Starting phenix.real_space_refine on Sun Jun 29 09:00:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xa1_38191/06_2025/8xa1_38191.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xa1_38191/06_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_38191/06_2025/8xa1_38191.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xa1_38191/06_2025/8xa1_38191.map" model { file = "/net/cci-nas-00/data/ceres_data/8xa1_38191/06_2025/8xa1_38191.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xa1_38191/06_2025/8xa1_38191.cif" } resolution = 4.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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): 0.71s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 2, 'ASP:plan': 4, 'ASN:plan1': 2, 'HIS:plan': 1, 'GLU:plan': 6, 'ARG:plan': 14} 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: {'TYR:plan': 1, 'GLU:plan': 4, 'ARG:plan': 12} 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 3, 'ARG:plan': 3} 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: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 9, 'GLU:plan': 3, 'ARG:plan': 3} 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: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 4} 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: {'GLN:plan1': 3, 'GLU:plan': 6, 'ARG:plan': 3, 'ASP:plan': 4} 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: {'GLN:plan1': 1, 'HIS:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 6, 'ARG:plan': 6} 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: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 6, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 98 Time building chain proxies: 19.24, per 1000 atoms: 0.57 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: 7.67 Conformation dependent library (CDL) restraints added in 5.3 seconds 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: 4.08 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: 12.79 Time building geometry restraints manager: 9.23 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: 2.200 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: 1.380 Check model and map are aligned: 0.230 Set scattering table: 0.300 Process input model: 73.450 Find NCS groups from input model: 1.320 Set up NCS constraints: 0.140 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 81.990 ------------------------------------------------------------------------------- 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 : 8.05 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.025 0.002 TRP I 276 HIS 0.011 0.001 HIS A1269 PHE 0.058 0.003 PHE C 634 TYR 0.043 0.002 TYR A 101 ARG 0.017 0.001 ARG A 718 Details of bonding type rmsd hydrogen bonds : bond 0.17421 ( 918) hydrogen bonds : angle 7.93265 ( 2547) SS BOND : bond 0.00313 ( 2) SS BOND : angle 0.74406 ( 4) covalent geometry : bond 0.00537 (34714) covalent geometry : angle 1.35305 (47341) *********************** 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 : 3.830 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: 0.9417 (pp) REVERT: A 87 LEU cc_start: 0.8497 (mm) cc_final: 0.8226 (tp) REVERT: A 115 MET cc_start: 0.2353 (mtm) cc_final: 0.1735 (ttt) REVERT: A 132 MET cc_start: 0.4285 (pmm) cc_final: 0.3998 (ptp) REVERT: A 145 PHE cc_start: 0.8034 (t80) cc_final: 0.7621 (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: 0.7383 (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: 0.7969 (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: 0.8670 (pp30) REVERT: A 400 ARG cc_start: 0.8900 (mtm110) cc_final: 0.8564 (mtm110) REVERT: A 441 PHE cc_start: 0.8267 (m-10) cc_final: 0.7961 (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: 0.7455 (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: 0.8623 (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: 0.7648 (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: 0.7422 (pp30) REVERT: A 1069 PHE cc_start: 0.8917 (m-10) cc_final: 0.8078 (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: 0.8061 (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: 0.8602 (p) REVERT: A 1261 LEU cc_start: 0.8756 (tp) cc_final: 0.8405 (tp) REVERT: A 1295 PHE cc_start: 0.8425 (m-10) cc_final: 0.8072 (m-80) REVERT: A 1344 CYS cc_start: 0.8393 (p) cc_final: 0.7384 (m) REVERT: A 1351 TYR cc_start: 0.9183 (m-10) cc_final: 0.8411 (m-10) REVERT: A 1358 ASP cc_start: 0.8517 (t70) cc_final: 0.8126 (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: 0.8949 (t80) REVERT: C 177 MET cc_start: 0.9451 (mmp) cc_final: 0.9239 (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: 0.8433 (pp30) REVERT: C 400 ARG cc_start: 0.4345 (tpt170) cc_final: 0.4025 (tpt170) REVERT: C 473 ASP cc_start: 0.8799 (p0) cc_final: 0.8476 (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: 0.7767 (m-70) REVERT: C 540 GLU cc_start: 0.7858 (pm20) cc_final: 0.7445 (mp0) REVERT: C 594 ILE cc_start: 0.8540 (mm) cc_final: 0.8123 (mt) REVERT: C 643 PHE cc_start: 0.9348 (m-10) cc_final: 0.8793 (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: 0.7133 (mmp) REVERT: C 917 MET cc_start: 0.8411 (mmp) cc_final: 0.7783 (mmm) REVERT: C 945 MET cc_start: 0.9019 (mtp) cc_final: 0.8698 (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: 0.8989 (p) REVERT: C 1084 TYR cc_start: 0.8482 (t80) cc_final: 0.8166 (t80) REVERT: C 1231 MET cc_start: 0.7813 (ppp) cc_final: 0.7541 (ppp) REVERT: C 1348 GLN cc_start: 0.9249 (mm-40) cc_final: 0.8127 (mm-40) REVERT: C 1361 MET cc_start: 0.8475 (mpp) cc_final: 0.8187 (mpp) REVERT: G 106 ASP cc_start: 0.6747 (m-30) cc_final: 0.6316 (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: 0.7780 (pmm) REVERT: G 273 ILE cc_start: 0.7277 (tp) cc_final: 0.6720 (pt) REVERT: G 282 ARG cc_start: 0.9019 (pmt170) cc_final: 0.8562 (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: 0.8271 (m-80) REVERT: I 69 MET cc_start: 0.9128 (mmm) cc_final: 0.8724 (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: 0.8241 (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: 0.8545 (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: 0.7924 (m-10) REVERT: P 64 LEU cc_start: 0.9560 (mm) cc_final: 0.9253 (pp) REVERT: P 143 GLN cc_start: 0.8715 (tp40) cc_final: 0.8499 (pm20) REVERT: P 218 ILE cc_start: 0.5914 (mm) cc_final: 0.5687 (pt) REVERT: P 290 ARG cc_start: 0.8054 (ptm-80) cc_final: 0.7677 (ttp80) REVERT: R 6 PHE cc_start: 0.8258 (t80) cc_final: 0.7855 (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: 0.8683 (tp) REVERT: d 142 HIS cc_start: 0.4208 (m-70) cc_final: 0.4004 (m-70) REVERT: d 253 GLU cc_start: 0.9281 (tt0) cc_final: 0.8886 (tt0) REVERT: d 335 ASN cc_start: 0.8830 (m-40) cc_final: 0.8434 (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: 0.4473 time to fit residues: 574.0458 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 : 3.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 374 optimal weight: 40.0000 chunk 336 optimal weight: 7.9990 chunk 186 optimal weight: 20.0000 chunk 114 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 chunk 179 optimal weight: 10.0000 chunk 348 optimal weight: 30.0000 chunk 134 optimal weight: 5.9990 chunk 211 optimal weight: 30.0000 chunk 259 optimal weight: 8.9990 chunk 403 optimal weight: 8.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 536 HIS ** 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 162 ASN I 162 ASN R 86 HIS Y 136 HIS ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.110088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.083733 restraints weight = 151642.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.086149 restraints weight = 94863.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.087847 restraints weight = 67214.851| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.1242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 34716 Z= 0.168 Angle : 0.835 15.033 47345 Z= 0.434 Chirality : 0.049 0.510 5553 Planarity : 0.006 0.124 6151 Dihedral : 6.378 36.610 4880 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 1.35 % Allowed : 11.06 % Favored : 87.59 % Rotamer: Outliers : 0.08 % Allowed : 6.00 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.12), residues: 4432 helix: -1.49 (0.13), residues: 1282 sheet: -1.29 (0.22), residues: 534 loop : -2.53 (0.11), residues: 2616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 672 HIS 0.005 0.001 HIS C 685 PHE 0.028 0.001 PHE C 458 TYR 0.020 0.001 TYR A 73 ARG 0.006 0.001 ARG C 718 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 918) hydrogen bonds : angle 6.03686 ( 2547) SS BOND : bond 0.00369 ( 2) SS BOND : angle 0.81260 ( 4) covalent geometry : bond 0.00348 (34714) covalent geometry : angle 0.83541 (47341) *********************** 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 734 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 731 time to evaluate : 3.843 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 81 ARG cc_start: 0.9315 (ptp-110) cc_final: 0.8970 (tpt170) REVERT: A 85 LEU cc_start: 0.9595 (pp) cc_final: 0.9340 (pp) REVERT: A 87 LEU cc_start: 0.8372 (mm) cc_final: 0.8171 (tp) REVERT: A 115 MET cc_start: 0.3972 (mtm) cc_final: 0.3243 (ttt) REVERT: A 132 MET cc_start: 0.4724 (pmm) cc_final: 0.4197 (ptp) REVERT: A 145 PHE cc_start: 0.8132 (t80) cc_final: 0.7672 (t80) REVERT: A 234 LEU cc_start: 0.9649 (mm) cc_final: 0.9134 (mm) REVERT: A 259 LEU cc_start: 0.9530 (mp) cc_final: 0.9283 (mp) REVERT: A 284 GLN cc_start: 0.8735 (pp30) cc_final: 0.8175 (pp30) REVERT: A 297 ARG cc_start: 0.9376 (ptt-90) cc_final: 0.8757 (ptt90) REVERT: A 301 GLN cc_start: 0.9095 (pp30) cc_final: 0.8671 (pp30) REVERT: A 400 ARG cc_start: 0.8895 (mtm110) cc_final: 0.8645 (mtm110) REVERT: A 441 PHE cc_start: 0.8257 (m-10) cc_final: 0.7859 (m-10) REVERT: A 475 MET cc_start: 0.8225 (mmp) cc_final: 0.8023 (mmm) REVERT: A 520 MET cc_start: 0.8563 (tpp) cc_final: 0.7958 (tpp) REVERT: A 531 MET cc_start: 0.8849 (tpt) cc_final: 0.8176 (tpt) REVERT: A 558 GLU cc_start: 0.8785 (tp30) cc_final: 0.8409 (tp30) REVERT: A 632 ASP cc_start: 0.8992 (t0) cc_final: 0.8662 (t0) REVERT: A 645 MET cc_start: 0.8586 (mtt) cc_final: 0.8160 (mtp) REVERT: A 676 HIS cc_start: 0.9001 (m-70) cc_final: 0.8067 (m90) REVERT: A 753 LEU cc_start: 0.9301 (tp) cc_final: 0.9091 (tp) REVERT: A 817 ILE cc_start: 0.8251 (mm) cc_final: 0.7686 (tt) REVERT: A 832 TYR cc_start: 0.9100 (t80) cc_final: 0.8524 (t80) REVERT: A 1069 PHE cc_start: 0.9047 (m-10) cc_final: 0.8380 (m-10) REVERT: A 1166 LEU cc_start: 0.9593 (mt) cc_final: 0.9356 (mt) REVERT: A 1227 ARG cc_start: 0.8231 (ttt180) cc_final: 0.8004 (ttt180) REVERT: A 1261 LEU cc_start: 0.8759 (tp) cc_final: 0.8373 (tp) REVERT: A 1295 PHE cc_start: 0.8709 (m-10) cc_final: 0.8464 (m-80) REVERT: A 1344 CYS cc_start: 0.8448 (p) cc_final: 0.8089 (p) REVERT: A 1358 ASP cc_start: 0.8518 (t70) cc_final: 0.8152 (t70) REVERT: A 1361 MET cc_start: 0.8897 (ppp) cc_final: 0.8628 (ppp) REVERT: A 1377 LEU cc_start: 0.9342 (tp) cc_final: 0.8941 (tp) REVERT: C 96 PHE cc_start: 0.9272 (t80) cc_final: 0.8945 (t80) REVERT: C 177 MET cc_start: 0.9451 (mmp) cc_final: 0.9213 (mmm) REVERT: C 202 GLU cc_start: 0.8518 (pm20) cc_final: 0.8298 (mp0) REVERT: C 400 ARG cc_start: 0.4566 (tpt170) cc_final: 0.4232 (tpt170) REVERT: C 473 ASP cc_start: 0.8882 (p0) cc_final: 0.8543 (p0) REVERT: C 520 MET cc_start: 0.8736 (tpp) cc_final: 0.8285 (tpp) REVERT: C 536 HIS cc_start: 0.7900 (m90) cc_final: 0.7660 (m-70) REVERT: C 537 TRP cc_start: 0.7837 (p-90) cc_final: 0.7250 (p-90) REVERT: C 540 GLU cc_start: 0.7878 (pm20) cc_final: 0.7589 (mp0) REVERT: C 643 PHE cc_start: 0.9313 (m-10) cc_final: 0.8306 (m-80) REVERT: C 724 PHE cc_start: 0.9330 (m-80) cc_final: 0.8990 (m-80) REVERT: C 848 MET cc_start: 0.8450 (mmp) cc_final: 0.7606 (mmp) REVERT: C 917 MET cc_start: 0.8423 (mmp) cc_final: 0.7932 (mmm) REVERT: C 945 MET cc_start: 0.9074 (mtp) cc_final: 0.8704 (mtp) REVERT: C 1231 MET cc_start: 0.8004 (ppp) cc_final: 0.7784 (ppp) REVERT: C 1348 GLN cc_start: 0.9297 (mm-40) cc_final: 0.8596 (mm110) REVERT: G 128 LEU cc_start: 0.7420 (mp) cc_final: 0.7215 (mp) REVERT: G 146 MET cc_start: 0.8205 (pmm) cc_final: 0.7910 (pmm) REVERT: G 273 ILE cc_start: 0.7262 (tp) cc_final: 0.6871 (pt) REVERT: I 67 TYR cc_start: 0.8725 (m-10) cc_final: 0.8281 (m-80) REVERT: I 69 MET cc_start: 0.9202 (mmm) cc_final: 0.8856 (mmm) REVERT: I 112 TYR cc_start: 0.8920 (m-10) cc_final: 0.8518 (m-80) REVERT: I 114 CYS cc_start: 0.9305 (m) cc_final: 0.9023 (m) REVERT: I 135 ILE cc_start: 0.9070 (mt) cc_final: 0.8651 (tp) REVERT: I 137 PHE cc_start: 0.8794 (m-80) cc_final: 0.8183 (m-80) REVERT: I 146 MET cc_start: 0.7109 (mtt) cc_final: 0.6600 (mtt) REVERT: I 147 ARG cc_start: 0.9067 (ppt170) cc_final: 0.8583 (tmm160) REVERT: I 219 LEU cc_start: 0.7595 (mt) cc_final: 0.7262 (mp) REVERT: I 298 PHE cc_start: 0.8351 (t80) cc_final: 0.7852 (m-10) REVERT: P 143 GLN cc_start: 0.8391 (tp40) cc_final: 0.8171 (pt0) REVERT: P 146 MET cc_start: 0.8933 (ppp) cc_final: 0.8472 (ppp) REVERT: P 290 ARG cc_start: 0.8191 (ptm-80) cc_final: 0.7906 (ttp80) REVERT: R 6 PHE cc_start: 0.8285 (t80) cc_final: 0.7864 (t80) REVERT: R 27 CYS cc_start: 0.9079 (m) cc_final: 0.8701 (m) REVERT: R 97 LEU cc_start: 0.8247 (mt) cc_final: 0.7992 (mm) REVERT: R 113 ILE cc_start: 0.9227 (mp) cc_final: 0.8867 (mp) REVERT: R 146 MET cc_start: 0.9408 (tpt) cc_final: 0.9205 (tpp) REVERT: R 189 ASN cc_start: 0.8065 (m-40) cc_final: 0.7804 (m110) REVERT: d 110 LEU cc_start: 0.8792 (mt) cc_final: 0.8395 (mt) REVERT: d 134 LEU cc_start: 0.9064 (tp) cc_final: 0.8769 (tp) REVERT: d 253 GLU cc_start: 0.9225 (tt0) cc_final: 0.8919 (mt-10) REVERT: d 335 ASN cc_start: 0.8971 (m-40) cc_final: 0.8542 (m-40) outliers start: 3 outliers final: 1 residues processed: 733 average time/residue: 0.4478 time to fit residues: 545.6336 Evaluate side-chains 578 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 577 time to evaluate : 3.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 92 optimal weight: 7.9990 chunk 189 optimal weight: 30.0000 chunk 427 optimal weight: 30.0000 chunk 188 optimal weight: 9.9990 chunk 375 optimal weight: 0.0270 chunk 384 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 271 optimal weight: 30.0000 chunk 58 optimal weight: 30.0000 chunk 423 optimal weight: 40.0000 chunk 35 optimal weight: 10.0000 overall best weight: 6.6046 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN ** A 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 451 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 HIS ** A1098 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 705 ASN ** 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 ** 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 = 0.3876 r_free = 0.3876 target = 0.108675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.082620 restraints weight = 150073.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.084998 restraints weight = 93604.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.086681 restraints weight = 66363.094| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 34716 Z= 0.169 Angle : 0.841 15.148 47345 Z= 0.431 Chirality : 0.049 0.556 5553 Planarity : 0.006 0.123 6151 Dihedral : 6.135 35.289 4880 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 1.22 % Allowed : 11.67 % Favored : 87.12 % Rotamer: Outliers : 0.00 % Allowed : 6.09 % Favored : 93.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.14 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.77 (0.12), residues: 4432 helix: -1.07 (0.14), residues: 1299 sheet: -1.29 (0.22), residues: 543 loop : -2.47 (0.12), residues: 2590 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 672 HIS 0.007 0.001 HIS A1057 PHE 0.027 0.002 PHE C 458 TYR 0.020 0.001 TYR G 112 ARG 0.008 0.001 ARG A 139 Details of bonding type rmsd hydrogen bonds : bond 0.03523 ( 918) hydrogen bonds : angle 5.65387 ( 2547) SS BOND : bond 0.00424 ( 2) SS BOND : angle 0.50336 ( 4) covalent geometry : bond 0.00355 (34714) covalent geometry : angle 0.84111 (47341) *********************** 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 731 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 731 time to evaluate : 3.690 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 47 ILE cc_start: 0.9248 (tt) cc_final: 0.8990 (pt) REVERT: A 81 ARG cc_start: 0.9369 (ptp-110) cc_final: 0.8906 (mpt180) REVERT: A 85 LEU cc_start: 0.9574 (pp) cc_final: 0.9362 (pp) REVERT: A 115 MET cc_start: 0.4167 (mtm) cc_final: 0.3113 (ttt) REVERT: A 132 MET cc_start: 0.4870 (pmm) cc_final: 0.4513 (ptp) REVERT: A 145 PHE cc_start: 0.8290 (t80) cc_final: 0.7800 (t80) REVERT: A 217 GLN cc_start: 0.8656 (tm130) cc_final: 0.8383 (tm-30) REVERT: A 234 LEU cc_start: 0.9652 (mm) cc_final: 0.9315 (mm) REVERT: A 259 LEU cc_start: 0.9580 (mp) cc_final: 0.9318 (mp) REVERT: A 297 ARG cc_start: 0.9335 (ptt-90) cc_final: 0.8827 (ptt90) REVERT: A 301 GLN cc_start: 0.9140 (pp30) cc_final: 0.8649 (pp30) REVERT: A 398 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8705 (mp0) REVERT: A 441 PHE cc_start: 0.8289 (m-10) cc_final: 0.7821 (m-10) REVERT: A 520 MET cc_start: 0.8515 (tpp) cc_final: 0.7941 (tpp) REVERT: A 531 MET cc_start: 0.8876 (tpt) cc_final: 0.8582 (tpt) REVERT: A 558 GLU cc_start: 0.8839 (tp30) cc_final: 0.8409 (tp30) REVERT: A 632 ASP cc_start: 0.8904 (t0) cc_final: 0.8597 (t0) REVERT: A 645 MET cc_start: 0.8597 (mtt) cc_final: 0.8145 (mtp) REVERT: A 676 HIS cc_start: 0.8935 (m-70) cc_final: 0.8574 (m-70) REVERT: A 753 LEU cc_start: 0.9364 (tp) cc_final: 0.9116 (tp) REVERT: A 817 ILE cc_start: 0.8167 (mm) cc_final: 0.7666 (tt) REVERT: A 832 TYR cc_start: 0.9155 (t80) cc_final: 0.8628 (t80) REVERT: A 928 LEU cc_start: 0.9414 (tt) cc_final: 0.8923 (mm) REVERT: A 958 MET cc_start: 0.7426 (ppp) cc_final: 0.7084 (ppp) REVERT: A 1055 LEU cc_start: 0.9199 (tt) cc_final: 0.8858 (tt) REVERT: A 1058 GLN cc_start: 0.8475 (pp30) cc_final: 0.8118 (pp30) REVERT: A 1166 LEU cc_start: 0.9627 (mt) cc_final: 0.9350 (mt) REVERT: A 1242 GLU cc_start: 0.8843 (pm20) cc_final: 0.8569 (pm20) REVERT: A 1245 MET cc_start: 0.9245 (ppp) cc_final: 0.8842 (ppp) REVERT: A 1261 LEU cc_start: 0.8718 (tp) cc_final: 0.8262 (tp) REVERT: A 1269 HIS cc_start: 0.8491 (m-70) cc_final: 0.8100 (m90) REVERT: A 1295 PHE cc_start: 0.8780 (m-10) cc_final: 0.8494 (m-80) REVERT: A 1358 ASP cc_start: 0.8491 (t70) cc_final: 0.8165 (t70) REVERT: A 1361 MET cc_start: 0.8832 (ppp) cc_final: 0.8485 (ppp) REVERT: A 1377 LEU cc_start: 0.9332 (tp) cc_final: 0.8969 (tt) REVERT: C 96 PHE cc_start: 0.9287 (t80) cc_final: 0.8932 (t80) REVERT: C 177 MET cc_start: 0.9508 (mmp) cc_final: 0.9243 (mmm) REVERT: C 400 ARG cc_start: 0.4476 (tpt170) cc_final: 0.4070 (tpt170) REVERT: C 473 ASP cc_start: 0.8938 (p0) cc_final: 0.8615 (p0) REVERT: C 520 MET cc_start: 0.8796 (tpp) cc_final: 0.8385 (tpp) REVERT: C 536 HIS cc_start: 0.8019 (m90) cc_final: 0.7747 (m-70) REVERT: C 537 TRP cc_start: 0.7915 (p-90) cc_final: 0.7162 (p-90) REVERT: C 643 PHE cc_start: 0.9393 (m-10) cc_final: 0.8367 (m-80) REVERT: C 724 PHE cc_start: 0.9366 (m-80) cc_final: 0.9023 (m-80) REVERT: C 762 ARG cc_start: 0.9126 (tmt-80) cc_final: 0.8548 (tmm160) REVERT: C 840 PHE cc_start: 0.8884 (m-80) cc_final: 0.8647 (m-80) REVERT: C 848 MET cc_start: 0.8487 (mmp) cc_final: 0.7571 (mmp) REVERT: C 917 MET cc_start: 0.8410 (mmp) cc_final: 0.7847 (mmm) REVERT: C 945 MET cc_start: 0.9130 (mtp) cc_final: 0.8766 (mtp) REVERT: C 1348 GLN cc_start: 0.9390 (mm-40) cc_final: 0.8401 (mm-40) REVERT: C 1361 MET cc_start: 0.8710 (mpp) cc_final: 0.8395 (mpp) REVERT: G 146 MET cc_start: 0.8004 (pmm) cc_final: 0.7758 (pmm) REVERT: G 273 ILE cc_start: 0.7175 (tp) cc_final: 0.6685 (pt) REVERT: I 67 TYR cc_start: 0.8723 (m-10) cc_final: 0.8348 (m-80) REVERT: I 69 MET cc_start: 0.9239 (mmm) cc_final: 0.8907 (mmm) REVERT: I 114 CYS cc_start: 0.9339 (m) cc_final: 0.9073 (m) REVERT: I 135 ILE cc_start: 0.9068 (mt) cc_final: 0.8641 (tp) REVERT: I 137 PHE cc_start: 0.8864 (m-80) cc_final: 0.8333 (m-80) REVERT: I 146 MET cc_start: 0.7251 (mtt) cc_final: 0.7016 (mtt) REVERT: I 147 ARG cc_start: 0.9140 (ppt170) cc_final: 0.8418 (ttp80) REVERT: P 52 TYR cc_start: 0.7979 (m-80) cc_final: 0.7291 (m-80) REVERT: P 57 PRO cc_start: 0.6571 (Cg_endo) cc_final: 0.6141 (Cg_exo) REVERT: P 146 MET cc_start: 0.8855 (ppp) cc_final: 0.8336 (ppp) REVERT: R 6 PHE cc_start: 0.8163 (t80) cc_final: 0.7643 (t80) REVERT: R 27 CYS cc_start: 0.9140 (m) cc_final: 0.8652 (m) REVERT: R 97 LEU cc_start: 0.8245 (mt) cc_final: 0.7991 (mm) REVERT: R 113 ILE cc_start: 0.9220 (mp) cc_final: 0.8847 (mp) REVERT: R 189 ASN cc_start: 0.8158 (m-40) cc_final: 0.7929 (m110) REVERT: Y 335 ASN cc_start: 0.9272 (t0) cc_final: 0.8852 (t0) REVERT: Y 418 MET cc_start: 0.5274 (mmp) cc_final: 0.4964 (mmp) REVERT: d 134 LEU cc_start: 0.9127 (tp) cc_final: 0.8832 (tp) REVERT: d 253 GLU cc_start: 0.9163 (tt0) cc_final: 0.8612 (mt-10) REVERT: d 335 ASN cc_start: 0.9000 (m-40) cc_final: 0.8601 (m-40) outliers start: 0 outliers final: 0 residues processed: 731 average time/residue: 0.4800 time to fit residues: 586.0251 Evaluate side-chains 558 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 3.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 4 optimal weight: 20.0000 chunk 80 optimal weight: 0.0980 chunk 153 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 19 optimal weight: 30.0000 chunk 233 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 chunk 420 optimal weight: 40.0000 chunk 312 optimal weight: 8.9990 chunk 129 optimal weight: 3.9990 chunk 154 optimal weight: 3.9990 overall best weight: 3.6188 ------------------------------------------------------------------------------- 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 595 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 820 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 988 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** ** G 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 HIS Y 136 HIS Y 238 HIS ** 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 = 0.3902 r_free = 0.3902 target = 0.109885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.083527 restraints weight = 150853.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.086019 restraints weight = 93642.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.087793 restraints weight = 65789.369| |-----------------------------------------------------------------------------| r_work (final): 0.3501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.1987 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= 0.141 Angle : 0.826 15.395 47345 Z= 0.418 Chirality : 0.049 0.438 5553 Planarity : 0.006 0.122 6151 Dihedral : 5.929 34.193 4880 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 1.26 % Allowed : 11.12 % Favored : 87.61 % Rotamer: Outliers : 0.08 % Allowed : 4.33 % Favored : 95.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.12), residues: 4432 helix: -0.85 (0.14), residues: 1290 sheet: -1.11 (0.22), residues: 532 loop : -2.46 (0.12), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 672 HIS 0.005 0.001 HIS A 820 PHE 0.024 0.001 PHE C 458 TYR 0.018 0.001 TYR C 689 ARG 0.007 0.000 ARG R 282 Details of bonding type rmsd hydrogen bonds : bond 0.03201 ( 918) hydrogen bonds : angle 5.43124 ( 2547) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.37595 ( 4) covalent geometry : bond 0.00299 (34714) covalent geometry : angle 0.82648 (47341) *********************** 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 740 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 737 time to evaluate : 3.525 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 47 ILE cc_start: 0.9192 (tt) cc_final: 0.8939 (pt) REVERT: A 81 ARG cc_start: 0.9283 (ptp-110) cc_final: 0.8903 (mpt180) REVERT: A 115 MET cc_start: 0.4416 (mtm) cc_final: 0.3442 (ttt) REVERT: A 132 MET cc_start: 0.4664 (pmm) cc_final: 0.4317 (ptp) REVERT: A 145 PHE cc_start: 0.8179 (t80) cc_final: 0.7703 (t80) REVERT: A 202 GLU cc_start: 0.9171 (mp0) cc_final: 0.8952 (mp0) REVERT: A 234 LEU cc_start: 0.9655 (mm) cc_final: 0.9124 (mm) REVERT: A 259 LEU cc_start: 0.9587 (mp) cc_final: 0.9327 (mp) REVERT: A 297 ARG cc_start: 0.9296 (ptt-90) cc_final: 0.8776 (ptt90) REVERT: A 301 GLN cc_start: 0.9111 (pp30) cc_final: 0.8597 (pp30) REVERT: A 386 ILE cc_start: 0.9339 (tt) cc_final: 0.9004 (mt) REVERT: A 398 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8922 (mm-30) REVERT: A 441 PHE cc_start: 0.8204 (m-10) cc_final: 0.7874 (m-10) REVERT: A 459 PHE cc_start: 0.9225 (p90) cc_final: 0.8853 (p90) REVERT: A 520 MET cc_start: 0.8463 (tpp) cc_final: 0.7845 (tpp) REVERT: A 531 MET cc_start: 0.8836 (tpt) cc_final: 0.8559 (tpt) REVERT: A 632 ASP cc_start: 0.8886 (t0) cc_final: 0.8543 (t0) REVERT: A 645 MET cc_start: 0.8675 (mtt) cc_final: 0.8259 (mtp) REVERT: A 676 HIS cc_start: 0.8855 (m-70) cc_final: 0.8536 (m-70) REVERT: A 753 LEU cc_start: 0.9355 (tp) cc_final: 0.9106 (tp) REVERT: A 817 ILE cc_start: 0.8423 (mm) cc_final: 0.7831 (tt) REVERT: A 832 TYR cc_start: 0.9086 (t80) cc_final: 0.8661 (t80) REVERT: A 928 LEU cc_start: 0.9409 (tt) cc_final: 0.8923 (mm) REVERT: A 1069 PHE cc_start: 0.8970 (m-10) cc_final: 0.8454 (m-10) REVERT: A 1093 PHE cc_start: 0.8581 (m-80) cc_final: 0.7890 (m-80) REVERT: A 1164 GLU cc_start: 0.9024 (tp30) cc_final: 0.8314 (tp30) REVERT: A 1166 LEU cc_start: 0.9594 (mt) cc_final: 0.9364 (mt) REVERT: A 1227 ARG cc_start: 0.8199 (ttt180) cc_final: 0.7956 (ttt180) REVERT: A 1234 MET cc_start: 0.4260 (ptt) cc_final: 0.2939 (tmm) REVERT: A 1261 LEU cc_start: 0.8694 (tp) cc_final: 0.8151 (tp) REVERT: A 1269 HIS cc_start: 0.8339 (m-70) cc_final: 0.7871 (m90) REVERT: A 1295 PHE cc_start: 0.8660 (m-10) cc_final: 0.8377 (m-80) REVERT: A 1344 CYS cc_start: 0.8776 (p) cc_final: 0.7234 (m) REVERT: A 1358 ASP cc_start: 0.8452 (t70) cc_final: 0.8225 (t70) REVERT: A 1377 LEU cc_start: 0.9288 (tp) cc_final: 0.8911 (tt) REVERT: C 96 PHE cc_start: 0.9253 (t80) cc_final: 0.8883 (t80) REVERT: C 177 MET cc_start: 0.9509 (mmp) cc_final: 0.9249 (mmm) REVERT: C 400 ARG cc_start: 0.4426 (tpt170) cc_final: 0.4056 (tpt170) REVERT: C 473 ASP cc_start: 0.8813 (p0) cc_final: 0.8526 (p0) REVERT: C 520 MET cc_start: 0.8756 (tpp) cc_final: 0.8389 (tpp) REVERT: C 536 HIS cc_start: 0.8063 (m90) cc_final: 0.7761 (m-70) REVERT: C 537 TRP cc_start: 0.7596 (p-90) cc_final: 0.6849 (p-90) REVERT: C 643 PHE cc_start: 0.9394 (m-10) cc_final: 0.8318 (m-80) REVERT: C 724 PHE cc_start: 0.9369 (m-80) cc_final: 0.8994 (m-80) REVERT: C 742 ILE cc_start: 0.9155 (mp) cc_final: 0.8672 (mm) REVERT: C 840 PHE cc_start: 0.8958 (m-80) cc_final: 0.8642 (m-10) REVERT: C 917 MET cc_start: 0.8414 (mmp) cc_final: 0.7893 (mmm) REVERT: C 945 MET cc_start: 0.9216 (mtp) cc_final: 0.8719 (mtp) REVERT: C 1231 MET cc_start: 0.8293 (ppp) cc_final: 0.8071 (ppp) REVERT: C 1348 GLN cc_start: 0.9425 (mm-40) cc_final: 0.8431 (mm-40) REVERT: C 1361 MET cc_start: 0.8732 (mpp) cc_final: 0.8403 (mpp) REVERT: G 128 LEU cc_start: 0.7420 (mp) cc_final: 0.7216 (mp) REVERT: G 146 MET cc_start: 0.8207 (pmm) cc_final: 0.7603 (pmm) REVERT: G 148 GLU cc_start: 0.8862 (pm20) cc_final: 0.8574 (mp0) REVERT: I 67 TYR cc_start: 0.8648 (m-10) cc_final: 0.8270 (m-80) REVERT: I 69 MET cc_start: 0.9274 (mmm) cc_final: 0.8995 (mmm) REVERT: I 114 CYS cc_start: 0.9348 (m) cc_final: 0.9085 (m) REVERT: I 135 ILE cc_start: 0.9062 (mt) cc_final: 0.8657 (pt) REVERT: I 137 PHE cc_start: 0.8839 (m-80) cc_final: 0.8343 (m-80) REVERT: I 147 ARG cc_start: 0.9073 (ppt170) cc_final: 0.8454 (ttp80) REVERT: P 52 TYR cc_start: 0.7949 (m-80) cc_final: 0.7356 (m-80) REVERT: P 57 PRO cc_start: 0.6391 (Cg_endo) cc_final: 0.5942 (Cg_exo) REVERT: R 6 PHE cc_start: 0.8164 (t80) cc_final: 0.7657 (t80) REVERT: R 97 LEU cc_start: 0.8179 (mt) cc_final: 0.7931 (mm) REVERT: R 113 ILE cc_start: 0.9230 (mp) cc_final: 0.8864 (mp) REVERT: R 189 ASN cc_start: 0.8168 (m-40) cc_final: 0.7953 (m110) REVERT: Y 335 ASN cc_start: 0.9175 (t0) cc_final: 0.8803 (t0) REVERT: Y 418 MET cc_start: 0.4975 (mmp) cc_final: 0.4497 (mmp) REVERT: d 253 GLU cc_start: 0.9189 (tt0) cc_final: 0.8717 (mt-10) REVERT: d 291 CYS cc_start: 0.8514 (m) cc_final: 0.7885 (m) REVERT: d 295 ASP cc_start: 0.7809 (m-30) cc_final: 0.7385 (m-30) REVERT: d 335 ASN cc_start: 0.9080 (m-40) cc_final: 0.8607 (m-40) outliers start: 3 outliers final: 0 residues processed: 739 average time/residue: 0.5180 time to fit residues: 638.0947 Evaluate side-chains 565 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 565 time to evaluate : 3.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 5 optimal weight: 30.0000 chunk 302 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 293 optimal weight: 0.0870 chunk 194 optimal weight: 20.0000 chunk 210 optimal weight: 0.0980 chunk 318 optimal weight: 2.9990 chunk 197 optimal weight: 10.0000 chunk 354 optimal weight: 40.0000 chunk 186 optimal weight: 8.9990 chunk 117 optimal weight: 30.0000 overall best weight: 0.9160 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 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 ** 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 309 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.111625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.085269 restraints weight = 149591.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.087782 restraints weight = 92730.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.089552 restraints weight = 65078.313| |-----------------------------------------------------------------------------| r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2128 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= 0.136 Angle : 0.827 15.332 47345 Z= 0.416 Chirality : 0.050 0.644 5553 Planarity : 0.006 0.120 6151 Dihedral : 5.759 34.359 4880 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 1.22 % Allowed : 11.10 % Favored : 87.68 % Rotamer: Outliers : 0.03 % Allowed : 2.75 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.12), residues: 4432 helix: -0.77 (0.14), residues: 1291 sheet: -0.98 (0.22), residues: 524 loop : -2.40 (0.12), residues: 2617 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP d 463 HIS 0.010 0.001 HIS d 242 PHE 0.031 0.001 PHE A 82 TYR 0.028 0.001 TYR G 52 ARG 0.006 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03084 ( 918) hydrogen bonds : angle 5.25029 ( 2547) SS BOND : bond 0.00126 ( 2) SS BOND : angle 0.35519 ( 4) covalent geometry : bond 0.00285 (34714) covalent geometry : angle 0.82676 (47341) *********************** 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 750 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 749 time to evaluate : 4.709 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 47 ILE cc_start: 0.9182 (tt) cc_final: 0.8882 (pt) REVERT: A 62 TYR cc_start: 0.2793 (t80) cc_final: 0.2289 (t80) REVERT: A 81 ARG cc_start: 0.9163 (ptp-110) cc_final: 0.8962 (tpt-90) REVERT: A 115 MET cc_start: 0.3581 (mtm) cc_final: 0.2709 (ttt) REVERT: A 132 MET cc_start: 0.4660 (pmm) cc_final: 0.4210 (ptp) REVERT: A 145 PHE cc_start: 0.8123 (t80) cc_final: 0.7884 (t80) REVERT: A 221 HIS cc_start: 0.8797 (m-70) cc_final: 0.7906 (m90) REVERT: A 223 ASN cc_start: 0.8158 (t0) cc_final: 0.7939 (t0) REVERT: A 234 LEU cc_start: 0.9655 (mm) cc_final: 0.9324 (mm) REVERT: A 259 LEU cc_start: 0.9526 (mp) cc_final: 0.9319 (mp) REVERT: A 297 ARG cc_start: 0.9259 (ptt-90) cc_final: 0.8730 (ptt90) REVERT: A 301 GLN cc_start: 0.9049 (pp30) cc_final: 0.8567 (pp30) REVERT: A 386 ILE cc_start: 0.9307 (tt) cc_final: 0.8998 (mt) REVERT: A 398 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8877 (mm-30) REVERT: A 441 PHE cc_start: 0.8150 (m-10) cc_final: 0.7796 (m-10) REVERT: A 459 PHE cc_start: 0.9205 (p90) cc_final: 0.8766 (p90) REVERT: A 520 MET cc_start: 0.8333 (tpp) cc_final: 0.7893 (tpp) REVERT: A 531 MET cc_start: 0.8741 (tpt) cc_final: 0.8440 (tpt) REVERT: A 541 HIS cc_start: 0.7706 (p-80) cc_final: 0.7382 (p-80) REVERT: A 632 ASP cc_start: 0.8948 (t0) cc_final: 0.8626 (t0) REVERT: A 645 MET cc_start: 0.8647 (mtt) cc_final: 0.8253 (mtp) REVERT: A 676 HIS cc_start: 0.8928 (m-70) cc_final: 0.8534 (m-70) REVERT: A 741 ASN cc_start: 0.8941 (t0) cc_final: 0.8065 (t0) REVERT: A 817 ILE cc_start: 0.8409 (mm) cc_final: 0.7841 (tt) REVERT: A 832 TYR cc_start: 0.9094 (t80) cc_final: 0.8518 (t80) REVERT: A 837 ILE cc_start: 0.9342 (mm) cc_final: 0.9095 (mm) REVERT: A 928 LEU cc_start: 0.9375 (tt) cc_final: 0.8869 (mm) REVERT: A 1058 GLN cc_start: 0.8205 (pp30) cc_final: 0.7825 (pp30) REVERT: A 1069 PHE cc_start: 0.8968 (m-10) cc_final: 0.8442 (m-10) REVERT: A 1093 PHE cc_start: 0.8611 (m-80) cc_final: 0.7904 (m-80) REVERT: A 1164 GLU cc_start: 0.8773 (tp30) cc_final: 0.8472 (tp30) REVERT: A 1166 LEU cc_start: 0.9575 (mt) cc_final: 0.9359 (mt) REVERT: A 1227 ARG cc_start: 0.8435 (ttt180) cc_final: 0.8026 (ttt180) REVERT: A 1234 MET cc_start: 0.4044 (ptt) cc_final: 0.2757 (tmm) REVERT: A 1242 GLU cc_start: 0.8873 (pm20) cc_final: 0.8525 (pm20) REVERT: A 1245 MET cc_start: 0.9138 (ppp) cc_final: 0.8655 (ppp) REVERT: A 1261 LEU cc_start: 0.8653 (tp) cc_final: 0.8056 (tp) REVERT: A 1269 HIS cc_start: 0.8335 (m-70) cc_final: 0.7918 (m90) REVERT: A 1295 PHE cc_start: 0.8631 (m-10) cc_final: 0.8303 (m-80) REVERT: A 1344 CYS cc_start: 0.8773 (p) cc_final: 0.7195 (m) REVERT: A 1358 ASP cc_start: 0.8591 (t70) cc_final: 0.8248 (t70) REVERT: A 1377 LEU cc_start: 0.9323 (tp) cc_final: 0.8979 (tt) REVERT: C 96 PHE cc_start: 0.9242 (t80) cc_final: 0.8819 (t80) REVERT: C 177 MET cc_start: 0.9496 (mmp) cc_final: 0.9244 (mmm) REVERT: C 400 ARG cc_start: 0.4337 (tpt170) cc_final: 0.4073 (tpt170) REVERT: C 473 ASP cc_start: 0.8640 (p0) cc_final: 0.8313 (p0) REVERT: C 520 MET cc_start: 0.8730 (tpp) cc_final: 0.8399 (tpp) REVERT: C 536 HIS cc_start: 0.8103 (m90) cc_final: 0.7831 (m-70) REVERT: C 537 TRP cc_start: 0.7562 (p-90) cc_final: 0.6808 (p-90) REVERT: C 594 ILE cc_start: 0.8589 (mm) cc_final: 0.8383 (mm) REVERT: C 643 PHE cc_start: 0.9428 (m-10) cc_final: 0.8378 (m-10) REVERT: C 712 GLN cc_start: 0.9426 (tm-30) cc_final: 0.9206 (tm-30) REVERT: C 724 PHE cc_start: 0.9389 (m-80) cc_final: 0.9014 (m-80) REVERT: C 742 ILE cc_start: 0.9125 (mp) cc_final: 0.8546 (mm) REVERT: C 840 PHE cc_start: 0.8991 (m-80) cc_final: 0.8630 (m-10) REVERT: C 848 MET cc_start: 0.8470 (mmp) cc_final: 0.7502 (mmp) REVERT: C 917 MET cc_start: 0.8228 (mmp) cc_final: 0.7603 (mmm) REVERT: C 945 MET cc_start: 0.9148 (mtp) cc_final: 0.8633 (mtp) REVERT: C 1168 ARG cc_start: 0.8975 (mmp80) cc_final: 0.8769 (mmp80) REVERT: C 1231 MET cc_start: 0.8007 (ppp) cc_final: 0.7776 (ppp) REVERT: C 1348 GLN cc_start: 0.9425 (mm-40) cc_final: 0.8383 (mm-40) REVERT: C 1361 MET cc_start: 0.8712 (mpp) cc_final: 0.8420 (mpp) REVERT: G 146 MET cc_start: 0.8122 (pmm) cc_final: 0.7879 (pmm) REVERT: G 282 ARG cc_start: 0.8948 (pmt170) cc_final: 0.8402 (tmt170) REVERT: G 287 LEU cc_start: 0.9215 (mt) cc_final: 0.9013 (mt) REVERT: I 67 TYR cc_start: 0.8589 (m-10) cc_final: 0.8234 (m-80) REVERT: I 69 MET cc_start: 0.9280 (mmm) cc_final: 0.9022 (mmm) REVERT: I 135 ILE cc_start: 0.9149 (mt) cc_final: 0.8794 (pt) REVERT: I 137 PHE cc_start: 0.8730 (m-80) cc_final: 0.8136 (m-80) REVERT: I 146 MET cc_start: 0.7173 (mtt) cc_final: 0.6486 (mtt) REVERT: I 147 ARG cc_start: 0.8973 (ppt170) cc_final: 0.8366 (tmm160) REVERT: P 52 TYR cc_start: 0.8042 (m-80) cc_final: 0.7465 (m-80) REVERT: P 57 PRO cc_start: 0.6368 (Cg_endo) cc_final: 0.5950 (Cg_exo) REVERT: P 257 MET cc_start: 0.1350 (ptt) cc_final: 0.1014 (ptp) REVERT: P 303 THR cc_start: 0.8953 (p) cc_final: 0.8677 (p) REVERT: R 6 PHE cc_start: 0.8062 (t80) cc_final: 0.7574 (t80) REVERT: R 97 LEU cc_start: 0.8129 (mt) cc_final: 0.7892 (mm) REVERT: R 189 ASN cc_start: 0.8200 (m-40) cc_final: 0.7982 (m110) REVERT: Y 212 VAL cc_start: 0.7327 (t) cc_final: 0.6899 (m) REVERT: Y 335 ASN cc_start: 0.9208 (t0) cc_final: 0.8923 (t0) REVERT: Y 418 MET cc_start: 0.5073 (mmp) cc_final: 0.4588 (mmp) REVERT: d 134 LEU cc_start: 0.9204 (tp) cc_final: 0.8915 (tp) REVERT: d 253 GLU cc_start: 0.9178 (tt0) cc_final: 0.8698 (mt-10) REVERT: d 291 CYS cc_start: 0.8596 (m) cc_final: 0.7942 (m) REVERT: d 295 ASP cc_start: 0.7713 (m-30) cc_final: 0.7329 (m-30) REVERT: d 335 ASN cc_start: 0.8735 (m-40) cc_final: 0.7932 (m-40) REVERT: d 439 MET cc_start: 0.5422 (tpt) cc_final: 0.5103 (tpt) outliers start: 1 outliers final: 0 residues processed: 749 average time/residue: 0.6373 time to fit residues: 806.2624 Evaluate side-chains 583 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 5.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 358 optimal weight: 30.0000 chunk 344 optimal weight: 30.0000 chunk 423 optimal weight: 2.9990 chunk 335 optimal weight: 20.0000 chunk 374 optimal weight: 0.7980 chunk 64 optimal weight: 20.0000 chunk 261 optimal weight: 50.0000 chunk 367 optimal weight: 40.0000 chunk 222 optimal weight: 7.9990 chunk 235 optimal weight: 0.9980 chunk 424 optimal weight: 6.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- 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 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 731 HIS ** 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 ** R 228 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** Y 126 HIS ** Y 136 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 238 HIS d 461 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.110134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.084009 restraints weight = 149131.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.086458 restraints weight = 92825.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.088197 restraints weight = 65310.277| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2356 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= 0.144 Angle : 0.822 15.440 47345 Z= 0.416 Chirality : 0.049 0.658 5553 Planarity : 0.005 0.118 6151 Dihedral : 5.677 33.598 4880 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 1.22 % Allowed : 11.15 % Favored : 87.64 % Rotamer: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.40 (0.12), residues: 4432 helix: -0.63 (0.15), residues: 1291 sheet: -0.94 (0.22), residues: 522 loop : -2.35 (0.12), residues: 2619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP Y 451 HIS 0.007 0.001 HIS d 242 PHE 0.022 0.001 PHE A 82 TYR 0.033 0.001 TYR A 707 ARG 0.009 0.000 ARG A 118 Details of bonding type rmsd hydrogen bonds : bond 0.03043 ( 918) hydrogen bonds : angle 5.19416 ( 2547) SS BOND : bond 0.00300 ( 2) SS BOND : angle 0.17608 ( 4) covalent geometry : bond 0.00308 (34714) covalent geometry : angle 0.82218 (47341) *********************** 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 728 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 728 time to evaluate : 5.378 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 47 ILE cc_start: 0.9167 (tt) cc_final: 0.8848 (pt) REVERT: A 115 MET cc_start: 0.4697 (mtm) cc_final: 0.3718 (ttt) REVERT: A 132 MET cc_start: 0.4842 (pmm) cc_final: 0.4489 (ptt) REVERT: A 145 PHE cc_start: 0.8302 (t80) cc_final: 0.8004 (t80) REVERT: A 221 HIS cc_start: 0.8540 (m-70) cc_final: 0.7738 (m90) REVERT: A 234 LEU cc_start: 0.9723 (mm) cc_final: 0.9212 (mm) REVERT: A 259 LEU cc_start: 0.9561 (mp) cc_final: 0.9329 (mp) REVERT: A 297 ARG cc_start: 0.9292 (ptt-90) cc_final: 0.8765 (ptt90) REVERT: A 301 GLN cc_start: 0.9084 (pp30) cc_final: 0.8575 (pp30) REVERT: A 386 ILE cc_start: 0.9200 (tt) cc_final: 0.8826 (mt) REVERT: A 441 PHE cc_start: 0.8169 (m-10) cc_final: 0.7835 (m-10) REVERT: A 475 MET cc_start: 0.8452 (mmp) cc_final: 0.8234 (mmm) REVERT: A 531 MET cc_start: 0.8755 (tpt) cc_final: 0.8468 (tpt) REVERT: A 645 MET cc_start: 0.8685 (mtt) cc_final: 0.8259 (mtp) REVERT: A 676 HIS cc_start: 0.8936 (m-70) cc_final: 0.8590 (m-70) REVERT: A 817 ILE cc_start: 0.8476 (mm) cc_final: 0.7888 (tt) REVERT: A 832 TYR cc_start: 0.9139 (t80) cc_final: 0.8574 (t80) REVERT: A 928 LEU cc_start: 0.9345 (tt) cc_final: 0.8848 (mm) REVERT: A 1058 GLN cc_start: 0.8363 (pp30) cc_final: 0.7934 (pp30) REVERT: A 1069 PHE cc_start: 0.8972 (m-10) cc_final: 0.8396 (m-10) REVERT: A 1164 GLU cc_start: 0.8793 (tp30) cc_final: 0.8327 (tp30) REVERT: A 1166 LEU cc_start: 0.9523 (mt) cc_final: 0.9241 (mt) REVERT: A 1227 ARG cc_start: 0.8425 (ttt180) cc_final: 0.8202 (ttt180) REVERT: A 1234 MET cc_start: 0.4204 (ptt) cc_final: 0.2899 (tmm) REVERT: A 1242 GLU cc_start: 0.8872 (pm20) cc_final: 0.8594 (pm20) REVERT: A 1261 LEU cc_start: 0.8729 (tp) cc_final: 0.8125 (tp) REVERT: A 1269 HIS cc_start: 0.8338 (m-70) cc_final: 0.7913 (m90) REVERT: A 1295 PHE cc_start: 0.8665 (m-10) cc_final: 0.8385 (m-80) REVERT: A 1344 CYS cc_start: 0.8467 (p) cc_final: 0.8092 (p) REVERT: A 1358 ASP cc_start: 0.8499 (t70) cc_final: 0.8191 (t70) REVERT: A 1377 LEU cc_start: 0.9281 (tp) cc_final: 0.8886 (tt) REVERT: C 96 PHE cc_start: 0.9241 (t80) cc_final: 0.8852 (t80) REVERT: C 177 MET cc_start: 0.9504 (mmp) cc_final: 0.9216 (mmm) REVERT: C 400 ARG cc_start: 0.4435 (tpt170) cc_final: 0.4095 (tpt170) REVERT: C 473 ASP cc_start: 0.8612 (p0) cc_final: 0.8293 (p0) REVERT: C 520 MET cc_start: 0.8729 (tpp) cc_final: 0.8428 (tpp) REVERT: C 536 HIS cc_start: 0.8042 (m90) cc_final: 0.7758 (m-70) REVERT: C 537 TRP cc_start: 0.7811 (p-90) cc_final: 0.6819 (p-90) REVERT: C 643 PHE cc_start: 0.9403 (m-10) cc_final: 0.8326 (m-10) REVERT: C 712 GLN cc_start: 0.9446 (tm-30) cc_final: 0.9238 (tm-30) REVERT: C 720 THR cc_start: 0.9472 (p) cc_final: 0.9158 (p) REVERT: C 724 PHE cc_start: 0.9372 (m-80) cc_final: 0.8948 (m-80) REVERT: C 742 ILE cc_start: 0.9135 (mp) cc_final: 0.8654 (mm) REVERT: C 832 TYR cc_start: 0.8900 (t80) cc_final: 0.8587 (t80) REVERT: C 840 PHE cc_start: 0.9023 (m-80) cc_final: 0.8679 (m-10) REVERT: C 945 MET cc_start: 0.9214 (mtp) cc_final: 0.8787 (mtp) REVERT: C 1049 LYS cc_start: 0.7924 (pttm) cc_final: 0.7462 (pttt) REVERT: C 1168 ARG cc_start: 0.8969 (mmp80) cc_final: 0.8764 (mmp80) REVERT: C 1231 MET cc_start: 0.8072 (ppp) cc_final: 0.7168 (ppp) REVERT: C 1348 GLN cc_start: 0.9413 (mm-40) cc_final: 0.8481 (mm-40) REVERT: C 1361 MET cc_start: 0.8738 (mpp) cc_final: 0.8453 (mpp) REVERT: G 128 LEU cc_start: 0.7386 (mp) cc_final: 0.7175 (mp) REVERT: I 67 TYR cc_start: 0.8587 (m-10) cc_final: 0.8234 (m-80) REVERT: I 134 GLU cc_start: 0.8458 (tp30) cc_final: 0.8167 (tp30) REVERT: I 135 ILE cc_start: 0.9180 (mt) cc_final: 0.8845 (pt) REVERT: I 137 PHE cc_start: 0.8832 (m-80) cc_final: 0.8272 (m-80) REVERT: I 147 ARG cc_start: 0.8706 (ppt170) cc_final: 0.8237 (ppt170) REVERT: P 52 TYR cc_start: 0.7805 (m-80) cc_final: 0.7185 (m-80) REVERT: P 57 PRO cc_start: 0.6404 (Cg_endo) cc_final: 0.5980 (Cg_exo) REVERT: P 257 MET cc_start: 0.1005 (ptt) cc_final: 0.0791 (ptp) REVERT: R 6 PHE cc_start: 0.8082 (t80) cc_final: 0.7589 (t80) REVERT: R 97 LEU cc_start: 0.8010 (mt) cc_final: 0.7782 (mm) REVERT: R 220 THR cc_start: 0.6581 (t) cc_final: 0.6340 (m) REVERT: R 257 MET cc_start: 0.0949 (tpt) cc_final: 0.0562 (tpp) REVERT: R 293 LEU cc_start: 0.8402 (tp) cc_final: 0.8188 (tp) REVERT: Y 335 ASN cc_start: 0.9233 (t0) cc_final: 0.8923 (t0) REVERT: Y 418 MET cc_start: 0.5244 (mmp) cc_final: 0.4711 (mmp) REVERT: d 253 GLU cc_start: 0.9176 (tt0) cc_final: 0.8697 (mt-10) REVERT: d 291 CYS cc_start: 0.8594 (m) cc_final: 0.7982 (m) REVERT: d 295 ASP cc_start: 0.7786 (m-30) cc_final: 0.7390 (m-30) REVERT: d 305 ASP cc_start: 0.8315 (m-30) cc_final: 0.8021 (t0) REVERT: d 335 ASN cc_start: 0.8959 (m-40) cc_final: 0.8593 (m-40) REVERT: d 337 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8459 (tt0) REVERT: d 439 MET cc_start: 0.5571 (tpt) cc_final: 0.5166 (tpt) outliers start: 0 outliers final: 0 residues processed: 728 average time/residue: 0.5680 time to fit residues: 697.5258 Evaluate side-chains 559 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 4.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 314 optimal weight: 9.9990 chunk 437 optimal weight: 20.0000 chunk 173 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 294 optimal weight: 30.0000 chunk 396 optimal weight: 30.0000 chunk 360 optimal weight: 8.9990 chunk 436 optimal weight: 5.9990 chunk 137 optimal weight: 7.9990 chunk 318 optimal weight: 9.9990 chunk 359 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 301 GLN 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 G 206 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 126 HIS Y 136 HIS ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 461 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.107919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.081925 restraints weight = 151132.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.084318 restraints weight = 94087.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.086012 restraints weight = 66414.359| |-----------------------------------------------------------------------------| r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 34716 Z= 0.168 Angle : 0.841 15.056 47345 Z= 0.428 Chirality : 0.050 0.693 5553 Planarity : 0.006 0.117 6151 Dihedral : 5.742 33.253 4880 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 16.63 Ramachandran Plot: Outliers : 1.26 % Allowed : 11.78 % Favored : 86.96 % Rotamer: Outliers : 0.03 % Allowed : 2.72 % Favored : 97.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.33 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.12), residues: 4432 helix: -0.61 (0.15), residues: 1303 sheet: -0.93 (0.23), residues: 507 loop : -2.34 (0.12), residues: 2622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP Y 451 HIS 0.005 0.001 HIS C1057 PHE 0.025 0.002 PHE A 82 TYR 0.024 0.002 TYR A 258 ARG 0.008 0.001 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03177 ( 918) hydrogen bonds : angle 5.24146 ( 2547) SS BOND : bond 0.00477 ( 2) SS BOND : angle 0.58883 ( 4) covalent geometry : bond 0.00356 (34714) covalent geometry : angle 0.84116 (47341) *********************** 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 721 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 720 time to evaluate : 3.671 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: A 62 TYR cc_start: 0.3077 (t80) cc_final: 0.2597 (t80) REVERT: A 115 MET cc_start: 0.4525 (mtm) cc_final: 0.3549 (ttt) REVERT: A 145 PHE cc_start: 0.8436 (t80) cc_final: 0.7869 (t80) REVERT: A 221 HIS cc_start: 0.8561 (m-70) cc_final: 0.7777 (m90) REVERT: A 234 LEU cc_start: 0.9622 (mm) cc_final: 0.9229 (mm) REVERT: A 259 LEU cc_start: 0.9591 (mp) cc_final: 0.9361 (mp) REVERT: A 297 ARG cc_start: 0.9224 (ptt-90) cc_final: 0.8822 (ptt90) REVERT: A 441 PHE cc_start: 0.8189 (m-10) cc_final: 0.7835 (m-10) REVERT: A 475 MET cc_start: 0.8540 (mmp) cc_final: 0.8306 (mmm) REVERT: A 531 MET cc_start: 0.8771 (tpt) cc_final: 0.8470 (tpt) REVERT: A 645 MET cc_start: 0.8671 (mtt) cc_final: 0.8238 (mtp) REVERT: A 676 HIS cc_start: 0.8979 (m-70) cc_final: 0.8679 (m-70) REVERT: A 817 ILE cc_start: 0.8373 (mm) cc_final: 0.7769 (tt) REVERT: A 832 TYR cc_start: 0.9024 (t80) cc_final: 0.8450 (t80) REVERT: A 928 LEU cc_start: 0.9356 (tt) cc_final: 0.8879 (mm) REVERT: A 1069 PHE cc_start: 0.8971 (m-10) cc_final: 0.8375 (m-10) REVERT: A 1164 GLU cc_start: 0.8829 (tp30) cc_final: 0.8414 (tp30) REVERT: A 1166 LEU cc_start: 0.9543 (mt) cc_final: 0.9263 (mt) REVERT: A 1227 ARG cc_start: 0.8395 (ttt180) cc_final: 0.8195 (ttt180) REVERT: A 1234 MET cc_start: 0.4395 (ptt) cc_final: 0.3185 (tmm) REVERT: A 1242 GLU cc_start: 0.8899 (pm20) cc_final: 0.8597 (pm20) REVERT: A 1245 MET cc_start: 0.9033 (ppp) cc_final: 0.8825 (ppp) REVERT: A 1261 LEU cc_start: 0.8738 (tp) cc_final: 0.8185 (tp) REVERT: A 1295 PHE cc_start: 0.8709 (m-10) cc_final: 0.8403 (m-80) REVERT: A 1344 CYS cc_start: 0.8679 (p) cc_final: 0.8187 (p) REVERT: A 1358 ASP cc_start: 0.8384 (t70) cc_final: 0.8122 (t70) REVERT: A 1377 LEU cc_start: 0.9288 (tp) cc_final: 0.8905 (tt) REVERT: C 96 PHE cc_start: 0.9328 (t80) cc_final: 0.8898 (t80) REVERT: C 177 MET cc_start: 0.9521 (mmp) cc_final: 0.9246 (mmm) REVERT: C 394 LEU cc_start: 0.9000 (tp) cc_final: 0.8798 (tt) REVERT: C 400 ARG cc_start: 0.4641 (tpt170) cc_final: 0.4259 (tpt170) REVERT: C 473 ASP cc_start: 0.8657 (p0) cc_final: 0.8378 (p0) REVERT: C 520 MET cc_start: 0.8760 (tpp) cc_final: 0.8471 (tpp) REVERT: C 530 MET cc_start: 0.8651 (ppp) cc_final: 0.8443 (ppp) REVERT: C 536 HIS cc_start: 0.8173 (m90) cc_final: 0.7845 (m-70) REVERT: C 537 TRP cc_start: 0.7723 (p-90) cc_final: 0.6898 (p-90) REVERT: C 643 PHE cc_start: 0.9431 (m-10) cc_final: 0.8366 (m-10) REVERT: C 724 PHE cc_start: 0.9410 (m-80) cc_final: 0.8939 (m-80) REVERT: C 832 TYR cc_start: 0.8915 (t80) cc_final: 0.8495 (t80) REVERT: C 840 PHE cc_start: 0.9073 (m-80) cc_final: 0.8850 (m-80) REVERT: C 848 MET cc_start: 0.8505 (mmp) cc_final: 0.7418 (mmp) REVERT: C 945 MET cc_start: 0.9181 (mtp) cc_final: 0.8806 (mtp) REVERT: C 1049 LYS cc_start: 0.8030 (pttm) cc_final: 0.7761 (pttt) REVERT: C 1168 ARG cc_start: 0.8965 (mmp80) cc_final: 0.8731 (mmp80) REVERT: C 1231 MET cc_start: 0.8226 (ppp) cc_final: 0.8018 (ppp) REVERT: C 1348 GLN cc_start: 0.9460 (mm-40) cc_final: 0.8188 (mm-40) REVERT: C 1361 MET cc_start: 0.8802 (mpp) cc_final: 0.8452 (mpp) REVERT: G 146 MET cc_start: 0.8090 (pmm) cc_final: 0.7880 (pmm) REVERT: I 67 TYR cc_start: 0.8610 (m-10) cc_final: 0.8083 (m-80) REVERT: I 69 MET cc_start: 0.9381 (mmp) cc_final: 0.9174 (mmm) REVERT: I 135 ILE cc_start: 0.9194 (mt) cc_final: 0.8802 (pt) REVERT: I 137 PHE cc_start: 0.8754 (m-80) cc_final: 0.8143 (m-80) REVERT: I 146 MET cc_start: 0.6468 (mtt) cc_final: 0.6107 (mtm) REVERT: P 52 TYR cc_start: 0.7900 (m-80) cc_final: 0.7344 (m-80) REVERT: P 57 PRO cc_start: 0.5998 (Cg_endo) cc_final: 0.5536 (Cg_exo) REVERT: P 303 THR cc_start: 0.8868 (p) cc_final: 0.8587 (p) REVERT: R 6 PHE cc_start: 0.8061 (t80) cc_final: 0.7574 (t80) REVERT: R 97 LEU cc_start: 0.8128 (mt) cc_final: 0.7890 (mm) REVERT: R 293 LEU cc_start: 0.8502 (tp) cc_final: 0.8269 (tp) REVERT: Y 335 ASN cc_start: 0.9214 (t0) cc_final: 0.8847 (t0) REVERT: Y 418 MET cc_start: 0.5790 (mmp) cc_final: 0.5293 (mmp) REVERT: d 253 GLU cc_start: 0.9202 (tt0) cc_final: 0.8740 (mt-10) REVERT: d 291 CYS cc_start: 0.8664 (m) cc_final: 0.8113 (m) REVERT: d 295 ASP cc_start: 0.7864 (m-30) cc_final: 0.7341 (m-30) REVERT: d 305 ASP cc_start: 0.8441 (m-30) cc_final: 0.8100 (t0) REVERT: d 335 ASN cc_start: 0.8780 (m-40) cc_final: 0.8455 (m-40) REVERT: d 337 GLN cc_start: 0.8702 (tm-30) cc_final: 0.8478 (tt0) REVERT: d 419 TYR cc_start: 0.8726 (p90) cc_final: 0.8489 (p90) outliers start: 1 outliers final: 0 residues processed: 721 average time/residue: 0.4393 time to fit residues: 526.7473 Evaluate side-chains 559 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 3.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 8 optimal weight: 8.9990 chunk 339 optimal weight: 8.9990 chunk 259 optimal weight: 3.9990 chunk 148 optimal weight: 20.0000 chunk 225 optimal weight: 0.7980 chunk 202 optimal weight: 50.0000 chunk 247 optimal weight: 0.2980 chunk 50 optimal weight: 8.9990 chunk 248 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 chunk 210 optimal weight: 30.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- 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** ** 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 C1102 HIS G 162 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 212 ASN R 86 HIS ** R 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 126 HIS ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 461 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.108858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082813 restraints weight = 149631.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.085221 restraints weight = 93162.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.086938 restraints weight = 65818.405| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 34716 Z= 0.146 Angle : 0.846 15.575 47345 Z= 0.425 Chirality : 0.050 0.686 5553 Planarity : 0.006 0.117 6151 Dihedral : 5.681 32.861 4880 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 15.60 Ramachandran Plot: Outliers : 1.22 % Allowed : 11.28 % Favored : 87.50 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.31 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.30 (0.12), residues: 4432 helix: -0.50 (0.15), residues: 1288 sheet: -0.96 (0.22), residues: 532 loop : -2.28 (0.12), residues: 2612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP Y 451 HIS 0.012 0.001 HIS C1057 PHE 0.023 0.001 PHE C 458 TYR 0.021 0.001 TYR A 258 ARG 0.010 0.000 ARG G 147 Details of bonding type rmsd hydrogen bonds : bond 0.03020 ( 918) hydrogen bonds : angle 5.17998 ( 2547) SS BOND : bond 0.00285 ( 2) SS BOND : angle 0.16574 ( 4) covalent geometry : bond 0.00310 (34714) covalent geometry : angle 0.84558 (47341) *********************** 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 720 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 720 time to evaluate : 3.992 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: A 115 MET cc_start: 0.4462 (mtm) cc_final: 0.3929 (pmm) REVERT: A 145 PHE cc_start: 0.8389 (t80) cc_final: 0.7829 (t80) REVERT: A 221 HIS cc_start: 0.8573 (m-70) cc_final: 0.7828 (m90) REVERT: A 234 LEU cc_start: 0.9663 (mm) cc_final: 0.9164 (mm) REVERT: A 259 LEU cc_start: 0.9582 (mp) cc_final: 0.9337 (mp) REVERT: A 284 GLN cc_start: 0.7310 (pp30) cc_final: 0.7085 (pp30) REVERT: A 297 ARG cc_start: 0.9262 (ptt-90) cc_final: 0.8783 (ptt90) REVERT: A 301 GLN cc_start: 0.8804 (pp30) cc_final: 0.8415 (pp30) REVERT: A 441 PHE cc_start: 0.8076 (m-10) cc_final: 0.7714 (m-10) REVERT: A 531 MET cc_start: 0.8793 (tpt) cc_final: 0.8492 (tpt) REVERT: A 645 MET cc_start: 0.8658 (mtt) cc_final: 0.8260 (mtp) REVERT: A 676 HIS cc_start: 0.8929 (m-70) cc_final: 0.8650 (m-70) REVERT: A 719 GLN cc_start: 0.8862 (tp-100) cc_final: 0.8644 (tp-100) REVERT: A 817 ILE cc_start: 0.8308 (mm) cc_final: 0.7690 (tt) REVERT: A 832 TYR cc_start: 0.8996 (t80) cc_final: 0.8237 (t80) REVERT: A 928 LEU cc_start: 0.9329 (tt) cc_final: 0.8844 (mm) REVERT: A 1058 GLN cc_start: 0.8363 (pp30) cc_final: 0.8060 (pp30) REVERT: A 1069 PHE cc_start: 0.9055 (m-10) cc_final: 0.8421 (m-10) REVERT: A 1164 GLU cc_start: 0.8794 (tp30) cc_final: 0.8519 (tp30) REVERT: A 1166 LEU cc_start: 0.9527 (mt) cc_final: 0.9258 (mt) REVERT: A 1234 MET cc_start: 0.4333 (ptt) cc_final: 0.3110 (tmm) REVERT: A 1242 GLU cc_start: 0.8930 (pm20) cc_final: 0.8599 (pm20) REVERT: A 1261 LEU cc_start: 0.8660 (tp) cc_final: 0.8108 (tp) REVERT: A 1295 PHE cc_start: 0.8619 (m-10) cc_final: 0.8236 (m-80) REVERT: A 1344 CYS cc_start: 0.8822 (p) cc_final: 0.7069 (m) REVERT: A 1358 ASP cc_start: 0.8410 (t70) cc_final: 0.8140 (t70) REVERT: A 1377 LEU cc_start: 0.9258 (tp) cc_final: 0.8878 (tt) REVERT: C 96 PHE cc_start: 0.9298 (t80) cc_final: 0.8853 (t80) REVERT: C 177 MET cc_start: 0.9514 (mmp) cc_final: 0.9209 (mmm) REVERT: C 400 ARG cc_start: 0.4594 (tpt170) cc_final: 0.4322 (tpt170) REVERT: C 473 ASP cc_start: 0.8676 (p0) cc_final: 0.8408 (p0) REVERT: C 520 MET cc_start: 0.8733 (tpp) cc_final: 0.8454 (tpp) REVERT: C 536 HIS cc_start: 0.8018 (m90) cc_final: 0.7703 (m-70) REVERT: C 537 TRP cc_start: 0.7728 (p-90) cc_final: 0.6743 (p-90) REVERT: C 643 PHE cc_start: 0.9446 (m-10) cc_final: 0.8313 (m-10) REVERT: C 712 GLN cc_start: 0.9402 (tm-30) cc_final: 0.9189 (tm-30) REVERT: C 720 THR cc_start: 0.9483 (p) cc_final: 0.9199 (p) REVERT: C 724 PHE cc_start: 0.9413 (m-80) cc_final: 0.8908 (m-80) REVERT: C 832 TYR cc_start: 0.8924 (t80) cc_final: 0.8515 (t80) REVERT: C 848 MET cc_start: 0.8486 (mmp) cc_final: 0.7363 (mmp) REVERT: C 945 MET cc_start: 0.9214 (mtp) cc_final: 0.8793 (mtp) REVERT: C 1049 LYS cc_start: 0.8056 (pttm) cc_final: 0.7795 (pttt) REVERT: C 1126 THR cc_start: 0.9351 (p) cc_final: 0.8981 (p) REVERT: C 1157 MET cc_start: 0.8093 (tpp) cc_final: 0.7839 (tpp) REVERT: C 1168 ARG cc_start: 0.8980 (mmp80) cc_final: 0.8757 (mmp80) REVERT: C 1231 MET cc_start: 0.8094 (ppp) cc_final: 0.7868 (ppp) REVERT: C 1348 GLN cc_start: 0.9423 (mm-40) cc_final: 0.8272 (mm-40) REVERT: C 1361 MET cc_start: 0.8789 (mpp) cc_final: 0.8419 (mpp) REVERT: G 106 ASP cc_start: 0.6163 (m-30) cc_final: 0.5722 (m-30) REVERT: G 146 MET cc_start: 0.8080 (pmm) cc_final: 0.7709 (pmm) REVERT: I 67 TYR cc_start: 0.8585 (m-10) cc_final: 0.8048 (m-80) REVERT: I 112 TYR cc_start: 0.8640 (m-80) cc_final: 0.8368 (m-10) REVERT: I 134 GLU cc_start: 0.8394 (tp30) cc_final: 0.8117 (tp30) REVERT: I 135 ILE cc_start: 0.9199 (mt) cc_final: 0.8997 (pt) REVERT: I 146 MET cc_start: 0.6503 (mtt) cc_final: 0.5912 (mtm) REVERT: I 147 ARG cc_start: 0.8592 (ppt170) cc_final: 0.8188 (tmm160) REVERT: I 293 LEU cc_start: 0.9514 (tp) cc_final: 0.9285 (tp) REVERT: P 52 TYR cc_start: 0.7863 (m-80) cc_final: 0.7355 (m-80) REVERT: P 57 PRO cc_start: 0.6000 (Cg_endo) cc_final: 0.5559 (Cg_exo) REVERT: P 303 THR cc_start: 0.8748 (p) cc_final: 0.8531 (p) REVERT: R 6 PHE cc_start: 0.8091 (t80) cc_final: 0.7629 (t80) REVERT: R 97 LEU cc_start: 0.8076 (mt) cc_final: 0.7865 (mm) REVERT: R 293 LEU cc_start: 0.8452 (tp) cc_final: 0.8235 (tp) REVERT: Y 308 LYS cc_start: 0.8146 (tptt) cc_final: 0.7837 (tppt) REVERT: Y 418 MET cc_start: 0.5800 (mmp) cc_final: 0.5295 (mmp) REVERT: d 253 GLU cc_start: 0.9199 (tt0) cc_final: 0.8696 (mt-10) REVERT: d 291 CYS cc_start: 0.8659 (m) cc_final: 0.8126 (m) REVERT: d 295 ASP cc_start: 0.7837 (m-30) cc_final: 0.7286 (m-30) REVERT: d 305 ASP cc_start: 0.8108 (m-30) cc_final: 0.7894 (m-30) REVERT: d 335 ASN cc_start: 0.8914 (m-40) cc_final: 0.8551 (m-40) REVERT: d 419 TYR cc_start: 0.8842 (p90) cc_final: 0.8529 (p90) outliers start: 0 outliers final: 0 residues processed: 720 average time/residue: 0.4526 time to fit residues: 540.8170 Evaluate side-chains 563 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 563 time to evaluate : 3.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 20 optimal weight: 20.0000 chunk 250 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 112 optimal weight: 8.9990 chunk 341 optimal weight: 50.0000 chunk 208 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 45 optimal weight: 20.0000 chunk 123 optimal weight: 9.9990 chunk 378 optimal weight: 0.2980 overall best weight: 3.8186 ------------------------------------------------------------------------------- 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** ** A1216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 126 HIS ** d 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 461 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.108819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.082847 restraints weight = 151274.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.085255 restraints weight = 94012.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.086973 restraints weight = 66285.263| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2915 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= 0.146 Angle : 0.849 15.187 47345 Z= 0.427 Chirality : 0.050 0.643 5553 Planarity : 0.006 0.116 6151 Dihedral : 5.655 32.919 4880 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 1.24 % Allowed : 11.80 % Favored : 86.96 % Rotamer: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.31 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.26 (0.12), residues: 4432 helix: -0.45 (0.15), residues: 1278 sheet: -0.87 (0.23), residues: 510 loop : -2.27 (0.12), residues: 2644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 451 HIS 0.012 0.001 HIS C1057 PHE 0.025 0.001 PHE C 458 TYR 0.021 0.001 TYR A 258 ARG 0.008 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.03010 ( 918) hydrogen bonds : angle 5.15705 ( 2547) SS BOND : bond 0.00283 ( 2) SS BOND : angle 0.18336 ( 4) covalent geometry : bond 0.00311 (34714) covalent geometry : angle 0.84903 (47341) *********************** 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 726 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 726 time to evaluate : 9.452 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 145 PHE cc_start: 0.8371 (t80) cc_final: 0.7833 (t80) REVERT: A 221 HIS cc_start: 0.8700 (m-70) cc_final: 0.7899 (m90) REVERT: A 259 LEU cc_start: 0.9583 (mp) cc_final: 0.9335 (mp) REVERT: A 286 ASP cc_start: 0.8745 (t0) cc_final: 0.8393 (t0) REVERT: A 297 ARG cc_start: 0.9235 (ptt-90) cc_final: 0.8769 (ptt90) REVERT: A 301 GLN cc_start: 0.8822 (pp30) cc_final: 0.8432 (pp30) REVERT: A 441 PHE cc_start: 0.8061 (m-10) cc_final: 0.7779 (m-10) REVERT: A 531 MET cc_start: 0.8779 (tpt) cc_final: 0.8471 (tpt) REVERT: A 632 ASP cc_start: 0.9230 (t70) cc_final: 0.8990 (t70) REVERT: A 645 MET cc_start: 0.8618 (mtt) cc_final: 0.8235 (mtp) REVERT: A 676 HIS cc_start: 0.9016 (m-70) cc_final: 0.8719 (m-70) REVERT: A 817 ILE cc_start: 0.8302 (mm) cc_final: 0.7682 (tt) REVERT: A 832 TYR cc_start: 0.9028 (t80) cc_final: 0.8239 (t80) REVERT: A 837 ILE cc_start: 0.9277 (mm) cc_final: 0.8993 (mm) REVERT: A 928 LEU cc_start: 0.9313 (tt) cc_final: 0.8832 (mm) REVERT: A 1058 GLN cc_start: 0.8429 (pp30) cc_final: 0.8041 (pp30) REVERT: A 1069 PHE cc_start: 0.9051 (m-10) cc_final: 0.8407 (m-10) REVERT: A 1164 GLU cc_start: 0.8828 (tp30) cc_final: 0.8294 (tp30) REVERT: A 1166 LEU cc_start: 0.9511 (mt) cc_final: 0.9247 (mt) REVERT: A 1218 PHE cc_start: 0.9620 (m-80) cc_final: 0.9251 (m-10) REVERT: A 1234 MET cc_start: 0.4362 (ptt) cc_final: 0.3196 (tmm) REVERT: A 1242 GLU cc_start: 0.8897 (pm20) cc_final: 0.8458 (pm20) REVERT: A 1245 MET cc_start: 0.8688 (ppp) cc_final: 0.8342 (ppp) REVERT: A 1261 LEU cc_start: 0.8667 (tp) cc_final: 0.8064 (tp) REVERT: A 1344 CYS cc_start: 0.8854 (p) cc_final: 0.7209 (m) REVERT: A 1351 TYR cc_start: 0.8720 (m-10) cc_final: 0.8507 (m-10) REVERT: A 1358 ASP cc_start: 0.8410 (t70) cc_final: 0.8132 (t70) REVERT: A 1377 LEU cc_start: 0.9251 (tp) cc_final: 0.8852 (tt) REVERT: C 96 PHE cc_start: 0.9290 (t80) cc_final: 0.8675 (t80) REVERT: C 177 MET cc_start: 0.9478 (mmp) cc_final: 0.9183 (mmm) REVERT: C 242 MET cc_start: 0.9257 (pmm) cc_final: 0.8112 (pmm) REVERT: C 400 ARG cc_start: 0.4547 (tpt170) cc_final: 0.4333 (tpt170) REVERT: C 473 ASP cc_start: 0.8691 (p0) cc_final: 0.8479 (p0) REVERT: C 520 MET cc_start: 0.8727 (tpp) cc_final: 0.8453 (tpp) REVERT: C 530 MET cc_start: 0.8794 (ppp) cc_final: 0.8545 (ppp) REVERT: C 536 HIS cc_start: 0.8089 (m90) cc_final: 0.7727 (m-70) REVERT: C 537 TRP cc_start: 0.7577 (p-90) cc_final: 0.6695 (p-90) REVERT: C 643 PHE cc_start: 0.9437 (m-10) cc_final: 0.8310 (m-10) REVERT: C 712 GLN cc_start: 0.9439 (tm-30) cc_final: 0.9203 (tm-30) REVERT: C 720 THR cc_start: 0.9445 (p) cc_final: 0.9126 (p) REVERT: C 724 PHE cc_start: 0.9406 (m-80) cc_final: 0.8902 (m-80) REVERT: C 848 MET cc_start: 0.8500 (mmp) cc_final: 0.7390 (mmp) REVERT: C 945 MET cc_start: 0.9170 (mtp) cc_final: 0.8709 (mtp) REVERT: C 1157 MET cc_start: 0.8151 (tpp) cc_final: 0.7943 (tpp) REVERT: C 1168 ARG cc_start: 0.9016 (mmp80) cc_final: 0.8765 (mmp80) REVERT: C 1231 MET cc_start: 0.7995 (ppp) cc_final: 0.7782 (ppp) REVERT: C 1348 GLN cc_start: 0.9479 (mm-40) cc_final: 0.8378 (mm-40) REVERT: C 1361 MET cc_start: 0.8794 (mpp) cc_final: 0.8370 (mpp) REVERT: C 1363 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.8159 (mtm-85) REVERT: G 146 MET cc_start: 0.7927 (pmm) cc_final: 0.7704 (pmm) REVERT: G 148 GLU cc_start: 0.9173 (pm20) cc_final: 0.8912 (mp0) REVERT: I 31 ILE cc_start: 0.9489 (mm) cc_final: 0.9183 (mm) REVERT: I 67 TYR cc_start: 0.8586 (m-10) cc_final: 0.8124 (m-80) REVERT: I 111 ASP cc_start: 0.7800 (m-30) cc_final: 0.7447 (m-30) REVERT: I 134 GLU cc_start: 0.8363 (tp30) cc_final: 0.8162 (tp30) REVERT: I 146 MET cc_start: 0.6953 (mtt) cc_final: 0.6153 (mtm) REVERT: I 147 ARG cc_start: 0.8625 (ppt170) cc_final: 0.8239 (tmm160) REVERT: P 52 TYR cc_start: 0.7880 (m-80) cc_final: 0.7398 (m-80) REVERT: P 57 PRO cc_start: 0.6520 (Cg_endo) cc_final: 0.6149 (Cg_exo) REVERT: P 186 LEU cc_start: 0.7702 (tp) cc_final: 0.7478 (tt) REVERT: P 303 THR cc_start: 0.8799 (p) cc_final: 0.8557 (p) REVERT: R 6 PHE cc_start: 0.8064 (t80) cc_final: 0.7618 (t80) REVERT: R 97 LEU cc_start: 0.8101 (mt) cc_final: 0.7890 (mm) REVERT: R 293 LEU cc_start: 0.8422 (tp) cc_final: 0.8185 (tp) REVERT: Y 308 LYS cc_start: 0.8165 (tptt) cc_final: 0.7842 (tppt) REVERT: Y 335 ASN cc_start: 0.8864 (t0) cc_final: 0.8621 (t0) REVERT: Y 418 MET cc_start: 0.5791 (mmp) cc_final: 0.5340 (mmp) REVERT: d 134 LEU cc_start: 0.9275 (tp) cc_final: 0.9055 (tp) REVERT: d 202 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8245 (tm-30) REVERT: d 253 GLU cc_start: 0.9196 (tt0) cc_final: 0.8703 (mt-10) REVERT: d 291 CYS cc_start: 0.8637 (m) cc_final: 0.8085 (m) REVERT: d 295 ASP cc_start: 0.7860 (m-30) cc_final: 0.7284 (m-30) REVERT: d 305 ASP cc_start: 0.8087 (m-30) cc_final: 0.7884 (m-30) REVERT: d 335 ASN cc_start: 0.8956 (m-40) cc_final: 0.8439 (m-40) REVERT: d 419 TYR cc_start: 0.8904 (p90) cc_final: 0.8557 (p90) outliers start: 0 outliers final: 0 residues processed: 726 average time/residue: 0.6944 time to fit residues: 848.9186 Evaluate side-chains 572 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 572 time to evaluate : 4.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 287 optimal weight: 0.0170 chunk 2 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 237 optimal weight: 20.0000 chunk 5 optimal weight: 0.0870 chunk 100 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 chunk 355 optimal weight: 50.0000 chunk 70 optimal weight: 9.9990 chunk 257 optimal weight: 0.9990 chunk 127 optimal weight: 9.9990 overall best weight: 3.0202 ------------------------------------------------------------------------------- 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** A 741 ASN C 451 GLN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C1028 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C1057 HIS ** C1269 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** I 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** Y 126 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 = 0.3896 r_free = 0.3896 target = 0.109419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.083438 restraints weight = 148928.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.085848 restraints weight = 92685.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.087536 restraints weight = 65341.005| |-----------------------------------------------------------------------------| r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3049 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= 0.142 Angle : 0.859 15.082 47345 Z= 0.429 Chirality : 0.050 0.604 5553 Planarity : 0.006 0.116 6151 Dihedral : 5.610 32.697 4880 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 1.24 % Allowed : 11.24 % Favored : 87.52 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.31 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.12), residues: 4432 helix: -0.36 (0.15), residues: 1265 sheet: -1.07 (0.22), residues: 553 loop : -2.28 (0.12), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP Y 451 HIS 0.013 0.001 HIS C1057 PHE 0.023 0.001 PHE C 458 TYR 0.020 0.001 TYR A 258 ARG 0.009 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.02972 ( 918) hydrogen bonds : angle 5.07923 ( 2547) SS BOND : bond 0.00213 ( 2) SS BOND : angle 0.21178 ( 4) covalent geometry : bond 0.00306 (34714) covalent geometry : angle 0.85861 (47341) ********************** 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 712 residues out of total 3760 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 712 time to evaluate : 4.928 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 130 ASN cc_start: 0.4171 (p0) cc_final: 0.3546 (p0) REVERT: A 145 PHE cc_start: 0.8315 (t80) cc_final: 0.7775 (t80) REVERT: A 221 HIS cc_start: 0.8689 (m-70) cc_final: 0.7899 (m90) REVERT: A 259 LEU cc_start: 0.9578 (mp) cc_final: 0.9347 (mp) REVERT: A 286 ASP cc_start: 0.8731 (t0) cc_final: 0.8398 (t0) REVERT: A 297 ARG cc_start: 0.9230 (ptt-90) cc_final: 0.8764 (ptt90) REVERT: A 301 GLN cc_start: 0.8825 (pp30) cc_final: 0.8421 (pp30) REVERT: A 386 ILE cc_start: 0.9254 (tt) cc_final: 0.8951 (mt) REVERT: A 441 PHE cc_start: 0.8001 (m-10) cc_final: 0.7743 (m-10) REVERT: A 531 MET cc_start: 0.8764 (tpt) cc_final: 0.8429 (tpt) REVERT: A 632 ASP cc_start: 0.9213 (t70) cc_final: 0.8970 (t70) REVERT: A 645 MET cc_start: 0.8619 (mtt) cc_final: 0.8371 (mtp) REVERT: A 676 HIS cc_start: 0.9012 (m-70) cc_final: 0.8694 (m-70) REVERT: A 680 PHE cc_start: 0.8002 (m-80) cc_final: 0.7619 (m-80) REVERT: A 817 ILE cc_start: 0.8306 (mm) cc_final: 0.7687 (tt) REVERT: A 832 TYR cc_start: 0.9036 (t80) cc_final: 0.8241 (t80) REVERT: A 837 ILE cc_start: 0.9269 (mm) cc_final: 0.8981 (mm) REVERT: A 928 LEU cc_start: 0.9290 (tt) cc_final: 0.8809 (mm) REVERT: A 1058 GLN cc_start: 0.8284 (pp30) cc_final: 0.7911 (pp30) REVERT: A 1069 PHE cc_start: 0.9010 (m-10) cc_final: 0.8453 (m-10) REVERT: A 1164 GLU cc_start: 0.8781 (tp30) cc_final: 0.8317 (tp30) REVERT: A 1166 LEU cc_start: 0.9514 (mt) cc_final: 0.9242 (mt) REVERT: A 1218 PHE cc_start: 0.9641 (m-80) cc_final: 0.9420 (m-80) REVERT: A 1227 ARG cc_start: 0.8376 (ttt180) cc_final: 0.8015 (ttt180) REVERT: A 1234 MET cc_start: 0.4430 (ptt) cc_final: 0.3177 (tmm) REVERT: A 1242 GLU cc_start: 0.8819 (pm20) cc_final: 0.8527 (pm20) REVERT: A 1261 LEU cc_start: 0.8623 (tp) cc_final: 0.8030 (tp) REVERT: A 1344 CYS cc_start: 0.8754 (p) cc_final: 0.7351 (m) REVERT: A 1351 TYR cc_start: 0.8746 (m-10) cc_final: 0.8480 (m-10) REVERT: A 1358 ASP cc_start: 0.8399 (t70) cc_final: 0.8078 (t70) REVERT: C 96 PHE cc_start: 0.9261 (t80) cc_final: 0.8834 (t80) REVERT: C 177 MET cc_start: 0.9469 (mmp) cc_final: 0.9178 (mmm) REVERT: C 400 ARG cc_start: 0.4504 (tpt170) cc_final: 0.4227 (tpt170) REVERT: C 473 ASP cc_start: 0.8671 (p0) cc_final: 0.8457 (p0) REVERT: C 520 MET cc_start: 0.8717 (tpp) cc_final: 0.8448 (tpp) REVERT: C 530 MET cc_start: 0.8776 (ppp) cc_final: 0.8539 (ppp) REVERT: C 536 HIS cc_start: 0.8050 (m90) cc_final: 0.7687 (m-70) REVERT: C 537 TRP cc_start: 0.7566 (p-90) cc_final: 0.6632 (p-90) REVERT: C 643 PHE cc_start: 0.9451 (m-10) cc_final: 0.8324 (m-10) REVERT: C 712 GLN cc_start: 0.9431 (tm-30) cc_final: 0.9188 (tm-30) REVERT: C 720 THR cc_start: 0.9374 (p) cc_final: 0.9011 (p) REVERT: C 724 PHE cc_start: 0.9407 (m-80) cc_final: 0.8904 (m-80) REVERT: C 848 MET cc_start: 0.8500 (mmp) cc_final: 0.7407 (mmp) REVERT: C 945 MET cc_start: 0.9158 (mtp) cc_final: 0.8653 (mtp) REVERT: C 1157 MET cc_start: 0.8143 (tpp) cc_final: 0.7902 (tpp) REVERT: C 1168 ARG cc_start: 0.9035 (mmp80) cc_final: 0.8727 (mmp80) REVERT: C 1231 MET cc_start: 0.8010 (ppp) cc_final: 0.7753 (ppp) REVERT: C 1348 GLN cc_start: 0.9484 (mm-40) cc_final: 0.8379 (mm-40) REVERT: C 1361 MET cc_start: 0.8789 (mpp) cc_final: 0.8398 (mpp) REVERT: C 1363 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.8166 (mtm-85) REVERT: G 146 MET cc_start: 0.7836 (pmm) cc_final: 0.7605 (pmm) REVERT: I 67 TYR cc_start: 0.8574 (m-10) cc_final: 0.8086 (m-80) REVERT: I 111 ASP cc_start: 0.8138 (m-30) cc_final: 0.7818 (m-30) REVERT: I 134 GLU cc_start: 0.8308 (tp30) cc_final: 0.8034 (tp30) REVERT: I 146 MET cc_start: 0.7106 (mtt) cc_final: 0.6638 (mtm) REVERT: I 147 ARG cc_start: 0.8649 (ppt170) cc_final: 0.8265 (tmm160) REVERT: I 276 TRP cc_start: 0.6629 (m100) cc_final: 0.6207 (m100) REVERT: P 52 TYR cc_start: 0.7888 (m-80) cc_final: 0.7400 (m-80) REVERT: P 57 PRO cc_start: 0.6518 (Cg_endo) cc_final: 0.6144 (Cg_exo) REVERT: P 186 LEU cc_start: 0.7679 (tp) cc_final: 0.7428 (tt) REVERT: P 303 THR cc_start: 0.8788 (p) cc_final: 0.8535 (p) REVERT: R 6 PHE cc_start: 0.8006 (t80) cc_final: 0.7566 (t80) REVERT: R 112 TYR cc_start: 0.7599 (m-10) cc_final: 0.7392 (m-10) REVERT: R 208 MET cc_start: 0.5785 (ppp) cc_final: 0.5559 (mmm) REVERT: R 293 LEU cc_start: 0.8179 (tp) cc_final: 0.7954 (tp) REVERT: Y 116 LEU cc_start: 0.9194 (mp) cc_final: 0.8780 (tp) REVERT: Y 308 LYS cc_start: 0.8120 (tptt) cc_final: 0.7816 (tppt) REVERT: Y 335 ASN cc_start: 0.8810 (t0) cc_final: 0.8577 (t0) REVERT: Y 418 MET cc_start: 0.5771 (mmp) cc_final: 0.5336 (mmp) REVERT: d 134 LEU cc_start: 0.9278 (tp) cc_final: 0.9066 (tp) REVERT: d 202 GLN cc_start: 0.8479 (tm-30) cc_final: 0.8243 (tm-30) REVERT: d 253 GLU cc_start: 0.9193 (tt0) cc_final: 0.8695 (mt-10) REVERT: d 291 CYS cc_start: 0.8600 (m) cc_final: 0.8046 (m) REVERT: d 295 ASP cc_start: 0.7772 (m-30) cc_final: 0.7127 (m-30) REVERT: d 305 ASP cc_start: 0.8066 (m-30) cc_final: 0.7861 (m-30) REVERT: d 335 ASN cc_start: 0.8772 (m-40) cc_final: 0.8261 (m-40) REVERT: d 419 TYR cc_start: 0.8822 (p90) cc_final: 0.8435 (p90) outliers start: 0 outliers final: 0 residues processed: 712 average time/residue: 0.4470 time to fit residues: 533.0954 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 : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 444 random chunks: chunk 188 optimal weight: 7.9990 chunk 101 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 161 optimal weight: 10.0000 chunk 425 optimal weight: 50.0000 chunk 120 optimal weight: 30.0000 chunk 253 optimal weight: 8.9990 chunk 127 optimal weight: 10.0000 chunk 2 optimal weight: 0.8980 chunk 195 optimal weight: 5.9990 chunk 142 optimal weight: 20.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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 ** A 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 885 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 ASN ** A 988 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1074 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN C 455 GLN ** C 696 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 782 GLN ** 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 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 126 HIS ** 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 = 0.3870 r_free = 0.3870 target = 0.107794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.081808 restraints weight = 152833.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.084183 restraints weight = 95091.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.085869 restraints weight = 67175.479| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7697 moved from start: 0.3250 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= 0.163 Angle : 0.862 15.058 47345 Z= 0.434 Chirality : 0.051 0.572 5553 Planarity : 0.006 0.116 6151 Dihedral : 5.680 32.403 4880 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 1.15 % Allowed : 12.18 % Favored : 86.67 % Rotamer: Outliers : 0.03 % Allowed : 0.48 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 2.31 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.21 (0.12), residues: 4432 helix: -0.30 (0.15), residues: 1248 sheet: -1.06 (0.22), residues: 547 loop : -2.25 (0.12), residues: 2637 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP Y 451 HIS 0.010 0.001 HIS C1057 PHE 0.024 0.002 PHE C 458 TYR 0.025 0.001 TYR C1084 ARG 0.009 0.001 ARG C 718 Details of bonding type rmsd hydrogen bonds : bond 0.03061 ( 918) hydrogen bonds : angle 5.14056 ( 2547) SS BOND : bond 0.00432 ( 2) SS BOND : angle 0.27882 ( 4) covalent geometry : bond 0.00346 (34714) covalent geometry : angle 0.86201 (47341) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14518.62 seconds wall clock time: 263 minutes 17.27 seconds (15797.27 seconds total)