47341) SS BOND : bond 0.00211 ( 2) SS BOND : angle 0.29468 ( 4) hydrogen bonds : bond 0.03089 ( 918) hydrogen bonds : angle 5.19814 ( 2547) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8864 Ramachandran restraints generated. 4432 Oldfield, 0 Emsley, 4432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 716 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 716 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 PHE cc_start: 0.9196 (t80) cc_final: 0.8894 (t80) REVERT: A 81 ARG cc_start: 0.9323 (ttm110) cc_final: 0.9098 (ttp-110) REVERT: A 101 TYR cc_start: 0.8458 (t80) cc_final: 0.8215 (t80) REVERT: A 115 MET cc_start: 0.6801 (mtt) cc_final: 0.6108 (pmm) REVERT: A 130 ASN cc_start: 0.5111 (p0) cc_final: 0.4860 (p0) REVERT: A 221 HIS cc_start: 0.8567 (m-70) cc_final: 0.7818 (m90) REVERT: A 231 LEU cc_start: 0.9538 (tt) cc_final: 0.9050 (tt) REVERT: A 235 LYS cc_start: 0.9085 (mmtt) cc_final: 0.8330 (mmmt) REVERT: A 244 PHE cc_start: 0.8164 (t80) cc_final: 0.7802 (t80) REVERT: A 259 LEU cc_start: 0.9586 (mp) cc_final: 0.9362 (mp) REVERT: A 286 ASP cc_start: 0.8640 (t0) cc_final: 0.8292 (t0) REVERT: A 297 ARG cc_start: 0.9232 (ptt-90) cc_final: 0.8739 (ptt90) REVERT: A 298 GLN cc_start: 0.9321 (tp40) cc_final: 0.8664 (tp40) REVERT: A 301 GLN cc_start: 0.9145 (pp30) cc_final: 0.8650 (pp30) REVERT: A 441 PHE cc_start: 0.7949 (m-10) cc_final: 0.7707 (m-10) REVERT: A 531 MET cc_start: 0.8745 (tpt) cc_final: 0.8429 (tpt) REVERT: A 676 HIS cc_start: 0.9043 (m-70) cc_final: 0.8671 (m-70) REVERT: A 817 ILE cc_start: 0.8371 (mm) cc_final: 0.7806 (tt) REVERT: A 832 TYR cc_start: 0.9040 (t80) cc_final: 0.8265 (t80) REVERT: A 928 LEU cc_start: 0.9305 (tt) cc_final: 0.8834 (mm) REVERT: A 1069 PHE cc_start: 0.9028 (m-10) cc_final: 0.8479 (m-10) REVERT: A 1084 TYR cc_start: 0.8689 (t80) cc_final: 0.8330 (t80) REVERT: A 1164 GLU cc_start: 0.8776 (tp30) cc_final: 0.8320 (tp30) REVERT: A 1166 LEU cc_start: 0.9530 (mt) cc_final: 0.9263 (mt) REVERT: A 1218 PHE cc_start: 0.9681 (m-80) cc_final: 0.9458 (m-80) REVERT: A 1227 ARG cc_start: 0.8429 (ttt180) cc_final: 0.8072 (ttt180) REVERT: A 1234 MET cc_start: 0.4355 (ptt) cc_final: 0.3123 (tmm) REVERT: A 1242 GLU cc_start: 0.8693 (pm20) cc_final: 0.8448 (pm20) REVERT: A 1245 MET cc_start: 0.8792 (ppp) cc_final: 0.8274 (ppp) REVERT: A 1246 PHE cc_start: 0.9188 (m-80) cc_final: 0.8878 (m-80) REVERT: A 1261 LEU cc_start: 0.8675 (tp) cc_final: 0.8107 (tp) REVERT: A 1269 HIS cc_start: 0.7262 (m-70) cc_final: 0.6874 (m90) REVERT: A 1281 ASN cc_start: 0.9377 (m110) cc_final: 0.9103 (m-40) REVERT: A 1295 PHE cc_start: 0.8711 (m-10) cc_final: 0.8348 (m-80) REVERT: A 1344 CYS cc_start: 0.8780 (p) cc_final: 0.8575 (p) REVERT: A 1358 ASP cc_start: 0.8333 (t70) cc_final: 0.8032 (t70) REVERT: C 96 PHE cc_start: 0.9267 (t80) cc_final: 0.8784 (t80) REVERT: C 177 MET cc_start: 0.9461 (mmp) cc_final: 0.9172 (mmm) REVERT: C 400 ARG cc_start: 0.4484 (tpt170) cc_final: 0.4249 (tpt170) REVERT: C 473 ASP cc_start: 0.8661 (p0) cc_final: 0.8428 (p0) REVERT: C 520 MET cc_start: 0.8654 (tpp) cc_final: 0.8363 (tpp) REVERT: C 530 MET cc_start: 0.8779 (ppp) cc_final: 0.8564 (ppp) REVERT: C 536 HIS cc_start: 0.8044 (m90) cc_final: 0.7745 (m-70) REVERT: C 537 TRP cc_start: 0.7683 (p-90) cc_final: 0.7384 (p-90) REVERT: C 643 PHE cc_start: 0.9442 (m-10) cc_final: 0.8323 (m-10) REVERT: C 712 GLN cc_start: 0.9411 (tm-30) cc_final: 0.9190 (tm-30) REVERT: C 724 PHE cc_start: 0.9424 (m-80) cc_final: 0.8932 (m-80) REVERT: C 832 TYR cc_start: 0.8880 (t80) cc_final: 0.8500 (t80) REVERT: C 848 MET cc_start: 0.8454 (mmp) cc_final: 0.7434 (mmp) REVERT: C 917 MET cc_start: 0.8411 (mmp) cc_final: 0.7724 (mmm) REVERT: C 945 MET cc_start: 0.9181 (mtp) cc_final: 0.8798 (mtp) REVERT: C 1231 MET cc_start: 0.8132 (ppp) cc_final: 0.7907 (ppp) REVERT: C 1245 MET cc_start: 0.9281 (ppp) cc_final: 0.8994 (ppp) REVERT: C 1348 GLN cc_start: 0.9274 (mm-40) cc_final: 0.8550 (mm-40) REVERT: C 1361 MET cc_start: 0.8665 (mpp) cc_final: 0.8255 (mpp) REVERT: G 128 LEU cc_start: 0.7465 (mp) cc_final: 0.7262 (mp) REVERT: G 146 MET cc_start: 0.7870 (pmm) cc_final: 0.7471 (pmm) REVERT: I 67 TYR cc_start: 0.8525 (m-10) cc_final: 0.8053 (m-80) REVERT: I 112 TYR cc_start: 0.8601 (m-80) cc_final: 0.8258 (m-80) REVERT: I 134 GLU cc_start: 0.8481 (tp30) cc_final: 0.7959 (tp30) REVERT: I 146 MET cc_start: 0.7326 (mtt) cc_final: 0.6714 (mtm) REVERT: I 147 ARG cc_start: 0.8834 (ppt170) cc_final: 0.8151 (ttp80) REVERT: I 219 LEU cc_start: 0.7396 (mt) cc_final: 0.7061 (mp) REVERT: I 276 TRP cc_start: 0.6610 (m100) cc_final: 0.6312 (m100) REVERT: I 314 GLN cc_start: 0.8841 (tm-30) cc_final: 0.8079 (tm-30) REVERT: P 4 MET cc_start: 0.3825 (tpt) cc_final: 0.3433 (tpp) REVERT: P 52 TYR cc_start: 0.7867 (m-80) cc_final: 0.7346 (m-80) REVERT: P 57 PRO cc_start: 0.6699 (Cg_endo) cc_final: 0.6301 (Cg_exo) REVERT: P 146 MET cc_start: 0.8283 (tpt) cc_final: 0.7909 (tpp) REVERT: P 150 ILE cc_start: 0.8960 (tt) cc_final: 0.8472 (tt) REVERT: P 295 VAL cc_start: 0.9071 (m) cc_final: 0.8850 (p) REVERT: P 303 THR cc_start: 0.8765 (p) cc_final: 0.8528 (p) REVERT: R 6 PHE cc_start: 0.8009 (t80) cc_final: 0.7544 (t80) REVERT: R 97 LEU cc_start: 0.8136 (mt) cc_final: 0.7918 (mm) REVERT: R 257 MET cc_start: 0.1810 (tpt) cc_final: 0.1422 (tpp) REVERT: Y 308 LYS cc_start: 0.8133 (tptt) cc_final: 0.7840 (tppt) REVERT: Y 335 ASN cc_start: 0.8810 (t0) cc_final: 0.8571 (t0) REVERT: Y 418 MET cc_start: 0.5703 (mmp) cc_final: 0.5254 (mmp) REVERT: d 134 LEU cc_start: 0.9119 (tp) cc_final: 0.8913 (tp) REVERT: d 202 GLN cc_start: 0.8495 (tm-30) cc_final: 0.8292 (tm-30) REVERT: d 253 GLU cc_start: 0.9170 (tt0) cc_final: 0.8726 (mt-10) REVERT: d 291 CYS cc_start: 0.8674 (m) cc_final: 0.8099 (m) REVERT: d 295 ASP cc_start: 0.7767 (m-30) cc_final: 0.7133 (m-30) REVERT: d 305 ASP cc_start: 0.8110 (m-30) cc_final: 0.7853 (m-30) REVERT: d 335 ASN cc_start: 0.8798 (m-40) cc_final: 0.8478 (m-40) outliers start: 0 outliers final: 0 residues processed: 716 average time/residue: 0.1655 time to fit residues: 197.3084 Evaluate side-chains 578 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 578 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 78 optimal weight: 7.9990 chunk 415 optimal weight: 0.0010 chunk 339 optimal weight: 0.0000 chunk 150 optimal weight: 0.0980 chunk 73 optimal weight: 8.9990 chunk 276 optimal weight: 8.9990 chunk 418 optimal weight: 5.9990 chunk 352 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 314 optimal weight: 8.9990 chunk 403 optimal weight: 6.9990 overall best weight: 2.4194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 427 GLN C 451 GLN C 455 GLN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 731 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 799 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 HIS G 162 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 ASN R 86 HIS ** R 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 461 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.109662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.083367 restraints weight = 148203.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.085793 restraints weight = 92322.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.087506 restraints weight = 65193.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 59)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.088773 restraints weight = 50146.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.089687 restraints weight = 41044.071| |-----------------------------------------------------------------------------| r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3107 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 34716 Z= 0.140 Angle : 0.850 15.072 47345 Z= 0.426 Chirality : 0.050 0.634 5553 Planarity : 0.006 0.116 6151 Dihedral : 5.611 32.646 4880 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 1.17 % Allowed : 11.62 % Favored : 87.21 % Rotamer: Outliers : 0.03 % Allowed : 0.51 % Favored : 99.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.31 % Twisted Proline : 0.00 % Twisted General : 0.12 % 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: -2.28 (0.12), residues: 4432 helix: -0.45 (0.15), residues: 1279 sheet: -0.99 (0.22), residues: 530 loop : -2.28 (0.12), residues: 2623 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A1189 TYR 0.020 0.001 TYR A 258 PHE 0.023 0.001 PHE A 51 TRP 0.022 0.001 TRP Y 451 HIS 0.013 0.001 HIS C1057 Details of bonding type rmsd covalent geometry : bond 0.00301 (34714) covalent geometry : angle 0.84999 (47341) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.38170 ( 4) hydrogen bonds : bond 0.02998 ( 918) hydrogen bonds : angle 5.08723 ( 2547) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5690.33 seconds wall clock time: 98 minutes 55.20 seconds (5935.20 seconds total)