Starting phenix.real_space_refine on Mon Oct 13 11:51:14 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5yfp_6827/10_2025/5yfp_6827.cif Found real_map, /net/cci-nas-00/data/ceres_data/5yfp_6827/10_2025/5yfp_6827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5yfp_6827/10_2025/5yfp_6827.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5yfp_6827/10_2025/5yfp_6827.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5yfp_6827/10_2025/5yfp_6827.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5yfp_6827/10_2025/5yfp_6827.map" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 436 atoms to isotropic. 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 37 5.16 5 C 20124 2.51 5 N 6346 2.21 5 O 6589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33096 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 672, 3345 Classifications: {'peptide': 672} Incomplete info: {'truncation_to_alanine': 635} Link IDs: {'CIS': 30, 'PCIS': 2, 'PTRANS': 15, 'TRANS': 624} Chain breaks: 4 Unresolved chain link angles: 17 Unresolved non-hydrogen bonds: 2246 Unresolved non-hydrogen angles: 2877 Unresolved non-hydrogen dihedrals: 1838 Unresolved non-hydrogen chiralities: 214 Planarities with less than four sites: {'GLU:plan': 66, 'ASN:plan1': 50, 'ASP:plan': 39, 'TRP:plan': 9, 'ARG:plan': 24, 'TYR:plan': 19, 'PHE:plan': 31, 'GLN:plan1': 33, 'HIS:plan': 12} Unresolved non-hydrogen planarities: 1243 Chain: "B" Number of atoms: 4610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 4610 Classifications: {'peptide': 928} Incomplete info: {'truncation_to_alanine': 874} Link IDs: {'CIS': 51, 'PCIS': 2, 'PTRANS': 25, 'TRANS': 849} Chain breaks: 2 Unresolved chain link angles: 27 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 3085 Unresolved non-hydrogen angles: 3936 Unresolved non-hydrogen dihedrals: 2546 Unresolved non-hydrogen chiralities: 280 Planarities with less than four sites: {'ASP:plan': 48, 'ARG:plan': 32, 'PHE:plan': 50, 'GLN:plan1': 55, 'GLU:plan': 61, 'TYR:plan': 31, 'ASN:plan1': 83, 'HIS:plan': 11, 'TRP:plan': 10} Unresolved non-hydrogen planarities: 1679 Chain: "C" Number of atoms: 4994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 794, 4994 Classifications: {'peptide': 794} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 9, 'n_c_alpha_c_only': 1, 'truncation_to_alanine': 399} Link IDs: {'CIS': 18, 'PCIS': 2, 'PTRANS': 16, 'TRANS': 757} Chain breaks: 2 Unresolved chain link angles: 12 Unresolved non-hydrogen bonds: 1558 Unresolved non-hydrogen angles: 1999 Unresolved non-hydrogen dihedrals: 1263 Unresolved non-hydrogen chiralities: 168 Planarities with less than four sites: {'ASP:plan': 31, 'GLN:plan1': 16, 'GLU:plan': 49, 'ARG:plan': 23, 'TYR:plan': 18, 'ASN:plan1': 23, 'PHE:plan': 16, 'HIS:plan': 8, 'TRP:plan': 2, 'GLN%COO:oxt': 1} Unresolved non-hydrogen planarities: 814 Chain: "D" Number of atoms: 4739 Number of conformers: 1 Conformer: "" Number of residues, atoms: 954, 4739 Classifications: {'peptide': 954} Incomplete info: {'truncation_to_alanine': 889} Link IDs: {'CIS': 53, 'PCIS': 3, 'PTRANS': 22, 'TRANS': 875} Chain breaks: 4 Unresolved chain link angles: 25 Unresolved non-hydrogen bonds: 3137 Unresolved non-hydrogen angles: 3996 Unresolved non-hydrogen dihedrals: 2580 Unresolved non-hydrogen chiralities: 292 Planarities with less than four sites: {'GLU:plan': 69, 'GLN:plan1': 43, 'ASN:plan1': 95, 'ASP:plan': 46, 'HIS:plan': 24, 'ARG:plan': 28, 'TRP:plan': 8, 'PHE:plan': 52, 'TYR:plan': 23} Unresolved non-hydrogen planarities: 1676 Chain: "E" Number of atoms: 3860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 776, 3860 Classifications: {'peptide': 776} Incomplete info: {'truncation_to_alanine': 729} Link IDs: {'CIS': 21, 'PCIS': 1, 'PTRANS': 14, 'TRANS': 739} Chain breaks: 2 Unresolved chain link angles: 15 Unresolved non-hydrogen bonds: 2553 Unresolved non-hydrogen angles: 3255 Unresolved non-hydrogen dihedrals: 2079 Unresolved non-hydrogen chiralities: 268 Planarities with less than four sites: {'TYR:plan': 24, 'GLU:plan': 59, 'ASP:plan': 43, 'TRP:plan': 5, 'ASN:plan1': 60, 'PHE:plan': 40, 'GLN:plan1': 33, 'HIS:plan': 13, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 1300 Chain: "F" Number of atoms: 3612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 725, 3612 Classifications: {'peptide': 725} Incomplete info: {'truncation_to_alanine': 690} Link IDs: {'CIS': 18, 'PTRANS': 16, 'TRANS': 690} Chain breaks: 4 Unresolved chain link angles: 16 Unresolved non-hydrogen bonds: 2475 Unresolved non-hydrogen angles: 3144 Unresolved non-hydrogen dihedrals: 2041 Unresolved non-hydrogen chiralities: 230 Planarities with less than four sites: {'HIS:plan': 8, 'GLU:plan': 60, 'GLN:plan1': 32, 'ASN:plan1': 50, 'ASP:plan': 49, 'PHE:plan': 48, 'TRP:plan': 5, 'ARG:plan': 23, 'TYR:plan': 24} Unresolved non-hydrogen planarities: 1321 Chain: "G" Number of atoms: 4696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4696 Classifications: {'peptide': 615} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 84} Link IDs: {'CIS': 2, 'PTRANS': 19, 'TRANS': 593} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 272 Unresolved non-hydrogen angles: 341 Unresolved non-hydrogen dihedrals: 218 Unresolved non-hydrogen chiralities: 27 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 3, 'GLN:plan1': 5, 'PHE:plan': 4, 'ASN:plan1': 8, 'ARG:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 131 Chain: "H" Number of atoms: 3240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 518, 3240 Classifications: {'peptide': 518} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 282} Link IDs: {'CIS': 7, 'PTRANS': 9, 'TRANS': 501} Chain breaks: 5 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 979 Unresolved non-hydrogen angles: 1233 Unresolved non-hydrogen dihedrals: 791 Unresolved non-hydrogen chiralities: 83 Planarities with less than four sites: {'ASN:plan1': 28, 'ARG:plan': 21, 'HIS:plan': 4, 'PHE:plan': 13, 'ASP:plan': 23, 'GLN:plan1': 17, 'GLU:plan': 20, 'TYR:plan': 4, 'TRP:plan': 2} Unresolved non-hydrogen planarities: 550 Time building chain proxies: 8.21, per 1000 atoms: 0.25 Number of scatterers: 33096 At special positions: 0 Unit cell: (185.529, 297.891, 233.871, 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 37 16.00 O 6589 8.00 N 6346 7.00 C 20124 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.00 Conformation dependent library (CDL) restraints added in 2.0 seconds Enol-peptide restraints added in 715.3 nanoseconds 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11596 Finding SS restraints... Secondary structure from input PDB file: 258 helices and 2 sheets defined 60.8% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.23 Creating SS restraints... Processing helix chain 'A' and resid 625 through 631 Processing helix chain 'A' and resid 639 through 664 Processing helix chain 'A' and resid 666 through 675 Proline residue: A 672 - end of helix Processing helix chain 'A' and resid 675 through 711 Proline residue: A 690 - end of helix Processing helix chain 'A' and resid 741 through 746 removed outlier: 4.293A pdb=" N ASN A 745 " --> pdb=" O GLU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 773 Processing helix chain 'A' and resid 788 through 791 Processing helix chain 'A' and resid 792 through 822 Processing helix chain 'A' and resid 830 through 838 Processing helix chain 'A' and resid 839 through 845 Processing helix chain 'A' and resid 854 through 860 Processing helix chain 'A' and resid 861 through 866 removed outlier: 4.598A pdb=" N SER A 865 " --> pdb=" O ASN A 861 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N ILE A 866 " --> pdb=" O TRP A 862 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 861 through 866' Processing helix chain 'A' and resid 867 through 879 removed outlier: 4.372A pdb=" N SER A 879 " --> pdb=" O THR A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 928 Processing helix chain 'A' and resid 931 through 936 Processing helix chain 'A' and resid 958 through 963 Processing helix chain 'A' and resid 982 through 993 removed outlier: 3.545A pdb=" N ALA A 986 " --> pdb=" O ASP A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 1003 through 1012 Processing helix chain 'A' and resid 1020 through 1030 Processing helix chain 'A' and resid 1041 through 1053 removed outlier: 3.631A pdb=" N VAL A1045 " --> pdb=" O LEU A1041 " (cutoff:3.500A) Processing helix chain 'A' and resid 1085 through 1094 removed outlier: 3.613A pdb=" N GLY A1089 " --> pdb=" O ASP A1085 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLU A1094 " --> pdb=" O LEU A1090 " (cutoff:3.500A) Processing helix chain 'A' and resid 1099 through 1103 removed outlier: 3.680A pdb=" N ARG A1102 " --> pdb=" O PHE A1099 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A1103 " --> pdb=" O ALA A1100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1099 through 1103' Processing helix chain 'A' and resid 1121 through 1133 Processing helix chain 'A' and resid 1157 through 1168 Processing helix chain 'A' and resid 1187 through 1195 Processing helix chain 'A' and resid 1195 through 1206 removed outlier: 3.762A pdb=" N ALA A1204 " --> pdb=" O LYS A1200 " (cutoff:3.500A) Processing helix chain 'A' and resid 1221 through 1226 Processing helix chain 'A' and resid 1300 through 1307 Processing helix chain 'A' and resid 1308 through 1310 No H-bonds generated for 'chain 'A' and resid 1308 through 1310' Processing helix chain 'B' and resid 11 through 15 removed outlier: 3.704A pdb=" N PHE B 14 " --> pdb=" O LEU B 11 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N TYR B 15 " --> pdb=" O LEU B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 15' Processing helix chain 'B' and resid 71 through 87 Proline residue: B 82 - end of helix Processing helix chain 'B' and resid 131 through 151 removed outlier: 3.732A pdb=" N LYS B 148 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLN B 149 " --> pdb=" O ILE B 145 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N VAL B 151 " --> pdb=" O LEU B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 171 removed outlier: 4.606A pdb=" N LEU B 165 " --> pdb=" O ILE B 161 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ILE B 168 " --> pdb=" O LYS B 164 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N TYR B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 192 through 197 Processing helix chain 'B' and resid 200 through 211 removed outlier: 3.757A pdb=" N LYS B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 211 through 231 Processing helix chain 'B' and resid 238 through 247 removed outlier: 3.987A pdb=" N LEU B 247 " --> pdb=" O LEU B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 267 removed outlier: 4.054A pdb=" N ARG B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 273 removed outlier: 3.984A pdb=" N SER B 273 " --> pdb=" O PHE B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 305 Processing helix chain 'B' and resid 310 through 331 Processing helix chain 'B' and resid 354 through 385 removed outlier: 4.345A pdb=" N ILE B 360 " --> pdb=" O ARG B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 407 Processing helix chain 'B' and resid 411 through 419 removed outlier: 6.063A pdb=" N ILE B 416 " --> pdb=" O PHE B 413 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N SER B 417 " --> pdb=" O GLN B 414 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N THR B 419 " --> pdb=" O ILE B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 494 removed outlier: 3.774A pdb=" N LEU B 493 " --> pdb=" O ILE B 489 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N ASP B 494 " --> pdb=" O GLU B 490 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 505 removed outlier: 3.903A pdb=" N GLU B 504 " --> pdb=" O SER B 500 " (cutoff:3.500A) Processing helix chain 'B' and resid 528 through 550 Processing helix chain 'B' and resid 595 through 618 Proline residue: B 602 - end of helix Proline residue: B 607 - end of helix Processing helix chain 'B' and resid 624 through 652 removed outlier: 3.982A pdb=" N SER B 633 " --> pdb=" O ARG B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 693 removed outlier: 3.650A pdb=" N GLU B 690 " --> pdb=" O THR B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 706 Processing helix chain 'B' and resid 707 through 709 No H-bonds generated for 'chain 'B' and resid 707 through 709' Processing helix chain 'B' and resid 725 through 754 Processing helix chain 'B' and resid 764 through 775 Processing helix chain 'B' and resid 777 through 784 Processing helix chain 'B' and resid 785 through 787 No H-bonds generated for 'chain 'B' and resid 785 through 787' Processing helix chain 'B' and resid 799 through 826 removed outlier: 3.785A pdb=" N GLY B 814 " --> pdb=" O SER B 810 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LYS B 821 " --> pdb=" O LEU B 817 " (cutoff:3.500A) Processing helix chain 'B' and resid 827 through 832 removed outlier: 3.651A pdb=" N LYS B 831 " --> pdb=" O THR B 827 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 832 " --> pdb=" O LEU B 828 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 827 through 832' Processing helix chain 'B' and resid 848 through 865 removed outlier: 3.535A pdb=" N GLU B 853 " --> pdb=" O ASP B 849 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA B 854 " --> pdb=" O TYR B 850 " (cutoff:3.500A) Processing helix chain 'B' and resid 874 through 891 Processing helix chain 'B' and resid 906 through 918 removed outlier: 3.557A pdb=" N ASP B 910 " --> pdb=" O GLN B 906 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET B 918 " --> pdb=" O PHE B 914 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 935 Processing helix chain 'B' and resid 942 through 952 removed outlier: 3.879A pdb=" N GLN B 946 " --> pdb=" O THR B 942 " (cutoff:3.500A) Processing helix chain 'B' and resid 952 through 960 removed outlier: 3.762A pdb=" N VAL B 956 " --> pdb=" O ILE B 952 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 971 removed outlier: 3.820A pdb=" N ALA B 969 " --> pdb=" O GLN B 966 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 11 Processing helix chain 'C' and resid 18 through 67 Processing helix chain 'C' and resid 70 through 78 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 105 through 123 removed outlier: 3.595A pdb=" N GLU C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 153 Processing helix chain 'C' and resid 177 through 182 removed outlier: 4.166A pdb=" N SER C 182 " --> pdb=" O PHE C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 200 Processing helix chain 'C' and resid 201 through 204 removed outlier: 3.660A pdb=" N ARG C 204 " --> pdb=" O GLU C 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 201 through 204' Processing helix chain 'C' and resid 210 through 235 removed outlier: 4.667A pdb=" N ARG C 223 " --> pdb=" O ASP C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 299 through 304 Processing helix chain 'C' and resid 308 through 313 Processing helix chain 'C' and resid 323 through 346 removed outlier: 3.953A pdb=" N ASN C 327 " --> pdb=" O ASP C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 368 removed outlier: 4.442A pdb=" N PHE C 357 " --> pdb=" O PHE C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 377 through 379 No H-bonds generated for 'chain 'C' and resid 377 through 379' Processing helix chain 'C' and resid 380 through 395 removed outlier: 3.863A pdb=" N ILE C 384 " --> pdb=" O ILE C 380 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU C 385 " --> pdb=" O ILE C 381 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 446 Processing helix chain 'C' and resid 463 through 476 Processing helix chain 'C' and resid 478 through 483 Processing helix chain 'C' and resid 489 through 526 removed outlier: 3.579A pdb=" N ILE C 526 " --> pdb=" O HIS C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 540 through 567 removed outlier: 3.975A pdb=" N TYR C 544 " --> pdb=" O GLY C 540 " (cutoff:3.500A) Processing helix chain 'C' and resid 571 through 580 Processing helix chain 'C' and resid 581 through 583 No H-bonds generated for 'chain 'C' and resid 581 through 583' Processing helix chain 'C' and resid 584 through 589 removed outlier: 3.919A pdb=" N GLY C 588 " --> pdb=" O GLY C 584 " (cutoff:3.500A) Processing helix chain 'C' and resid 590 through 606 removed outlier: 4.752A pdb=" N LEU C 598 " --> pdb=" O GLN C 594 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY C 599 " --> pdb=" O CYS C 595 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE C 605 " --> pdb=" O ILE C 601 " (cutoff:3.500A) Processing helix chain 'C' and resid 610 through 615 removed outlier: 3.718A pdb=" N GLU C 614 " --> pdb=" O LYS C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 617 through 623 removed outlier: 3.734A pdb=" N TYR C 621 " --> pdb=" O SER C 617 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N MET C 622 " --> pdb=" O LYS C 618 " (cutoff:3.500A) Processing helix chain 'C' and resid 624 through 637 Processing helix chain 'C' and resid 640 through 644 removed outlier: 4.120A pdb=" N MET C 644 " --> pdb=" O LYS C 641 " (cutoff:3.500A) Processing helix chain 'C' and resid 645 through 663 removed outlier: 4.023A pdb=" N ASN C 651 " --> pdb=" O VAL C 647 " (cutoff:3.500A) Processing helix chain 'C' and resid 676 through 678 No H-bonds generated for 'chain 'C' and resid 676 through 678' Processing helix chain 'C' and resid 679 through 692 removed outlier: 4.510A pdb=" N ASP C 688 " --> pdb=" O ALA C 684 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N PHE C 689 " --> pdb=" O MET C 685 " (cutoff:3.500A) Processing helix chain 'C' and resid 693 through 698 Processing helix chain 'C' and resid 710 through 725 removed outlier: 4.245A pdb=" N VAL C 716 " --> pdb=" O GLN C 712 " (cutoff:3.500A) Processing helix chain 'C' and resid 727 through 730 Processing helix chain 'C' and resid 731 through 742 Processing helix chain 'C' and resid 747 through 754 removed outlier: 3.837A pdb=" N VAL C 751 " --> pdb=" O ILE C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 761 through 783 Processing helix chain 'D' and resid 33 through 40 removed outlier: 3.949A pdb=" N ASN D 37 " --> pdb=" O ASP D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 46 removed outlier: 3.669A pdb=" N LEU D 44 " --> pdb=" O ARG D 41 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N GLN D 45 " --> pdb=" O ILE D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 47 through 52 Processing helix chain 'D' and resid 73 through 83 Processing helix chain 'D' and resid 104 through 120 removed outlier: 4.322A pdb=" N VAL D 111 " --> pdb=" O TYR D 107 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER D 112 " --> pdb=" O GLY D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 133 Processing helix chain 'D' and resid 140 through 175 removed outlier: 4.979A pdb=" N ASN D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LYS D 154 " --> pdb=" O LEU D 150 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN D 161 " --> pdb=" O ASP D 157 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU D 165 " --> pdb=" O ASN D 161 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 168 " --> pdb=" O GLU D 164 " (cutoff:3.500A) Proline residue: D 169 - end of helix removed outlier: 3.678A pdb=" N ILE D 172 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU D 173 " --> pdb=" O PRO D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 196 removed outlier: 3.791A pdb=" N GLN D 185 " --> pdb=" O PHE D 181 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN D 196 " --> pdb=" O PHE D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 227 Processing helix chain 'D' and resid 275 through 293 removed outlier: 3.938A pdb=" N LEU D 286 " --> pdb=" O ILE D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 321 through 333 removed outlier: 4.376A pdb=" N ARG D 325 " --> pdb=" O GLU D 321 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 369 removed outlier: 4.411A pdb=" N VAL D 341 " --> pdb=" O ASN D 337 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE D 343 " --> pdb=" O LEU D 339 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR D 362 " --> pdb=" O ILE D 358 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS D 369 " --> pdb=" O ILE D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 374 through 380 removed outlier: 3.844A pdb=" N THR D 377 " --> pdb=" O LYS D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 393 through 422 removed outlier: 4.365A pdb=" N LEU D 397 " --> pdb=" O LEU D 393 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG D 398 " --> pdb=" O SER D 394 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU D 399 " --> pdb=" O ILE D 395 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER D 422 " --> pdb=" O ILE D 418 " (cutoff:3.500A) Processing helix chain 'D' and resid 432 through 441 removed outlier: 3.502A pdb=" N LYS D 436 " --> pdb=" O LYS D 432 " (cutoff:3.500A) Processing helix chain 'D' and resid 442 through 456 removed outlier: 3.635A pdb=" N ILE D 448 " --> pdb=" O LEU D 444 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL D 453 " --> pdb=" O GLU D 449 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 515 Processing helix chain 'D' and resid 561 through 564 Processing helix chain 'D' and resid 565 through 570 Processing helix chain 'D' and resid 593 through 607 Processing helix chain 'D' and resid 626 through 643 Processing helix chain 'D' and resid 653 through 674 removed outlier: 3.709A pdb=" N LEU D 673 " --> pdb=" O TYR D 669 " (cutoff:3.500A) Processing helix chain 'D' and resid 687 through 692 Processing helix chain 'D' and resid 696 through 704 Processing helix chain 'D' and resid 714 through 723 Processing helix chain 'D' and resid 724 through 729 removed outlier: 4.229A pdb=" N TYR D 729 " --> pdb=" O PRO D 726 " (cutoff:3.500A) Processing helix chain 'D' and resid 745 through 768 Proline residue: D 764 - end of helix Processing helix chain 'D' and resid 819 through 854 Processing helix chain 'D' and resid 855 through 858 Processing helix chain 'D' and resid 875 through 896 removed outlier: 3.654A pdb=" N ALA D 879 " --> pdb=" O ASP D 875 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU D 896 " --> pdb=" O LEU D 892 " (cutoff:3.500A) Processing helix chain 'D' and resid 897 through 921 removed outlier: 3.735A pdb=" N LYS D 901 " --> pdb=" O PRO D 897 " (cutoff:3.500A) Processing helix chain 'D' and resid 927 through 949 removed outlier: 3.748A pdb=" N LYS D 932 " --> pdb=" O HIS D 928 " (cutoff:3.500A) Processing helix chain 'D' and resid 955 through 969 Processing helix chain 'D' and resid 971 through 978 Processing helix chain 'D' and resid 987 through 1004 Processing helix chain 'D' and resid 1046 through 1054 Processing helix chain 'E' and resid 4 through 9 Proline residue: E 9 - end of helix Processing helix chain 'E' and resid 10 through 15 Processing helix chain 'E' and resid 16 through 21 Processing helix chain 'E' and resid 59 through 64 Processing helix chain 'E' and resid 70 through 96 Processing helix chain 'E' and resid 100 through 141 Processing helix chain 'E' and resid 141 through 149 removed outlier: 3.846A pdb=" N GLY E 145 " --> pdb=" O VAL E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 154 through 171 Processing helix chain 'E' and resid 198 through 203 Processing helix chain 'E' and resid 215 through 240 removed outlier: 3.603A pdb=" N ASN E 219 " --> pdb=" O PRO E 215 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N THR E 220 " --> pdb=" O LYS E 216 " (cutoff:3.500A) Processing helix chain 'E' and resid 251 through 256 removed outlier: 3.572A pdb=" N ALA E 255 " --> pdb=" O LEU E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 270 Processing helix chain 'E' and resid 318 through 339 Processing helix chain 'E' and resid 343 through 348 removed outlier: 3.919A pdb=" N VAL E 347 " --> pdb=" O LYS E 343 " (cutoff:3.500A) Processing helix chain 'E' and resid 352 through 359 Processing helix chain 'E' and resid 361 through 375 removed outlier: 3.507A pdb=" N GLU E 365 " --> pdb=" O GLU E 361 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER E 375 " --> pdb=" O SER E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 376 through 404 Processing helix chain 'E' and resid 406 through 411 Processing helix chain 'E' and resid 413 through 427 Processing helix chain 'E' and resid 436 through 453 Processing helix chain 'E' and resid 455 through 460 Processing helix chain 'E' and resid 570 through 591 Processing helix chain 'E' and resid 595 through 610 Processing helix chain 'E' and resid 641 through 668 Proline residue: E 666 - end of helix Processing helix chain 'E' and resid 674 through 679 Processing helix chain 'E' and resid 682 through 694 Processing helix chain 'E' and resid 700 through 713 Processing helix chain 'E' and resid 732 through 742 Processing helix chain 'E' and resid 757 through 774 Processing helix chain 'E' and resid 785 through 794 Processing helix chain 'E' and resid 794 through 802 removed outlier: 3.828A pdb=" N THR E 799 " --> pdb=" O ILE E 795 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ALA E 800 " --> pdb=" O GLY E 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 814 through 821 Processing helix chain 'E' and resid 837 through 842 removed outlier: 3.867A pdb=" N ALA E 840 " --> pdb=" O GLY E 837 " (cutoff:3.500A) Processing helix chain 'E' and resid 849 through 853 removed outlier: 4.065A pdb=" N ASN E 853 " --> pdb=" O TYR E 850 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 69 Proline residue: F 66 - end of helix Processing helix chain 'F' and resid 77 through 102 removed outlier: 3.752A pdb=" N ILE F 81 " --> pdb=" O LEU F 77 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ASP F 82 " --> pdb=" O ASP F 78 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASP F 102 " --> pdb=" O GLN F 98 " (cutoff:3.500A) Processing helix chain 'F' and resid 109 through 145 removed outlier: 3.915A pdb=" N ILE F 113 " --> pdb=" O LEU F 109 " (cutoff:3.500A) Processing helix chain 'F' and resid 153 through 187 removed outlier: 3.945A pdb=" N THR F 187 " --> pdb=" O GLN F 183 " (cutoff:3.500A) Processing helix chain 'F' and resid 192 through 203 removed outlier: 4.232A pdb=" N GLN F 196 " --> pdb=" O PHE F 192 " (cutoff:3.500A) Processing helix chain 'F' and resid 207 through 211 removed outlier: 3.867A pdb=" N ASN F 211 " --> pdb=" O GLU F 208 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 224 Processing helix chain 'F' and resid 224 through 240 removed outlier: 3.615A pdb=" N GLN F 228 " --> pdb=" O ILE F 224 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 248 Processing helix chain 'F' and resid 251 through 266 Processing helix chain 'F' and resid 266 through 274 Processing helix chain 'F' and resid 284 through 291 Processing helix chain 'F' and resid 308 through 319 Processing helix chain 'F' and resid 323 through 326 Processing helix chain 'F' and resid 327 through 341 removed outlier: 3.955A pdb=" N GLU F 331 " --> pdb=" O VAL F 327 " (cutoff:3.500A) Processing helix chain 'F' and resid 383 through 387 Processing helix chain 'F' and resid 389 through 406 Processing helix chain 'F' and resid 422 through 442 removed outlier: 3.536A pdb=" N ASP F 434 " --> pdb=" O ASP F 430 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU F 436 " --> pdb=" O LEU F 432 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER F 437 " --> pdb=" O MET F 433 " (cutoff:3.500A) Proline residue: F 438 - end of helix Processing helix chain 'F' and resid 443 through 450 removed outlier: 3.890A pdb=" N LYS F 447 " --> pdb=" O ILE F 444 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU F 448 " --> pdb=" O ASP F 445 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N THR F 450 " --> pdb=" O LYS F 447 " (cutoff:3.500A) Processing helix chain 'F' and resid 454 through 460 Processing helix chain 'F' and resid 461 through 467 Processing helix chain 'F' and resid 475 through 496 removed outlier: 3.733A pdb=" N LEU F 482 " --> pdb=" O LEU F 478 " (cutoff:3.500A) Processing helix chain 'F' and resid 502 through 507 Processing helix chain 'F' and resid 520 through 528 Processing helix chain 'F' and resid 559 through 575 removed outlier: 4.673A pdb=" N LYS F 566 " --> pdb=" O THR F 562 " (cutoff:3.500A) Processing helix chain 'F' and resid 589 through 597 Processing helix chain 'F' and resid 601 through 603 No H-bonds generated for 'chain 'F' and resid 601 through 603' Processing helix chain 'F' and resid 604 through 612 removed outlier: 4.401A pdb=" N SER F 608 " --> pdb=" O LYS F 604 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N LEU F 610 " --> pdb=" O ILE F 606 " (cutoff:3.500A) Processing helix chain 'F' and resid 622 through 627 Processing helix chain 'F' and resid 629 through 636 Processing helix chain 'F' and resid 654 through 679 removed outlier: 3.648A pdb=" N ILE F 679 " --> pdb=" O ILE F 675 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 713 Processing helix chain 'F' and resid 728 through 733 Processing helix chain 'F' and resid 735 through 745 Processing helix chain 'F' and resid 756 through 763 Processing helix chain 'F' and resid 767 through 771 removed outlier: 4.394A pdb=" N ILE F 771 " --> pdb=" O LEU F 768 " (cutoff:3.500A) Processing helix chain 'F' and resid 839 through 848 Processing helix chain 'F' and resid 862 through 867 removed outlier: 3.969A pdb=" N HIS F 866 " --> pdb=" O SER F 862 " (cutoff:3.500A) Processing helix chain 'F' and resid 878 through 886 removed outlier: 4.080A pdb=" N SER F 884 " --> pdb=" O SER F 880 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 67 removed outlier: 4.197A pdb=" N ALA G 10 " --> pdb=" O ASP G 6 " (cutoff:3.500A) Proline residue: G 49 - end of helix removed outlier: 4.915A pdb=" N ARG G 62 " --> pdb=" O THR G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 68 through 70 No H-bonds generated for 'chain 'G' and resid 68 through 70' Processing helix chain 'G' and resid 74 through 88 removed outlier: 3.857A pdb=" N ALA G 78 " --> pdb=" O VAL G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 91 No H-bonds generated for 'chain 'G' and resid 89 through 91' Processing helix chain 'G' and resid 96 through 109 Processing helix chain 'G' and resid 112 through 116 removed outlier: 4.078A pdb=" N GLN G 115 " --> pdb=" O GLU G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 154 removed outlier: 3.665A pdb=" N HIS G 128 " --> pdb=" O ASN G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 162 through 167 Processing helix chain 'G' and resid 175 through 192 removed outlier: 4.173A pdb=" N ALA G 181 " --> pdb=" O GLN G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 194 through 217 Processing helix chain 'G' and resid 218 through 223 removed outlier: 4.011A pdb=" N GLU G 223 " --> pdb=" O PRO G 219 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 260 removed outlier: 4.598A pdb=" N LEU G 260 " --> pdb=" O LEU G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 294 Proline residue: G 278 - end of helix Processing helix chain 'G' and resid 304 through 317 removed outlier: 3.534A pdb=" N LEU G 308 " --> pdb=" O PHE G 304 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 358 Processing helix chain 'G' and resid 369 through 382 removed outlier: 3.895A pdb=" N VAL G 373 " --> pdb=" O THR G 369 " (cutoff:3.500A) Processing helix chain 'G' and resid 385 through 393 Processing helix chain 'G' and resid 397 through 402 Processing helix chain 'G' and resid 407 through 411 Processing helix chain 'G' and resid 422 through 451 removed outlier: 3.526A pdb=" N LEU G 426 " --> pdb=" O ASP G 422 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER G 428 " --> pdb=" O ASN G 424 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N MET G 451 " --> pdb=" O GLN G 447 " (cutoff:3.500A) Processing helix chain 'G' and resid 468 through 488 Processing helix chain 'G' and resid 491 through 496 Processing helix chain 'G' and resid 498 through 515 removed outlier: 4.141A pdb=" N SER G 502 " --> pdb=" O GLY G 498 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N TYR G 511 " --> pdb=" O LEU G 507 " (cutoff:3.500A) Processing helix chain 'G' and resid 516 through 533 removed outlier: 3.962A pdb=" N ASP G 533 " --> pdb=" O SER G 529 " (cutoff:3.500A) Processing helix chain 'G' and resid 541 through 564 removed outlier: 3.600A pdb=" N ILE G 545 " --> pdb=" O ASP G 541 " (cutoff:3.500A) Processing helix chain 'G' and resid 570 through 597 Proline residue: G 587 - end of helix Processing helix chain 'G' and resid 602 through 606 Processing helix chain 'G' and resid 610 through 620 Processing helix chain 'H' and resid 196 through 257 Processing helix chain 'H' and resid 260 through 272 Processing helix chain 'H' and resid 328 through 335 Processing helix chain 'H' and resid 399 through 401 No H-bonds generated for 'chain 'H' and resid 399 through 401' Processing helix chain 'H' and resid 430 through 440 Processing helix chain 'H' and resid 446 through 451 Processing helix chain 'H' and resid 455 through 466 Processing helix chain 'H' and resid 527 through 533 Processing helix chain 'H' and resid 533 through 548 Processing helix chain 'H' and resid 551 through 569 removed outlier: 4.202A pdb=" N ALA H 555 " --> pdb=" O ARG H 551 " (cutoff:3.500A) Processing helix chain 'H' and resid 579 through 603 removed outlier: 4.325A pdb=" N LEU H 583 " --> pdb=" O MET H 579 " (cutoff:3.500A) Processing helix chain 'H' and resid 609 through 623 Processing helix chain 'H' and resid 624 through 645 removed outlier: 3.702A pdb=" N LEU H 645 " --> pdb=" O GLN H 641 " (cutoff:3.500A) Processing helix chain 'H' and resid 652 through 679 Processing helix chain 'H' and resid 684 through 708 removed outlier: 3.759A pdb=" N GLN H 708 " --> pdb=" O LEU H 704 " (cutoff:3.500A) Processing helix chain 'H' and resid 717 through 731 Processing helix chain 'H' and resid 737 through 748 removed outlier: 3.544A pdb=" N LEU H 741 " --> pdb=" O PHE H 737 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 350 through 357 removed outlier: 6.644A pdb=" N ASN H 350 " --> pdb=" O PHE H 371 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE H 371 " --> pdb=" O ASN H 350 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N ALA H 352 " --> pdb=" O GLN H 369 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLN H 369 " --> pdb=" O ALA H 352 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N TRP H 354 " --> pdb=" O MET H 367 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N MET H 367 " --> pdb=" O TRP H 354 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N GLU H 356 " --> pdb=" O LEU H 365 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 403 through 404 removed outlier: 3.655A pdb=" N PHE H 415 " --> pdb=" O THR H 404 " (cutoff:3.500A) 2458 hydrogen bonds defined for protein. 7257 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.05 Time building geometry restraints manager: 3.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 6554 1.32 - 1.44: 6957 1.44 - 1.57: 19630 1.57 - 1.69: 6 1.69 - 1.81: 62 Bond restraints: 33209 Sorted by residual: bond pdb=" CA PHE A 948 " pdb=" C PHE A 948 " ideal model delta sigma weight residual 1.522 1.559 -0.037 9.30e-03 1.16e+04 1.61e+01 bond pdb=" CA ASN F 75 " pdb=" C ASN F 75 " ideal model delta sigma weight residual 1.525 1.598 -0.073 2.10e-02 2.27e+03 1.20e+01 bond pdb=" N ASN D 708 " pdb=" CA ASN D 708 " ideal model delta sigma weight residual 1.461 1.429 0.032 9.70e-03 1.06e+04 1.08e+01 bond pdb=" N ASP D 138 " pdb=" CA ASP D 138 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.28e-02 6.10e+03 7.81e+00 bond pdb=" CA VAL D 550 " pdb=" CB VAL D 550 " ideal model delta sigma weight residual 1.540 1.502 0.038 1.36e-02 5.41e+03 7.80e+00 ... (remaining 33204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.68: 45435 5.68 - 11.37: 378 11.37 - 17.05: 64 17.05 - 22.73: 2 22.73 - 28.41: 1 Bond angle restraints: 45880 Sorted by residual: angle pdb=" C ASN B 758 " pdb=" N PRO B 759 " pdb=" CA PRO B 759 " ideal model delta sigma weight residual 127.00 155.41 -28.41 2.40e+00 1.74e-01 1.40e+02 angle pdb=" C ILE A1116 " pdb=" N GLU A1117 " pdb=" CA GLU A1117 " ideal model delta sigma weight residual 121.70 141.13 -19.43 1.80e+00 3.09e-01 1.16e+02 angle pdb=" C ILE F 444 " pdb=" N ASP F 445 " pdb=" CA ASP F 445 " ideal model delta sigma weight residual 121.70 139.70 -18.00 1.80e+00 3.09e-01 1.00e+02 angle pdb=" C ASN D 649 " pdb=" N THR D 650 " pdb=" CA THR D 650 " ideal model delta sigma weight residual 121.70 137.65 -15.95 1.80e+00 3.09e-01 7.85e+01 angle pdb=" C SER F 275 " pdb=" N LYS F 276 " pdb=" CA LYS F 276 " ideal model delta sigma weight residual 121.70 137.51 -15.81 1.80e+00 3.09e-01 7.71e+01 ... (remaining 45875 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.31: 18694 16.31 - 32.62: 976 32.62 - 48.93: 135 48.93 - 65.25: 17 65.25 - 81.56: 16 Dihedral angle restraints: 19838 sinusoidal: 2258 harmonic: 17580 Sorted by residual: dihedral pdb=" CA THR D 261 " pdb=" C THR D 261 " pdb=" N SER D 262 " pdb=" CA SER D 262 " ideal model delta harmonic sigma weight residual 180.00 103.63 76.37 0 5.00e+00 4.00e-02 2.33e+02 dihedral pdb=" CA ASN F 643 " pdb=" C ASN F 643 " pdb=" N ILE F 644 " pdb=" CA ILE F 644 " ideal model delta harmonic sigma weight residual -180.00 -105.66 -74.34 0 5.00e+00 4.00e-02 2.21e+02 dihedral pdb=" CA ASN D 799 " pdb=" C ASN D 799 " pdb=" N TYR D 800 " pdb=" CA TYR D 800 " ideal model delta harmonic sigma weight residual 180.00 -108.51 -71.49 0 5.00e+00 4.00e-02 2.04e+02 ... (remaining 19835 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 5122 0.070 - 0.140: 837 0.140 - 0.210: 118 0.210 - 0.280: 22 0.280 - 0.350: 4 Chirality restraints: 6103 Sorted by residual: chirality pdb=" CA LYS F 276 " pdb=" N LYS F 276 " pdb=" C LYS F 276 " pdb=" CB LYS F 276 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" CA ASN B 940 " pdb=" N ASN B 940 " pdb=" C ASN B 940 " pdb=" CB ASN B 940 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CA GLN D 390 " pdb=" N GLN D 390 " pdb=" C GLN D 390 " pdb=" CB GLN D 390 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.54e+00 ... (remaining 6100 not shown) Planarity restraints: 6402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B 347 " -0.022 2.00e-02 2.50e+03 4.42e-02 1.95e+01 pdb=" C SER B 347 " 0.076 2.00e-02 2.50e+03 pdb=" O SER B 347 " -0.028 2.00e-02 2.50e+03 pdb=" N SER B 348 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS B 592 " -0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C CYS B 592 " 0.073 2.00e-02 2.50e+03 pdb=" O CYS B 592 " -0.028 2.00e-02 2.50e+03 pdb=" N ASN B 593 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN D 708 " -0.017 2.00e-02 2.50e+03 3.45e-02 1.19e+01 pdb=" C ASN D 708 " 0.060 2.00e-02 2.50e+03 pdb=" O ASN D 708 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY D 709 " -0.020 2.00e-02 2.50e+03 ... (remaining 6399 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 5747 2.75 - 3.29: 35306 3.29 - 3.83: 57369 3.83 - 4.36: 64533 4.36 - 4.90: 95229 Nonbonded interactions: 258184 Sorted by model distance: nonbonded pdb=" O LEU H 612 " pdb=" OG1 THR H 616 " model vdw 2.215 3.040 nonbonded pdb=" OH TYR G 589 " pdb=" O TYR G 609 " model vdw 2.232 3.040 nonbonded pdb=" O VAL C 428 " pdb=" OG1 THR C 431 " model vdw 2.242 3.040 nonbonded pdb=" O LEU G 559 " pdb=" OG1 THR G 563 " model vdw 2.252 3.040 nonbonded pdb=" O SER G 572 " pdb=" OG1 THR G 576 " model vdw 2.257 3.040 ... (remaining 258179 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 30.690 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3490 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 : 0.006 0.073 33209 Z= 0.330 Angle : 1.355 28.413 45880 Z= 0.778 Chirality : 0.056 0.350 6103 Planarity : 0.006 0.068 6402 Dihedral : 12.261 81.558 8242 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.69 % Allowed : 17.80 % Favored : 81.51 % Rotamer: Outliers : 0.10 % Allowed : 2.55 % Favored : 97.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 3.03 % Twisted Proline : 6.16 % Twisted General : 2.31 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -6.11 (0.08), residues: 5916 helix: -3.77 (0.05), residues: 3477 sheet: -5.81 (0.86), residues: 10 loop : -4.39 (0.10), residues: 2429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 320 TYR 0.034 0.003 TYR C 558 PHE 0.038 0.003 PHE C 674 TRP 0.038 0.003 TRP C 735 HIS 0.010 0.003 HIS C 581 Details of bonding type rmsd covalent geometry : bond 0.00564 (33209) covalent geometry : angle 1.35495 (45880) hydrogen bonds : bond 0.15927 ( 2458) hydrogen bonds : angle 14.26538 ( 7257) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 231 time to evaluate : 1.341 Fit side-chains TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 471 " (corrupted residue). Skipping it. 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: C 562 ILE cc_start: 0.5629 (mt) cc_final: 0.5293 (mm) REVERT: C 732 LEU cc_start: 0.6803 (mt) cc_final: 0.6542 (mm) REVERT: G 496 LEU cc_start: 0.1876 (mt) cc_final: 0.1345 (mt) REVERT: H 619 MET cc_start: 0.2975 (tpt) cc_final: 0.1933 (ttt) REVERT: H 664 ARG cc_start: 0.8362 (ttm-80) cc_final: 0.8081 (ttp80) REVERT: H 690 LEU cc_start: 0.9308 (tp) cc_final: 0.8878 (tp) outliers start: 1 outliers final: 0 residues processed: 232 average time/residue: 0.1933 time to fit residues: 76.3221 Evaluate side-chains 180 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 394 optimal weight: 20.0000 chunk 430 optimal weight: 10.0000 chunk 41 optimal weight: 30.0000 chunk 265 optimal weight: 20.0000 chunk 523 optimal weight: 4.9990 chunk 497 optimal weight: 6.9990 chunk 414 optimal weight: 20.0000 chunk 310 optimal weight: 30.0000 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 4.9990 chunk 223 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 475 GLN C 484 GLN C 505 ASN C 517 GLN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 625 GLN C 694 GLN C 771 GLN C 777 HIS G 144 GLN G 178 GLN G 190 HIS G 270 HIS G 313 ASN G 331 GLN H 611 HIS ** H 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 634 GLN H 638 ASN ** H 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 708 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.077406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.054300 restraints weight = 409163.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.054227 restraints weight = 396080.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.053866 restraints weight = 387706.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.053899 restraints weight = 378012.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.053946 restraints weight = 363298.218| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 moved from start: 0.4239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.138 33209 Z= 0.340 Angle : 1.107 16.159 45880 Z= 0.631 Chirality : 0.051 0.269 6103 Planarity : 0.007 0.212 6402 Dihedral : 9.889 68.222 6026 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 0.42 % Allowed : 17.06 % Favored : 82.52 % Rotamer: Outliers : 0.51 % Allowed : 3.56 % Favored : 95.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 3.38 % Twisted Proline : 4.11 % Twisted General : 1.14 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.82 (0.09), residues: 5916 helix: -2.42 (0.07), residues: 3642 sheet: -4.88 (0.64), residues: 26 loop : -4.46 (0.11), residues: 2248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.002 ARG G 338 TYR 0.032 0.002 TYR G 566 PHE 0.032 0.002 PHE G 304 TRP 0.046 0.003 TRP C 735 HIS 0.012 0.003 HIS C 581 Details of bonding type rmsd covalent geometry : bond 0.00586 (33209) covalent geometry : angle 1.10744 (45880) hydrogen bonds : bond 0.06788 ( 2458) hydrogen bonds : angle 7.95659 ( 7257) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 187 time to evaluate : 1.340 Fit side-chains TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 471 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ARG C 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 717 MET cc_start: 0.4740 (mmt) cc_final: 0.4037 (mmt) REVERT: G 166 THR cc_start: 0.8882 (p) cc_final: 0.8595 (p) REVERT: G 168 LYS cc_start: 0.9532 (ptpp) cc_final: 0.9181 (tppt) REVERT: G 209 LEU cc_start: 0.6102 (OUTLIER) cc_final: 0.5801 (mt) REVERT: H 693 TRP cc_start: 0.9167 (t60) cc_final: 0.8779 (t60) outliers start: 5 outliers final: 2 residues processed: 191 average time/residue: 0.1678 time to fit residues: 58.5938 Evaluate side-chains 169 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 102 optimal weight: 30.0000 chunk 268 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 129 optimal weight: 20.0000 chunk 376 optimal weight: 40.0000 chunk 338 optimal weight: 0.0980 chunk 378 optimal weight: 5.9990 chunk 572 optimal weight: 50.0000 chunk 321 optimal weight: 8.9990 chunk 512 optimal weight: 7.9990 overall best weight: 5.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 ASN C 581 HIS C 771 GLN G 154 ASN G 263 GLN G 325 GLN ** G 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 ASN ** G 441 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 501 HIS G 602 ASN ** H 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.063982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.044708 restraints weight = 474144.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.044856 restraints weight = 422194.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.044850 restraints weight = 367812.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.044923 restraints weight = 342979.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.044923 restraints weight = 313970.722| |-----------------------------------------------------------------------------| r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6838 moved from start: 0.9061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.133 33209 Z= 0.334 Angle : 1.106 14.908 45880 Z= 0.623 Chirality : 0.052 0.396 6103 Planarity : 0.006 0.138 6402 Dihedral : 9.376 63.185 6026 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 20.16 Ramachandran Plot: Outliers : 0.47 % Allowed : 16.23 % Favored : 83.30 % Rotamer: Outliers : 1.53 % Allowed : 7.43 % Favored : 91.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.34 % Twisted Proline : 2.05 % Twisted General : 1.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.98 (0.10), residues: 5916 helix: -1.72 (0.07), residues: 3678 sheet: -4.17 (1.11), residues: 14 loop : -4.22 (0.12), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG G 206 TYR 0.025 0.003 TYR G 188 PHE 0.041 0.003 PHE G 600 TRP 0.040 0.003 TRP C 735 HIS 0.014 0.003 HIS H 611 Details of bonding type rmsd covalent geometry : bond 0.00605 (33209) covalent geometry : angle 1.10639 (45880) hydrogen bonds : bond 0.07031 ( 2458) hydrogen bonds : angle 7.55362 ( 7257) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 195 time to evaluate : 1.243 Fit side-chains TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 471 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG C 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 717 MET cc_start: 0.5981 (mmt) cc_final: 0.4099 (mmt) REVERT: C 721 MET cc_start: 0.8573 (mmp) cc_final: 0.8266 (mmp) REVERT: H 593 GLU cc_start: 0.9529 (tm-30) cc_final: 0.9309 (mm-30) REVERT: H 619 MET cc_start: 0.9029 (tpt) cc_final: 0.8501 (tpp) REVERT: H 639 PHE cc_start: 0.9872 (t80) cc_final: 0.9568 (t80) outliers start: 15 outliers final: 4 residues processed: 207 average time/residue: 0.1747 time to fit residues: 65.1419 Evaluate side-chains 177 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 173 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 316 optimal weight: 0.0870 chunk 159 optimal weight: 0.0670 chunk 107 optimal weight: 40.0000 chunk 498 optimal weight: 8.9990 chunk 119 optimal weight: 20.0000 chunk 480 optimal weight: 0.6980 chunk 58 optimal weight: 50.0000 chunk 472 optimal weight: 50.0000 chunk 508 optimal weight: 0.9990 chunk 206 optimal weight: 0.9980 chunk 285 optimal weight: 10.0000 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 771 GLN G 89 GLN ** G 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 GLN ** G 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 ASN G 454 GLN G 501 HIS H 627 GLN H 652 ASN H 708 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.065360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.044863 restraints weight = 460412.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.045505 restraints weight = 395524.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.045705 restraints weight = 317265.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.045926 restraints weight = 294647.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.045897 restraints weight = 278327.927| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.9242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 33209 Z= 0.172 Angle : 0.846 14.201 45880 Z= 0.472 Chirality : 0.045 0.217 6103 Planarity : 0.004 0.049 6402 Dihedral : 8.206 63.424 6026 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 12.19 Ramachandran Plot: Outliers : 0.25 % Allowed : 14.44 % Favored : 85.31 % Rotamer: Outliers : 0.31 % Allowed : 1.93 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.41 % Twisted Proline : 2.74 % Twisted General : 0.67 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.74 (0.11), residues: 5916 helix: -0.55 (0.08), residues: 3719 sheet: -5.21 (0.59), residues: 24 loop : -4.14 (0.12), residues: 2173 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 471 TYR 0.035 0.001 TYR G 188 PHE 0.027 0.001 PHE G 474 TRP 0.027 0.001 TRP C 735 HIS 0.017 0.002 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00304 (33209) covalent geometry : angle 0.84628 (45880) hydrogen bonds : bond 0.04971 ( 2458) hydrogen bonds : angle 6.17356 ( 7257) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 190 time to evaluate : 1.325 Fit side-chains TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 471 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG C 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 451 MET cc_start: 0.8616 (pmm) cc_final: 0.8334 (pmm) REVERT: H 563 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8555 (mm-30) REVERT: H 593 GLU cc_start: 0.9452 (tm-30) cc_final: 0.9232 (mm-30) REVERT: H 639 PHE cc_start: 0.9833 (t80) cc_final: 0.9565 (t80) outliers start: 3 outliers final: 1 residues processed: 192 average time/residue: 0.1728 time to fit residues: 59.8562 Evaluate side-chains 173 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 172 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 176 optimal weight: 30.0000 chunk 316 optimal weight: 6.9990 chunk 186 optimal weight: 0.9990 chunk 346 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 101 optimal weight: 4.9990 chunk 195 optimal weight: 20.0000 chunk 167 optimal weight: 20.0000 chunk 166 optimal weight: 9.9990 chunk 558 optimal weight: 30.0000 chunk 497 optimal weight: 1.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 89 GLN ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 240 ASN ** G 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.059533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.042564 restraints weight = 483812.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.042788 restraints weight = 437208.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 18)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.042812 restraints weight = 398863.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.042827 restraints weight = 393722.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.042931 restraints weight = 383198.635| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 1.0553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.105 33209 Z= 0.276 Angle : 0.919 14.176 45880 Z= 0.521 Chirality : 0.047 0.234 6103 Planarity : 0.004 0.102 6402 Dihedral : 8.255 61.995 6026 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.27 % Allowed : 16.65 % Favored : 83.08 % Rotamer: Outliers : 0.31 % Allowed : 3.67 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.39 % Twisted Proline : 0.68 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.75 (0.11), residues: 5916 helix: -0.58 (0.08), residues: 3738 sheet: -3.91 (1.19), residues: 16 loop : -4.14 (0.12), residues: 2162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.002 ARG G 140 TYR 0.025 0.002 TYR G 283 PHE 0.033 0.002 PHE C 674 TRP 0.030 0.002 TRP C 735 HIS 0.008 0.002 HIS G 128 Details of bonding type rmsd covalent geometry : bond 0.00475 (33209) covalent geometry : angle 0.91873 (45880) hydrogen bonds : bond 0.05410 ( 2458) hydrogen bonds : angle 6.17482 ( 7257) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 1.327 Fit side-chains TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 471 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG C 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 271 VAL cc_start: 0.5535 (OUTLIER) cc_final: 0.5312 (t) REVERT: G 393 MET cc_start: 0.4735 (ttt) cc_final: 0.4506 (ttt) REVERT: G 588 MET cc_start: 0.5476 (tpt) cc_final: 0.5202 (tpt) REVERT: H 593 GLU cc_start: 0.9582 (tm-30) cc_final: 0.9381 (mm-30) REVERT: H 639 PHE cc_start: 0.9842 (t80) cc_final: 0.9601 (t80) outliers start: 3 outliers final: 1 residues processed: 182 average time/residue: 0.1613 time to fit residues: 53.6161 Evaluate side-chains 174 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 172 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 411 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 583 optimal weight: 0.9980 chunk 475 optimal weight: 0.9990 chunk 436 optimal weight: 9.9990 chunk 565 optimal weight: 30.0000 chunk 189 optimal weight: 30.0000 chunk 588 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 572 optimal weight: 30.0000 chunk 522 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN ** G 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.060489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.043296 restraints weight = 474541.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.043443 restraints weight = 425671.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.043507 restraints weight = 381228.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.043340 restraints weight = 331497.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.043383 restraints weight = 334348.916| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 1.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 33209 Z= 0.167 Angle : 0.813 14.071 45880 Z= 0.454 Chirality : 0.044 0.219 6103 Planarity : 0.003 0.050 6402 Dihedral : 7.754 61.307 6026 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.24 % Allowed : 14.18 % Favored : 85.58 % Rotamer: Outliers : 0.10 % Allowed : 1.83 % Favored : 98.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.43 % Twisted Proline : 1.37 % Twisted General : 0.50 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.11 (0.11), residues: 5916 helix: 0.02 (0.09), residues: 3714 sheet: -4.90 (0.74), residues: 26 loop : -4.02 (0.12), residues: 2176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 146 TYR 0.024 0.001 TYR G 188 PHE 0.027 0.001 PHE G 474 TRP 0.027 0.001 TRP C 735 HIS 0.004 0.001 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.00288 (33209) covalent geometry : angle 0.81315 (45880) hydrogen bonds : bond 0.04710 ( 2458) hydrogen bonds : angle 5.74444 ( 7257) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.553 Fit side-chains TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 471 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG C 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 393 MET cc_start: 0.4893 (ttt) cc_final: 0.4684 (ttt) REVERT: G 451 MET cc_start: 0.8928 (pmm) cc_final: 0.8693 (pmm) REVERT: G 588 MET cc_start: 0.4973 (tpt) cc_final: 0.4549 (tpt) REVERT: H 619 MET cc_start: 0.8924 (mmt) cc_final: 0.8545 (mmt) REVERT: H 639 PHE cc_start: 0.9834 (t80) cc_final: 0.9564 (t80) outliers start: 1 outliers final: 1 residues processed: 185 average time/residue: 0.1676 time to fit residues: 56.6048 Evaluate side-chains 174 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 173 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 160 optimal weight: 0.5980 chunk 463 optimal weight: 6.9990 chunk 565 optimal weight: 30.0000 chunk 272 optimal weight: 10.0000 chunk 532 optimal weight: 5.9990 chunk 512 optimal weight: 5.9990 chunk 24 optimal weight: 20.0000 chunk 380 optimal weight: 0.0670 chunk 546 optimal weight: 40.0000 chunk 388 optimal weight: 40.0000 chunk 374 optimal weight: 30.0000 overall best weight: 3.9324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 178 GLN G 190 HIS G 342 GLN ** G 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.058532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.042057 restraints weight = 483727.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.042012 restraints weight = 447123.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.041787 restraints weight = 426619.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.041772 restraints weight = 412660.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.041813 restraints weight = 392783.915| |-----------------------------------------------------------------------------| r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 1.1887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 33209 Z= 0.221 Angle : 0.857 14.011 45880 Z= 0.483 Chirality : 0.045 0.265 6103 Planarity : 0.004 0.051 6402 Dihedral : 7.739 62.571 6026 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.20 % Allowed : 16.06 % Favored : 83.74 % Rotamer: Outliers : 0.10 % Allowed : 2.34 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.39 % Twisted Proline : 0.68 % Twisted General : 0.55 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.06 (0.11), residues: 5916 helix: 0.04 (0.09), residues: 3759 sheet: -3.78 (1.54), residues: 13 loop : -4.07 (0.12), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG G 471 TYR 0.024 0.002 TYR G 283 PHE 0.048 0.002 PHE C 689 TRP 0.034 0.002 TRP G 184 HIS 0.006 0.002 HIS G 190 Details of bonding type rmsd covalent geometry : bond 0.00380 (33209) covalent geometry : angle 0.85659 (45880) hydrogen bonds : bond 0.04956 ( 2458) hydrogen bonds : angle 5.71375 ( 7257) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 1.404 Fit side-chains TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET C 471 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ARG C 790 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 393 MET cc_start: 0.5424 (ttt) cc_final: 0.5219 (ttt) REVERT: G 588 MET cc_start: 0.6368 (tpt) cc_final: 0.5970 (tpt) REVERT: H 526 MET cc_start: 0.8792 (ptt) cc_final: 0.8495 (ptt) REVERT: H 563 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8932 (pp20) REVERT: H 619 MET cc_start: 0.9042 (mmt) cc_final: 0.8719 (mmm) REVERT: H 639 PHE cc_start: 0.9812 (t80) cc_final: 0.9528 (t80) REVERT: H 693 TRP cc_start: 0.8999 (t60) cc_final: 0.8737 (t60) outliers start: 1 outliers final: 1 residues processed: 178 average time/residue: 0.1667 time to fit residues: 54.3012 Evaluate side-chains 166 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 147 optimal weight: 30.0000 chunk 102 optimal weight: 30.0000 chunk 364 optimal weight: 20.0000 chunk 528 optimal weight: 5.9990 chunk 448 optimal weight: 9.9990 chunk 447 optimal weight: 20.0000 chunk 255 optimal weight: 5.9990 chunk 480 optimal weight: 50.0000 chunk 46 optimal weight: 50.0000 chunk 3 optimal weight: 6.9990 chunk 323 optimal weight: 20.0000 overall best weight: 9.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 519 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 93 ASN G 105 HIS ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 190 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 290 ASN ** G 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 493 ASN ** G 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 646 GLN H 655 ASN ** H 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.054608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.039051 restraints weight = 508667.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.039119 restraints weight = 477503.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.038626 restraints weight = 428447.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.038652 restraints weight = 442692.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.038680 restraints weight = 407824.121| |-----------------------------------------------------------------------------| r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 1.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.148 33209 Z= 0.421 Angle : 1.092 14.380 45880 Z= 0.629 Chirality : 0.051 0.400 6103 Planarity : 0.006 0.119 6402 Dihedral : 8.841 66.040 6026 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 29.38 Ramachandran Plot: Outliers : 0.27 % Allowed : 18.91 % Favored : 80.81 % Rotamer: Outliers : 0.20 % Allowed : 1.83 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 3.43 % Twisted Proline : 3.42 % Twisted General : 0.79 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.34 (0.10), residues: 5916 helix: -1.19 (0.08), residues: 3771 sheet: -3.71 (1.74), residues: 13 loop : -4.12 (0.12), residues: 2132 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.002 ARG C 687 TYR 0.048 0.003 TYR G 566 PHE 0.059 0.003 PHE C 689 TRP 0.073 0.005 TRP G 184 HIS 0.013 0.004 HIS G 133 Details of bonding type rmsd covalent geometry : bond 0.00711 (33209) covalent geometry : angle 1.09205 (45880) hydrogen bonds : bond 0.07025 ( 2458) hydrogen bonds : angle 6.63024 ( 7257) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 174 time to evaluate : 1.152 Fit side-chains TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 471 " (corrupted residue). Skipping it. 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: C 717 MET cc_start: 0.6336 (mmm) cc_final: 0.5830 (mmt) REVERT: G 393 MET cc_start: 0.6565 (ttt) cc_final: 0.6314 (ttt) REVERT: G 405 ASN cc_start: 0.9502 (m110) cc_final: 0.9299 (p0) REVERT: H 619 MET cc_start: 0.9448 (mmt) cc_final: 0.9137 (mmt) REVERT: H 639 PHE cc_start: 0.9788 (t80) cc_final: 0.9584 (t80) REVERT: H 693 TRP cc_start: 0.9437 (t60) cc_final: 0.9180 (t60) outliers start: 2 outliers final: 2 residues processed: 176 average time/residue: 0.1612 time to fit residues: 51.9984 Evaluate side-chains 156 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 110 optimal weight: 8.9990 chunk 476 optimal weight: 50.0000 chunk 111 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 551 optimal weight: 10.0000 chunk 452 optimal weight: 9.9990 chunk 225 optimal weight: 5.9990 chunk 321 optimal weight: 10.0000 chunk 401 optimal weight: 40.0000 chunk 591 optimal weight: 3.9990 chunk 149 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 102 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 357 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.054216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.038447 restraints weight = 503072.568| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.038596 restraints weight = 472070.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.038453 restraints weight = 421867.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.038518 restraints weight = 416925.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.038406 restraints weight = 422840.107| |-----------------------------------------------------------------------------| r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 1.5335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 33209 Z= 0.286 Angle : 0.931 14.006 45880 Z= 0.529 Chirality : 0.047 0.291 6103 Planarity : 0.004 0.060 6402 Dihedral : 8.308 67.204 6026 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 20.99 Ramachandran Plot: Outliers : 0.24 % Allowed : 16.92 % Favored : 82.84 % Rotamer: Outliers : 0.20 % Allowed : 1.22 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 3.39 % Twisted Proline : 2.05 % Twisted General : 0.71 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.86 (0.11), residues: 5916 helix: -0.73 (0.08), residues: 3804 sheet: -3.72 (1.74), residues: 13 loop : -4.15 (0.12), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 595 TYR 0.024 0.002 TYR G 283 PHE 0.047 0.002 PHE C 689 TRP 0.062 0.004 TRP C 433 HIS 0.009 0.002 HIS G 606 Details of bonding type rmsd covalent geometry : bond 0.00487 (33209) covalent geometry : angle 0.93147 (45880) hydrogen bonds : bond 0.06083 ( 2458) hydrogen bonds : angle 6.18640 ( 7257) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 166 time to evaluate : 1.425 Fit side-chains TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 471 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 430 MET cc_start: 0.4045 (mtp) cc_final: 0.2250 (mtm) REVERT: C 717 MET cc_start: 0.6595 (mmm) cc_final: 0.5681 (mmt) REVERT: G 393 MET cc_start: 0.6239 (ttt) cc_final: 0.5944 (ttt) REVERT: G 581 ILE cc_start: 0.8302 (mt) cc_final: 0.7968 (mt) REVERT: H 619 MET cc_start: 0.9300 (mmt) cc_final: 0.8828 (mmm) REVERT: H 639 PHE cc_start: 0.9784 (t80) cc_final: 0.9528 (t80) REVERT: H 693 TRP cc_start: 0.9000 (t60) cc_final: 0.8721 (t60) outliers start: 2 outliers final: 2 residues processed: 168 average time/residue: 0.1714 time to fit residues: 53.2119 Evaluate side-chains 159 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 157 time to evaluate : 1.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 72 optimal weight: 20.0000 chunk 531 optimal weight: 9.9990 chunk 460 optimal weight: 30.0000 chunk 558 optimal weight: 40.0000 chunk 389 optimal weight: 30.0000 chunk 560 optimal weight: 30.0000 chunk 227 optimal weight: 2.9990 chunk 382 optimal weight: 20.0000 chunk 344 optimal weight: 30.0000 chunk 493 optimal weight: 5.9990 chunk 13 optimal weight: 50.0000 overall best weight: 11.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 643 GLN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 655 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 GLN ** G 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 493 ASN ** G 501 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 611 HIS ** H 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.051996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.037216 restraints weight = 531542.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.037183 restraints weight = 511310.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.037066 restraints weight = 509074.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.036893 restraints weight = 517635.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.036709 restraints weight = 561978.320| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 1.6967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.133 33209 Z= 0.493 Angle : 1.166 19.768 45880 Z= 0.673 Chirality : 0.054 0.402 6103 Planarity : 0.006 0.087 6402 Dihedral : 9.268 70.015 6026 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 35.74 Ramachandran Plot: Outliers : 0.44 % Allowed : 21.30 % Favored : 78.26 % Rotamer: Outliers : 0.10 % Allowed : 0.51 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 3.39 % Twisted Proline : 2.74 % Twisted General : 0.98 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.77 (0.10), residues: 5916 helix: -1.54 (0.08), residues: 3771 sheet: -6.17 (0.75), residues: 10 loop : -4.25 (0.12), residues: 2135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG G 471 TYR 0.048 0.003 TYR G 566 PHE 0.054 0.004 PHE C 719 TRP 0.089 0.005 TRP G 184 HIS 0.016 0.005 HIS G 133 Details of bonding type rmsd covalent geometry : bond 0.00819 (33209) covalent geometry : angle 1.16644 (45880) hydrogen bonds : bond 0.07706 ( 2458) hydrogen bonds : angle 6.98022 ( 7257) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11832 Ramachandran restraints generated. 5916 Oldfield, 0 Emsley, 5916 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 1.387 Fit side-chains TARDY: cannot create tardy model for: "MET B 1 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET C 471 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 430 MET cc_start: 0.4869 (mtp) cc_final: 0.4366 (mtm) REVERT: C 717 MET cc_start: 0.5495 (mmm) cc_final: 0.4943 (mmt) REVERT: G 393 MET cc_start: 0.6607 (ttt) cc_final: 0.5983 (ttt) REVERT: G 550 ARG cc_start: 0.9338 (mpt180) cc_final: 0.9058 (mmp-170) REVERT: H 619 MET cc_start: 0.9545 (mmt) cc_final: 0.9291 (mmt) REVERT: H 693 TRP cc_start: 0.9332 (t60) cc_final: 0.9058 (t60) outliers start: 1 outliers final: 1 residues processed: 163 average time/residue: 0.1651 time to fit residues: 49.4225 Evaluate side-chains 153 residues out of total 5598 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 152 time to evaluate : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 375 optimal weight: 50.0000 chunk 532 optimal weight: 5.9990 chunk 175 optimal weight: 30.0000 chunk 292 optimal weight: 1.9990 chunk 76 optimal weight: 30.0000 chunk 470 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 219 optimal weight: 5.9990 chunk 272 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 432 optimal weight: 9.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 552 GLN C 643 GLN C 651 ASN C 655 ASN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 154 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 GLN ** G 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 618 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.053128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.037804 restraints weight = 502992.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.037730 restraints weight = 466390.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.037679 restraints weight = 419207.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.037653 restraints weight = 398988.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.037653 restraints weight = 372640.333| |-----------------------------------------------------------------------------| r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 1.7064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.085 33209 Z= 0.209 Angle : 0.891 20.179 45880 Z= 0.497 Chirality : 0.046 0.246 6103 Planarity : 0.004 0.072 6402 Dihedral : 8.263 67.896 6026 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 15.75 % Favored : 84.01 % Rotamer: Outliers : 0.20 % Allowed : 0.81 % Favored : 98.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.41 % Twisted Proline : 1.37 % Twisted General : 0.64 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.61 (0.11), residues: 5916 helix: -0.46 (0.08), residues: 3796 sheet: -5.62 (0.84), residues: 21 loop : -4.17 (0.12), residues: 2099 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG G 595 TYR 0.026 0.002 TYR G 283 PHE 0.058 0.002 PHE C 689 TRP 0.046 0.003 TRP G 184 HIS 0.007 0.002 HIS C 522 Details of bonding type rmsd covalent geometry : bond 0.00368 (33209) covalent geometry : angle 0.89134 (45880) hydrogen bonds : bond 0.05812 ( 2458) hydrogen bonds : angle 6.08313 ( 7257) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9140.87 seconds wall clock time: 156 minutes 7.39 seconds (9367.39 seconds total)