Starting phenix.real_space_refine on Fri Mar 22 13:03:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yfp_6827/03_2024/5yfp_6827.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yfp_6827/03_2024/5yfp_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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yfp_6827/03_2024/5yfp_6827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yfp_6827/03_2024/5yfp_6827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yfp_6827/03_2024/5yfp_6827.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5yfp_6827/03_2024/5yfp_6827.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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 Residue "G PHE 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/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: {'GLN:plan1': 33, 'HIS:plan': 12, 'TYR:plan': 19, 'ASN:plan1': 50, 'TRP:plan': 9, 'ASP:plan': 39, 'PHE:plan': 31, 'GLU:plan': 66, 'ARG:plan': 24} 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: {'GLN:plan1': 55, 'HIS:plan': 11, 'TYR:plan': 31, 'ASN:plan1': 83, 'TRP:plan': 10, 'ASP:plan': 48, 'PHE:plan': 50, 'GLU:plan': 61, 'ARG:plan': 32} 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: {'GLN:plan1': 16, 'HIS:plan': 8, 'GLN%COO:oxt': 1, 'TYR:plan': 18, 'ASN:plan1': 23, 'TRP:plan': 2, 'ASP:plan': 31, 'PHE:plan': 16, 'GLU:plan': 49, 'ARG:plan': 23} 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: {'GLN:plan1': 43, 'ASP:plan': 46, 'TYR:plan': 23, 'ASN:plan1': 95, 'TRP:plan': 8, 'HIS:plan': 24, 'PHE:plan': 52, 'GLU:plan': 69, 'ARG:plan': 28} 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: {'GLN:plan1': 33, 'ARG:plan': 21, 'TYR:plan': 24, 'ASN:plan1': 60, 'TRP:plan': 5, 'ASP:plan': 43, 'PHE:plan': 40, 'GLU:plan': 59, 'HIS:plan': 13} 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: {'GLN:plan1': 32, 'ARG:plan': 23, 'TYR:plan': 24, 'ASN:plan1': 50, 'TRP:plan': 5, 'ASP:plan': 49, 'PHE:plan': 48, 'GLU:plan': 60, 'HIS:plan': 8} 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: {'GLN:plan1': 5, 'TYR:plan': 1, 'ASN:plan1': 8, 'ASP:plan': 3, 'PHE:plan': 4, 'GLU:plan': 8, 'ARG:plan': 3} 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: {'GLN:plan1': 17, 'ARG:plan': 21, 'TYR:plan': 4, 'ASN:plan1': 28, 'TRP:plan': 2, 'HIS:plan': 4, 'PHE:plan': 13, 'GLU:plan': 20, 'ASP:plan': 23} Unresolved non-hydrogen planarities: 550 Time building chain proxies: 18.60, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 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: 14.43 Conformation dependent library (CDL) restraints added in 8.0 seconds 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: 3.72 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: 12.62 Time building geometry restraints manager: 15.41 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: 95.29 - 107.32: 569 107.32 - 119.34: 27202 119.34 - 131.36: 17995 131.36 - 143.39: 113 143.39 - 155.41: 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 2.440 nonbonded pdb=" OH TYR G 589 " pdb=" O TYR G 609 " model vdw 2.232 2.440 nonbonded pdb=" O VAL C 428 " pdb=" OG1 THR C 431 " model vdw 2.242 2.440 nonbonded pdb=" O LEU G 559 " pdb=" OG1 THR G 563 " model vdw 2.252 2.440 nonbonded pdb=" O SER G 572 " pdb=" OG1 THR G 576 " model vdw 2.257 2.440 ... (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 ========== 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: 2.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.220 Construct map_model_manager: 0.020 Extract box with map and model: 11.600 Check model and map are aligned: 0.540 Set scattering table: 0.330 Process input model: 91.670 Find NCS groups from input model: 1.950 Set up NCS constraints: 0.190 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.440 ------------------------------------------------------------------------------- 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= 0.390 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 : 17.82 % Favored : 81.49 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.038 0.003 TRP C 735 HIS 0.010 0.003 HIS C 581 PHE 0.038 0.003 PHE C 674 TYR 0.034 0.003 TYR C 558 ARG 0.011 0.001 ARG G 320 *********************** 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 fitting. rotamer outliers: 1 poor density : 231 time to evaluate : 3.919 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: 0.4276 time to fit residues: 170.2306 Evaluate side-chains 180 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 3.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 501 optimal weight: 0.7980 chunk 450 optimal weight: 0.8980 chunk 249 optimal weight: 9.9990 chunk 153 optimal weight: 20.0000 chunk 303 optimal weight: 7.9990 chunk 240 optimal weight: 50.0000 chunk 465 optimal weight: 0.7980 chunk 180 optimal weight: 30.0000 chunk 283 optimal weight: 30.0000 chunk 346 optimal weight: 1.9990 chunk 539 optimal weight: 0.0670 overall best weight: 0.9120 ------------------------------------------------------------------------------- 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 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 594 GLN C 625 GLN C 655 ASN C 694 GLN C 771 GLN G 178 GLN G 270 HIS ** G 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 634 GLN ** H 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3512 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.099 33209 Z= 0.238 Angle : 0.902 14.816 45880 Z= 0.511 Chirality : 0.045 0.246 6103 Planarity : 0.005 0.074 6402 Dihedral : 9.448 65.981 6026 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 15.23 Ramachandran Plot: Outliers : 0.39 % Allowed : 16.13 % Favored : 83.49 % Rotamer: Outliers : 0.20 % Allowed : 2.65 % Favored : 97.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.16 % Cis-general : 3.36 % Twisted Proline : 3.42 % Twisted General : 0.98 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.52 (0.09), residues: 5916 helix: -2.17 (0.07), residues: 3572 sheet: -5.87 (0.79), residues: 10 loop : -4.32 (0.11), residues: 2334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 735 HIS 0.014 0.002 HIS G 606 PHE 0.017 0.001 PHE C 445 TYR 0.033 0.002 TYR G 188 ARG 0.029 0.001 ARG G 338 *********************** 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 195 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 193 time to evaluate : 4.366 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: C 553 MET cc_start: -0.0039 (mmt) cc_final: -0.0281 (mmt) REVERT: C 721 MET cc_start: 0.6846 (mmt) cc_final: 0.6449 (mmp) REVERT: G 166 THR cc_start: 0.8718 (p) cc_final: 0.8452 (p) REVERT: G 168 LYS cc_start: 0.9419 (ptpp) cc_final: 0.9130 (tppt) REVERT: H 690 LEU cc_start: 0.8920 (tp) cc_final: 0.8616 (tp) outliers start: 2 outliers final: 0 residues processed: 195 average time/residue: 0.3843 time to fit residues: 133.5826 Evaluate side-chains 167 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 167 time to evaluate : 4.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 299 optimal weight: 20.0000 chunk 167 optimal weight: 30.0000 chunk 448 optimal weight: 20.0000 chunk 367 optimal weight: 8.9990 chunk 148 optimal weight: 9.9990 chunk 540 optimal weight: 4.9990 chunk 583 optimal weight: 5.9990 chunk 481 optimal weight: 9.9990 chunk 535 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 433 optimal weight: 0.1980 overall best weight: 3.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 436 ASN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 777 HIS G 105 HIS G 144 GLN ** G 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 GLN G 342 GLN G 424 ASN G 501 HIS H 611 HIS ** H 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 638 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 666 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 708 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3744 moved from start: 0.5802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.260 33209 Z= 0.370 Angle : 1.000 21.799 45880 Z= 0.559 Chirality : 0.051 1.372 6103 Planarity : 0.006 0.171 6402 Dihedral : 8.564 62.908 6026 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 22.68 Ramachandran Plot: Outliers : 0.37 % Allowed : 16.43 % Favored : 83.20 % Rotamer: Outliers : 1.12 % Allowed : 5.09 % Favored : 93.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.39 % Twisted Proline : 2.05 % Twisted General : 0.79 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.42 (0.10), residues: 5916 helix: -1.11 (0.08), residues: 3683 sheet: -4.91 (0.62), residues: 26 loop : -4.32 (0.12), residues: 2207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP G 184 HIS 0.007 0.002 HIS C 581 PHE 0.028 0.002 PHE G 149 TYR 0.040 0.002 TYR G 174 ARG 0.029 0.002 ARG G 378 *********************** 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 194 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 183 time to evaluate : 3.952 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: C 721 MET cc_start: 0.6073 (mmt) cc_final: 0.5550 (mmp) REVERT: G 166 THR cc_start: 0.8555 (p) cc_final: 0.8253 (p) REVERT: G 168 LYS cc_start: 0.9360 (ptpp) cc_final: 0.9051 (tppt) REVERT: H 556 VAL cc_start: 0.6426 (t) cc_final: 0.5854 (t) REVERT: H 639 PHE cc_start: 0.8998 (t80) cc_final: 0.8775 (t80) REVERT: H 672 VAL cc_start: 0.8025 (t) cc_final: 0.7710 (t) REVERT: H 675 PHE cc_start: 0.8010 (t80) cc_final: 0.7691 (t80) REVERT: H 690 LEU cc_start: 0.8855 (tp) cc_final: 0.8324 (tp) outliers start: 11 outliers final: 0 residues processed: 192 average time/residue: 0.3654 time to fit residues: 127.6237 Evaluate side-chains 164 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 3.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 533 optimal weight: 2.9990 chunk 406 optimal weight: 50.0000 chunk 280 optimal weight: 0.4980 chunk 59 optimal weight: 50.0000 chunk 257 optimal weight: 20.0000 chunk 362 optimal weight: 20.0000 chunk 542 optimal weight: 6.9990 chunk 574 optimal weight: 0.7980 chunk 283 optimal weight: 40.0000 chunk 513 optimal weight: 6.9990 chunk 154 optimal weight: 7.9990 overall best weight: 3.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 517 GLN ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN G 190 HIS G 199 GLN ** G 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 325 GLN ** G 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 638 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3796 moved from start: 0.7165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 33209 Z= 0.269 Angle : 0.869 14.072 45880 Z= 0.487 Chirality : 0.045 0.290 6103 Planarity : 0.004 0.120 6402 Dihedral : 7.965 59.794 6026 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.95 Ramachandran Plot: Outliers : 0.29 % Allowed : 14.99 % Favored : 84.72 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.39 % Twisted Proline : 1.37 % Twisted General : 0.55 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.11), residues: 5916 helix: -0.38 (0.08), residues: 3680 sheet: -4.72 (0.69), residues: 24 loop : -4.07 (0.12), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 735 HIS 0.016 0.002 HIS G 128 PHE 0.021 0.002 PHE H 552 TYR 0.027 0.001 TYR G 566 ARG 0.023 0.001 ARG G 471 *********************** 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 174 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 174 time to evaluate : 4.032 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: H 556 VAL cc_start: 0.7186 (t) cc_final: 0.6883 (t) REVERT: H 672 VAL cc_start: 0.8013 (t) cc_final: 0.7755 (t) REVERT: H 675 PHE cc_start: 0.6995 (t80) cc_final: 0.6434 (t80) REVERT: H 690 LEU cc_start: 0.8792 (tp) cc_final: 0.8293 (tp) outliers start: 0 outliers final: 0 residues processed: 174 average time/residue: 0.3427 time to fit residues: 110.7709 Evaluate side-chains 162 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 3.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 478 optimal weight: 20.0000 chunk 325 optimal weight: 20.0000 chunk 8 optimal weight: 10.0000 chunk 427 optimal weight: 20.0000 chunk 236 optimal weight: 4.9990 chunk 489 optimal weight: 30.0000 chunk 396 optimal weight: 50.0000 chunk 0 optimal weight: 30.0000 chunk 293 optimal weight: 9.9990 chunk 515 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 overall best weight: 9.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 550 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 736 GLN G 199 GLN ** G 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 708 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 726 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3937 moved from start: 1.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.207 33209 Z= 0.518 Angle : 1.138 20.400 45880 Z= 0.651 Chirality : 0.052 0.489 6103 Planarity : 0.006 0.084 6402 Dihedral : 8.991 64.714 6026 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 36.72 Ramachandran Plot: Outliers : 0.63 % Allowed : 19.73 % Favored : 79.65 % Rotamer: Outliers : 0.41 % Allowed : 5.40 % Favored : 94.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.39 % Twisted Proline : 1.37 % Twisted General : 0.72 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.62 (0.10), residues: 5916 helix: -1.38 (0.08), residues: 3687 sheet: -3.72 (1.31), residues: 12 loop : -4.21 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP G 184 HIS 0.015 0.003 HIS H 611 PHE 0.034 0.002 PHE H 552 TYR 0.030 0.003 TYR G 566 ARG 0.134 0.005 ARG G 140 *********************** 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 179 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 175 time to evaluate : 3.792 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: G 393 MET cc_start: 0.6845 (ttt) cc_final: 0.6625 (ttt) REVERT: H 593 GLU cc_start: 0.9290 (tm-30) cc_final: 0.9077 (mm-30) REVERT: H 639 PHE cc_start: 0.9104 (t80) cc_final: 0.8888 (t80) REVERT: H 675 PHE cc_start: 0.7748 (t80) cc_final: 0.7402 (t80) outliers start: 4 outliers final: 3 residues processed: 179 average time/residue: 0.3441 time to fit residues: 114.1238 Evaluate side-chains 170 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 167 time to evaluate : 3.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 193 optimal weight: 9.9990 chunk 517 optimal weight: 30.0000 chunk 113 optimal weight: 0.0570 chunk 337 optimal weight: 0.0870 chunk 141 optimal weight: 10.0000 chunk 574 optimal weight: 5.9990 chunk 477 optimal weight: 40.0000 chunk 266 optimal weight: 5.9990 chunk 47 optimal weight: 0.5980 chunk 190 optimal weight: 30.0000 chunk 301 optimal weight: 0.0050 overall best weight: 1.3492 ------------------------------------------------------------------------------- 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 550 ASN C 581 HIS ** C 594 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 ASN G 192 ASN G 199 GLN G 240 ASN ** G 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 454 GLN G 606 HIS ** G 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3925 moved from start: 1.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 33209 Z= 0.219 Angle : 0.846 15.882 45880 Z= 0.469 Chirality : 0.045 0.229 6103 Planarity : 0.004 0.050 6402 Dihedral : 8.054 61.275 6026 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.30 % Allowed : 14.54 % Favored : 85.16 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.39 % Twisted Proline : 1.37 % Twisted General : 0.57 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.11), residues: 5916 helix: -0.06 (0.09), residues: 3699 sheet: -3.49 (1.36), residues: 12 loop : -4.00 (0.13), residues: 2205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 735 HIS 0.004 0.001 HIS G 468 PHE 0.022 0.002 PHE H 675 TYR 0.031 0.002 TYR G 566 ARG 0.009 0.001 ARG G 595 *********************** 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 181 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 3.721 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: C 644 MET cc_start: 0.0083 (tpt) cc_final: -0.0323 (tpt) REVERT: C 685 MET cc_start: 0.6878 (mmp) cc_final: 0.6555 (mmp) REVERT: H 556 VAL cc_start: 0.8025 (t) cc_final: 0.7677 (t) REVERT: H 593 GLU cc_start: 0.9139 (tm-30) cc_final: 0.8871 (mm-30) outliers start: 0 outliers final: 0 residues processed: 181 average time/residue: 0.3417 time to fit residues: 114.7566 Evaluate side-chains 171 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 3.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 554 optimal weight: 50.0000 chunk 64 optimal weight: 50.0000 chunk 327 optimal weight: 20.0000 chunk 419 optimal weight: 9.9990 chunk 325 optimal weight: 20.0000 chunk 483 optimal weight: 6.9990 chunk 320 optimal weight: 8.9990 chunk 572 optimal weight: 30.0000 chunk 358 optimal weight: 20.0000 chunk 349 optimal weight: 9.9990 chunk 264 optimal weight: 20.0000 overall best weight: 11.1992 ------------------------------------------------------------------------------- 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** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 192 ASN G 199 GLN G 290 ASN ** G 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 748 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3988 moved from start: 1.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.124 33209 Z= 0.561 Angle : 1.174 22.228 45880 Z= 0.679 Chirality : 0.054 0.343 6103 Planarity : 0.007 0.079 6402 Dihedral : 9.227 68.571 6026 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 43.75 Ramachandran Plot: Outliers : 0.90 % Allowed : 21.06 % Favored : 78.04 % Rotamer: Outliers : 0.20 % Allowed : 3.56 % Favored : 96.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.39 % Twisted Proline : 2.05 % Twisted General : 0.88 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.57 (0.10), residues: 5916 helix: -1.34 (0.08), residues: 3677 sheet: None (None), residues: 0 loop : -4.18 (0.12), residues: 2239 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP C 735 HIS 0.023 0.004 HIS G 133 PHE 0.043 0.003 PHE G 216 TYR 0.033 0.003 TYR G 566 ARG 0.018 0.002 ARG G 320 *********************** 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 fitting. rotamer outliers: 2 poor density : 176 time to evaluate : 3.981 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: C 553 MET cc_start: 0.0633 (mmt) cc_final: 0.0421 (mmt) REVERT: C 685 MET cc_start: 0.7606 (mmp) cc_final: 0.7338 (mmp) REVERT: C 717 MET cc_start: 0.2836 (mmp) cc_final: 0.2060 (mmp) REVERT: G 495 MET cc_start: 0.7993 (mmp) cc_final: 0.7629 (tpp) REVERT: G 581 ILE cc_start: 0.6591 (mt) cc_final: 0.6317 (mt) REVERT: G 588 MET cc_start: 0.3281 (tpt) cc_final: 0.3057 (tpt) REVERT: H 593 GLU cc_start: 0.9451 (tm-30) cc_final: 0.9178 (mm-30) REVERT: H 693 TRP cc_start: 0.6245 (t60) cc_final: 0.5675 (t60) outliers start: 2 outliers final: 1 residues processed: 178 average time/residue: 0.3668 time to fit residues: 119.9964 Evaluate side-chains 158 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 157 time to evaluate : 3.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 354 optimal weight: 40.0000 chunk 228 optimal weight: 10.0000 chunk 341 optimal weight: 20.0000 chunk 172 optimal weight: 50.0000 chunk 112 optimal weight: 0.6980 chunk 110 optimal weight: 5.9990 chunk 363 optimal weight: 20.0000 chunk 390 optimal weight: 0.1980 chunk 283 optimal weight: 40.0000 chunk 53 optimal weight: 1.9990 chunk 450 optimal weight: 9.9990 overall best weight: 3.7786 ------------------------------------------------------------------------------- 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** G 93 ASN G 199 GLN ** G 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 606 HIS ** G 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 726 GLN H 748 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3995 moved from start: 1.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.104 33209 Z= 0.262 Angle : 0.883 14.043 45880 Z= 0.494 Chirality : 0.046 0.396 6103 Planarity : 0.004 0.065 6402 Dihedral : 8.332 65.086 6026 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 25.68 Ramachandran Plot: Outliers : 0.30 % Allowed : 16.73 % Favored : 82.96 % Rotamer: Outliers : 0.10 % Allowed : 1.63 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.38 % Twisted Proline : 2.05 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.11), residues: 5916 helix: -0.37 (0.08), residues: 3727 sheet: -3.49 (1.73), residues: 11 loop : -4.18 (0.12), residues: 2178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP G 184 HIS 0.005 0.001 HIS G 133 PHE 0.056 0.002 PHE G 474 TYR 0.028 0.002 TYR G 566 ARG 0.007 0.001 ARG G 595 *********************** 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 177 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 176 time to evaluate : 4.135 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 430 MET cc_start: -0.0693 (mtp) cc_final: -0.2548 (mtm) REVERT: C 717 MET cc_start: 0.1964 (mmp) cc_final: 0.1121 (mmt) REVERT: G 588 MET cc_start: 0.3648 (tpt) cc_final: 0.3270 (tpt) REVERT: H 593 GLU cc_start: 0.9331 (tm-30) cc_final: 0.9128 (mm-30) REVERT: H 599 LEU cc_start: 0.8854 (mp) cc_final: 0.8465 (tp) REVERT: H 639 PHE cc_start: 0.9130 (t80) cc_final: 0.8895 (t80) REVERT: H 693 TRP cc_start: 0.5284 (t60) cc_final: 0.4944 (t60) outliers start: 1 outliers final: 1 residues processed: 177 average time/residue: 0.3528 time to fit residues: 115.8102 Evaluate side-chains 163 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 162 time to evaluate : 4.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 520 optimal weight: 6.9990 chunk 548 optimal weight: 5.9990 chunk 500 optimal weight: 0.7980 chunk 533 optimal weight: 0.8980 chunk 321 optimal weight: 20.0000 chunk 232 optimal weight: 5.9990 chunk 418 optimal weight: 50.0000 chunk 163 optimal weight: 20.0000 chunk 482 optimal weight: 30.0000 chunk 504 optimal weight: 20.0000 chunk 531 optimal weight: 6.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- 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** G 102 GLN ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4037 moved from start: 1.4568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 33209 Z= 0.270 Angle : 0.884 21.295 45880 Z= 0.494 Chirality : 0.046 0.370 6103 Planarity : 0.004 0.092 6402 Dihedral : 7.946 65.320 6026 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 26.92 Ramachandran Plot: Outliers : 0.27 % Allowed : 18.36 % Favored : 81.37 % Rotamer: Outliers : 0.10 % Allowed : 0.81 % Favored : 99.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.39 % Twisted Proline : 0.68 % Twisted General : 0.53 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.11), residues: 5916 helix: 0.04 (0.09), residues: 3751 sheet: -5.09 (0.93), residues: 21 loop : -4.16 (0.13), residues: 2144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP G 184 HIS 0.005 0.001 HIS G 133 PHE 0.042 0.002 PHE G 474 TYR 0.030 0.002 TYR G 283 ARG 0.009 0.001 ARG G 471 *********************** 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 176 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 175 time to evaluate : 4.185 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: C 430 MET cc_start: -0.1486 (mtp) cc_final: -0.2390 (mtm) REVERT: C 685 MET cc_start: 0.7692 (mmp) cc_final: 0.7452 (mmp) REVERT: C 717 MET cc_start: 0.2025 (mmp) cc_final: 0.1569 (mmt) REVERT: G 588 MET cc_start: 0.4426 (tpt) cc_final: 0.3996 (tpt) REVERT: H 599 LEU cc_start: 0.8833 (mp) cc_final: 0.8466 (tp) REVERT: H 639 PHE cc_start: 0.9111 (t80) cc_final: 0.8857 (t80) REVERT: H 672 VAL cc_start: 0.9105 (t) cc_final: 0.8870 (t) REVERT: H 693 TRP cc_start: 0.5220 (t60) cc_final: 0.4874 (t60) outliers start: 1 outliers final: 1 residues processed: 176 average time/residue: 0.3529 time to fit residues: 115.2875 Evaluate side-chains 164 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 163 time to evaluate : 4.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 350 optimal weight: 8.9990 chunk 564 optimal weight: 50.0000 chunk 344 optimal weight: 30.0000 chunk 267 optimal weight: 9.9990 chunk 392 optimal weight: 20.0000 chunk 591 optimal weight: 4.9990 chunk 544 optimal weight: 20.0000 chunk 471 optimal weight: 30.0000 chunk 48 optimal weight: 50.0000 chunk 363 optimal weight: 20.0000 chunk 288 optimal weight: 10.0000 overall best weight: 10.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 ASN ** C 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 713 ASN ** C 736 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 GLN ** G 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 627 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 726 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4036 moved from start: 1.6477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.138 33209 Z= 0.520 Angle : 1.120 21.329 45880 Z= 0.641 Chirality : 0.052 0.504 6103 Planarity : 0.006 0.069 6402 Dihedral : 9.133 65.400 6026 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 43.36 Ramachandran Plot: Outliers : 0.49 % Allowed : 21.84 % Favored : 77.67 % Rotamer: Outliers : 0.10 % Allowed : 0.61 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.38 % Twisted Proline : 2.05 % Twisted General : 0.83 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.10), residues: 5916 helix: -1.16 (0.08), residues: 3720 sheet: None (None), residues: 0 loop : -4.25 (0.12), residues: 2196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.080 0.005 TRP G 184 HIS 0.020 0.004 HIS G 133 PHE 0.057 0.003 PHE G 474 TYR 0.052 0.004 TYR G 566 ARG 0.015 0.002 ARG G 471 ********************** 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 168 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 167 time to evaluate : 3.781 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 430 MET cc_start: 0.3152 (mtp) cc_final: 0.2470 (mtp) REVERT: C 553 MET cc_start: 0.3177 (mmt) cc_final: 0.2965 (mmt) REVERT: C 685 MET cc_start: 0.8488 (mmp) cc_final: 0.8172 (mmp) REVERT: C 717 MET cc_start: 0.4249 (mmp) cc_final: 0.2993 (mmt) REVERT: G 495 MET cc_start: 0.8618 (mmp) cc_final: 0.8164 (tpt) REVERT: G 588 MET cc_start: 0.4842 (tpt) cc_final: 0.4449 (tpt) REVERT: H 639 PHE cc_start: 0.9096 (t80) cc_final: 0.8890 (t80) REVERT: H 693 TRP cc_start: 0.5612 (t60) cc_final: 0.5201 (t60) outliers start: 1 outliers final: 1 residues processed: 168 average time/residue: 0.3546 time to fit residues: 111.1566 Evaluate side-chains 156 residues out of total 5598 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 3.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 594 random chunks: chunk 374 optimal weight: 20.0000 chunk 501 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 chunk 434 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 130 optimal weight: 20.0000 chunk 471 optimal weight: 0.5980 chunk 197 optimal weight: 40.0000 chunk 484 optimal weight: 9.9990 chunk 59 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 424 ASN ** C 651 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 GLN ** G 313 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 601 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 627 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 = 0.3579 r_free = 0.3579 target = 0.053735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.038198 restraints weight = 506024.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.038140 restraints weight = 473839.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.038111 restraints weight = 434285.297| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 1.6552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33209 Z= 0.235 Angle : 0.871 14.182 45880 Z= 0.484 Chirality : 0.046 0.326 6103 Planarity : 0.004 0.082 6402 Dihedral : 8.147 66.313 6026 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 24.83 Ramachandran Plot: Outliers : 0.24 % Allowed : 16.26 % Favored : 83.50 % Rotamer: Outliers : 0.10 % Allowed : 0.51 % Favored : 99.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.85 % Cis-general : 3.41 % Twisted Proline : 1.37 % Twisted General : 0.52 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.11), residues: 5916 helix: -0.11 (0.09), residues: 3726 sheet: -5.94 (0.58), residues: 21 loop : -4.10 (0.12), residues: 2169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP G 184 HIS 0.004 0.001 HIS G 133 PHE 0.039 0.002 PHE G 474 TYR 0.027 0.002 TYR G 283 ARG 0.009 0.001 ARG G 471 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5684.46 seconds wall clock time: 102 minutes 49.08 seconds (6169.08 seconds total)