Starting phenix.real_space_refine on Thu Aug 6 10:54:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7o_41987/08_2026/8u7o_41987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7o_41987/08_2026/8u7o_41987.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u7o_41987/08_2026/8u7o_41987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7o_41987/08_2026/8u7o_41987.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u7o_41987/08_2026/8u7o_41987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7o_41987/08_2026/8u7o_41987.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.017 sd= 0.106 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 65 5.16 5 C 9703 2.51 5 N 2434 2.21 5 O 2722 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14929 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 978, 7227 Classifications: {'peptide': 978} Incomplete info: {'truncation_to_alanine': 135} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 949} Chain breaks: 5 Unresolved non-hydrogen bonds: 518 Unresolved non-hydrogen angles: 654 Unresolved non-hydrogen dihedrals: 417 Unresolved non-hydrogen chiralities: 58 Planarities with less than four sites: {'PHE:plan': 9, 'GLU:plan': 16, 'ASN:plan1': 4, 'ASP:plan': 6, 'ARG:plan': 13, 'TYR:plan': 3, 'HIS:plan': 4, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 269 Chain: "B" Number of atoms: 7248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 981, 7248 Classifications: {'peptide': 981} Incomplete info: {'truncation_to_alanine': 136} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 952} Chain breaks: 5 Unresolved non-hydrogen bonds: 521 Unresolved non-hydrogen angles: 657 Unresolved non-hydrogen dihedrals: 420 Unresolved non-hydrogen chiralities: 57 Planarities with less than four sites: {'PHE:plan': 9, 'GLU:plan': 17, 'ASN:plan1': 5, 'ASP:plan': 6, 'ARG:plan': 13, 'TYR:plan': 3, 'HIS:plan': 4, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 272 Chain: "A" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 134 Unusual residues: {'AJP': 1, 'POV': 1} Classifications: {'RNAv2': 1, 'undetermined': 2} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 320 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 320 Unusual residues: {'AJP': 3, 'POV': 2} Classifications: {'RNAv2': 1, 'undetermined': 5} Modifications used: {'rna3p': 1} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 15 Time building chain proxies: 3.70, per 1000 atoms: 0.25 Number of scatterers: 14929 At special positions: 0 Unit cell: (111.78, 142.14, 133.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 65 16.00 P 5 15.00 O 2722 8.00 N 2434 7.00 C 9703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.43 Conformation dependent library (CDL) restraints added in 573.0 milliseconds 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3690 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 8 sheets defined 73.8% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 77 through 95 Processing helix chain 'A' and resid 102 through 118 removed outlier: 3.677A pdb=" N LEU A 106 " --> pdb=" O TYR A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 134 through 151 removed outlier: 3.939A pdb=" N LEU A 138 " --> pdb=" O ASP A 134 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Proline residue: A 144 - end of helix Processing helix chain 'A' and resid 155 through 161 Processing helix chain 'A' and resid 162 through 189 Processing helix chain 'A' and resid 194 through 207 removed outlier: 3.817A pdb=" N ALA A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 221 Processing helix chain 'A' and resid 224 through 253 removed outlier: 3.700A pdb=" N THR A 228 " --> pdb=" O LYS A 224 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N MET A 251 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 253 " --> pdb=" O MET A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 291 removed outlier: 3.904A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N GLY A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix Processing helix chain 'A' and resid 297 through 319 removed outlier: 3.507A pdb=" N ILE A 301 " --> pdb=" O ALA A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 337 removed outlier: 4.070A pdb=" N LEU A 325 " --> pdb=" O VAL A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 376 Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 381 through 414 removed outlier: 3.955A pdb=" N TRP A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N ILE A 389 " --> pdb=" O TRP A 385 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE A 403 " --> pdb=" O ARG A 399 " (cutoff:3.500A) Proline residue: A 408 - end of helix Processing helix chain 'A' and resid 418 through 427 removed outlier: 4.188A pdb=" N TRP A 427 " --> pdb=" O VAL A 423 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 Processing helix chain 'A' and resid 449 through 482 removed outlier: 4.217A pdb=" N SER A 453 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N VAL A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 482 " --> pdb=" O LEU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 487 through 514 removed outlier: 3.839A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 removed outlier: 3.528A pdb=" N ALA A 526 " --> pdb=" O ASP A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 601 Processing helix chain 'A' and resid 605 through 618 removed outlier: 3.680A pdb=" N ALA A 618 " --> pdb=" O HIS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 636 Processing helix chain 'A' and resid 639 through 652 removed outlier: 4.322A pdb=" N TRP A 643 " --> pdb=" O GLY A 639 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP A 650 " --> pdb=" O ARG A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 692 Processing helix chain 'A' and resid 694 through 700 Processing helix chain 'A' and resid 730 through 753 Processing helix chain 'A' and resid 761 through 774 removed outlier: 3.886A pdb=" N PHE A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 858 Proline residue: A 819 - end of helix removed outlier: 3.565A pdb=" N GLN A 832 " --> pdb=" O LYS A 828 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ILE A 853 " --> pdb=" O GLU A 849 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ASP A 855 " --> pdb=" O GLY A 851 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N MET A 857 " --> pdb=" O ILE A 853 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N VAL A 858 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 889 removed outlier: 3.882A pdb=" N LYS A 880 " --> pdb=" O LEU A 876 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLU A 881 " --> pdb=" O GLN A 877 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N HIS A 889 " --> pdb=" O LEU A 885 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 919 removed outlier: 3.536A pdb=" N VAL A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ILE A 902 " --> pdb=" O THR A 898 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A 903 " --> pdb=" O ARG A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 943 removed outlier: 3.915A pdb=" N THR A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL A 934 " --> pdb=" O LEU A 930 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 954 through 962 removed outlier: 3.995A pdb=" N TRP A 962 " --> pdb=" O LYS A 958 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 975 Processing helix chain 'A' and resid 1044 through 1049 removed outlier: 3.603A pdb=" N LEU A1048 " --> pdb=" O GLU A1044 " (cutoff:3.500A) Processing helix chain 'A' and resid 1070 through 1080 removed outlier: 3.577A pdb=" N PHE A1080 " --> pdb=" O ALA A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1100 Processing helix chain 'A' and resid 1100 through 1105 removed outlier: 3.920A pdb=" N MET A1104 " --> pdb=" O THR A1100 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLU A1105 " --> pdb=" O PRO A1101 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1100 through 1105' Processing helix chain 'A' and resid 1113 through 1121 Processing helix chain 'B' and resid 77 through 95 Processing helix chain 'B' and resid 102 through 118 removed outlier: 3.666A pdb=" N LEU B 106 " --> pdb=" O TYR B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.984A pdb=" N HIS B 132 " --> pdb=" O ARG B 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 134 through 151 removed outlier: 3.827A pdb=" N LEU B 138 " --> pdb=" O ASP B 134 " (cutoff:3.500A) removed outlier: 5.089A pdb=" N LEU B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Proline residue: B 144 - end of helix Processing helix chain 'B' and resid 155 through 161 Processing helix chain 'B' and resid 162 through 189 Processing helix chain 'B' and resid 194 through 207 removed outlier: 3.724A pdb=" N ALA B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 224 through 254 removed outlier: 3.714A pdb=" N THR B 228 " --> pdb=" O LYS B 224 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE B 254 " --> pdb=" O LYS B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 291 removed outlier: 3.919A pdb=" N LEU B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N GLY B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix Processing helix chain 'B' and resid 297 through 319 removed outlier: 3.520A pdb=" N ILE B 301 " --> pdb=" O ALA B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 337 removed outlier: 4.010A pdb=" N LEU B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 376 Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 381 through 414 removed outlier: 3.983A pdb=" N TRP B 385 " --> pdb=" O ASP B 381 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE B 389 " --> pdb=" O TRP B 385 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 403 " --> pdb=" O ARG B 399 " (cutoff:3.500A) Proline residue: B 408 - end of helix Processing helix chain 'B' and resid 418 through 427 removed outlier: 4.067A pdb=" N TRP B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 445 Processing helix chain 'B' and resid 449 through 482 removed outlier: 4.224A pdb=" N SER B 453 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY B 482 " --> pdb=" O LEU B 478 " (cutoff:3.500A) Processing helix chain 'B' and resid 487 through 514 removed outlier: 3.793A pdb=" N SER B 514 " --> pdb=" O ASN B 510 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 530 removed outlier: 3.529A pdb=" N ALA B 526 " --> pdb=" O ASP B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 601 Processing helix chain 'B' and resid 605 through 618 removed outlier: 3.602A pdb=" N ALA B 618 " --> pdb=" O HIS B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 636 Processing helix chain 'B' and resid 639 through 652 removed outlier: 4.363A pdb=" N TRP B 643 " --> pdb=" O GLY B 639 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP B 650 " --> pdb=" O ARG B 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 691 Processing helix chain 'B' and resid 691 through 700 removed outlier: 3.596A pdb=" N ILE B 695 " --> pdb=" O ASN B 691 " (cutoff:3.500A) Processing helix chain 'B' and resid 730 through 753 Processing helix chain 'B' and resid 754 through 756 No H-bonds generated for 'chain 'B' and resid 754 through 756' Processing helix chain 'B' and resid 763 through 774 removed outlier: 4.139A pdb=" N ASP B 767 " --> pdb=" O TRP B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 808 through 812 removed outlier: 4.516A pdb=" N LEU B 811 " --> pdb=" O LEU B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 813 through 852 Proline residue: B 819 - end of helix removed outlier: 3.763A pdb=" N ILE B 822 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY B 827 " --> pdb=" O LEU B 823 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N GLN B 832 " --> pdb=" O LYS B 828 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LYS B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 853 through 858 removed outlier: 3.539A pdb=" N MET B 857 " --> pdb=" O ILE B 853 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 858 " --> pdb=" O ILE B 854 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 853 through 858' Processing helix chain 'B' and resid 860 through 889 removed outlier: 3.568A pdb=" N LYS B 880 " --> pdb=" O LEU B 876 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 881 " --> pdb=" O GLN B 877 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS B 889 " --> pdb=" O LEU B 885 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 919 removed outlier: 3.533A pdb=" N VAL B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE B 902 " --> pdb=" O THR B 898 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG B 903 " --> pdb=" O ARG B 899 " (cutoff:3.500A) Processing helix chain 'B' and resid 923 through 943 removed outlier: 3.893A pdb=" N THR B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N VAL B 934 " --> pdb=" O LEU B 930 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 954 through 962 removed outlier: 4.042A pdb=" N TRP B 962 " --> pdb=" O LYS B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 975 Processing helix chain 'B' and resid 1044 through 1049 Processing helix chain 'B' and resid 1070 through 1080 removed outlier: 3.600A pdb=" N PHE B1080 " --> pdb=" O ALA B1076 " (cutoff:3.500A) Processing helix chain 'B' and resid 1084 through 1100 Processing helix chain 'B' and resid 1100 through 1105 removed outlier: 3.848A pdb=" N MET B1104 " --> pdb=" O THR B1100 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLU B1105 " --> pdb=" O PRO B1101 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 1100 through 1105' Processing helix chain 'B' and resid 1113 through 1121 Processing sheet with id=AA1, first strand: chain 'A' and resid 980 through 982 removed outlier: 6.500A pdb=" N TYR A1066 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ILE A1001 " --> pdb=" O TYR A1066 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ILE A1068 " --> pdb=" O PHE A 999 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE A 999 " --> pdb=" O ILE A1068 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 987 through 989 removed outlier: 6.682A pdb=" N VAL A 987 " --> pdb=" O CYS A1059 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N CYS A1059 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N VAL A 989 " --> pdb=" O VAL A1057 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL A1057 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 1124 through 1126 removed outlier: 6.815A pdb=" N PHE A1187 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 5.613A pdb=" N LEU A1147 " --> pdb=" O PHE A1187 " (cutoff:3.500A) removed outlier: 7.518A pdb=" N VAL A1189 " --> pdb=" O VAL A1145 " (cutoff:3.500A) removed outlier: 5.600A pdb=" N VAL A1145 " --> pdb=" O VAL A1189 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LEU A1147 " --> pdb=" O CYS A1165 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N CYS A1165 " --> pdb=" O LEU A1147 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1135 through 1137 Processing sheet with id=AA5, first strand: chain 'B' and resid 980 through 982 removed outlier: 6.477A pdb=" N TYR B1066 " --> pdb=" O ILE B1001 " (cutoff:3.500A) removed outlier: 5.788A pdb=" N ILE B1001 " --> pdb=" O TYR B1066 " (cutoff:3.500A) removed outlier: 7.478A pdb=" N ILE B1068 " --> pdb=" O PHE B 999 " (cutoff:3.500A) removed outlier: 5.198A pdb=" N PHE B 999 " --> pdb=" O ILE B1068 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 987 through 989 removed outlier: 3.888A pdb=" N ILE B 988 " --> pdb=" O VAL B1057 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N VAL B1057 " --> pdb=" O ILE B 988 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 1124 through 1126 removed outlier: 6.041A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N LEU B1147 " --> pdb=" O CYS B1165 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N CYS B1165 " --> pdb=" O LEU B1147 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 1135 through 1137 1067 hydrogen bonds defined for protein. 3171 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: 2.97 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2544 1.33 - 1.45: 3738 1.45 - 1.57: 8830 1.57 - 1.69: 8 1.69 - 1.81: 118 Bond restraints: 15238 Sorted by residual: bond pdb=" C26 AJP B1404 " pdb=" O25 AJP B1404 " ideal model delta sigma weight residual 1.375 1.413 -0.038 2.00e-02 2.50e+03 3.59e+00 bond pdb=" C26 AJP B1403 " pdb=" O25 AJP B1403 " ideal model delta sigma weight residual 1.375 1.412 -0.037 2.00e-02 2.50e+03 3.47e+00 bond pdb=" C26 AJP B1405 " pdb=" O25 AJP B1405 " ideal model delta sigma weight residual 1.375 1.412 -0.037 2.00e-02 2.50e+03 3.45e+00 bond pdb=" C45 AJP B1404 " pdb=" O44 AJP B1404 " ideal model delta sigma weight residual 1.375 1.410 -0.035 2.00e-02 2.50e+03 3.14e+00 bond pdb=" C45 AJP B1405 " pdb=" O44 AJP B1405 " ideal model delta sigma weight residual 1.375 1.410 -0.035 2.00e-02 2.50e+03 3.03e+00 ... (remaining 15233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.07: 20456 2.07 - 4.14: 291 4.14 - 6.20: 48 6.20 - 8.27: 16 8.27 - 10.34: 9 Bond angle restraints: 20820 Sorted by residual: angle pdb=" C1' CMP B1406 " pdb=" C2' CMP B1406 " pdb=" C3' CMP B1406 " ideal model delta sigma weight residual 111.00 100.66 10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" C1' CMP A1403 " pdb=" C2' CMP A1403 " pdb=" C3' CMP A1403 " ideal model delta sigma weight residual 111.00 100.66 10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" O1P CMP B1406 " pdb=" P CMP B1406 " pdb=" O2P CMP B1406 " ideal model delta sigma weight residual 109.50 118.76 -9.26 3.00e+00 1.11e-01 9.53e+00 angle pdb=" O1P CMP A1403 " pdb=" P CMP A1403 " pdb=" O2P CMP A1403 " ideal model delta sigma weight residual 109.50 118.75 -9.25 3.00e+00 1.11e-01 9.52e+00 angle pdb=" C2' CMP B1406 " pdb=" C3' CMP B1406 " pdb=" C4' CMP B1406 " ideal model delta sigma weight residual 111.00 101.78 9.22 3.00e+00 1.11e-01 9.44e+00 ... (remaining 20815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.89: 9037 24.89 - 49.79: 387 49.79 - 74.68: 65 74.68 - 99.58: 20 99.58 - 124.47: 105 Dihedral angle restraints: 9614 sinusoidal: 3926 harmonic: 5688 Sorted by residual: dihedral pdb=" O31 AJP B1404 " pdb=" C30 AJP B1404 " pdb=" C32 AJP B1404 " pdb=" O33 AJP B1404 " ideal model delta sinusoidal sigma weight residual 177.28 52.81 124.47 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C45 AJP A1402 " pdb=" C49 AJP A1402 " pdb=" O50 AJP A1402 " pdb=" C48 AJP A1402 " ideal model delta sinusoidal sigma weight residual -62.82 61.40 -124.22 1 3.00e+01 1.11e-03 1.67e+01 dihedral pdb=" C46 AJP A1402 " pdb=" C45 AJP A1402 " pdb=" O50 AJP A1402 " pdb=" C49 AJP A1402 " ideal model delta sinusoidal sigma weight residual -62.83 60.12 -122.95 1 3.00e+01 1.11e-03 1.65e+01 ... (remaining 9611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 2127 0.055 - 0.110: 431 0.110 - 0.166: 27 0.166 - 0.221: 6 0.221 - 0.276: 8 Chirality restraints: 2599 Sorted by residual: chirality pdb=" C2' CMP B1406 " pdb=" C1' CMP B1406 " pdb=" C3' CMP B1406 " pdb=" O2' CMP B1406 " both_signs ideal model delta sigma weight residual False -2.51 -2.79 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" C2' CMP A1403 " pdb=" C1' CMP A1403 " pdb=" C3' CMP A1403 " pdb=" O2' CMP A1403 " both_signs ideal model delta sigma weight residual False -2.51 -2.78 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" C22 AJP B1404 " pdb=" C21 AJP B1404 " pdb=" C23 AJP B1404 " pdb=" O79 AJP B1404 " both_signs ideal model delta sigma weight residual False 2.47 2.23 0.24 2.00e-01 2.50e+01 1.47e+00 ... (remaining 2596 not shown) Planarity restraints: 2529 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 138 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C LEU B 138 " -0.029 2.00e-02 2.50e+03 pdb=" O LEU B 138 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU B 139 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 138 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C LEU A 138 " 0.028 2.00e-02 2.50e+03 pdb=" O LEU A 138 " -0.011 2.00e-02 2.50e+03 pdb=" N LEU A 139 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 944 " 0.026 5.00e-02 4.00e+02 3.94e-02 2.48e+00 pdb=" N PRO A 945 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO A 945 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 945 " 0.022 5.00e-02 4.00e+02 ... (remaining 2526 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1768 2.75 - 3.29: 15040 3.29 - 3.83: 24475 3.83 - 4.36: 24606 4.36 - 4.90: 44195 Nonbonded interactions: 110084 Sorted by model distance: nonbonded pdb=" O62 AJP B1403 " pdb=" O63 AJP B1403 " model vdw 2.218 3.040 nonbonded pdb=" O42 AJP A1402 " pdb=" O52 AJP A1402 " model vdw 2.268 3.040 nonbonded pdb=" O32 POV B1402 " pdb=" O79 AJP B1405 " model vdw 2.270 3.040 nonbonded pdb=" O32 POV A1401 " pdb=" O79 AJP B1403 " model vdw 2.306 3.040 nonbonded pdb=" OG1 THR B 208 " pdb=" O LEU B 430 " model vdw 2.319 3.040 ... (remaining 110079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 76 through 382 or (resid 383 and (name N or name CA or nam \ e C or name O or name CB )) or resid 384 through 652 or resid 678 through 690 or \ (resid 691 through 693 and (name N or name CA or name C or name O or name CB )) \ or resid 694 through 1076 or (resid 1077 through 1079 and (name N or name CA or \ name C or name O or name CB )) or resid 1080 through 1190 or resid 1402 through \ 1403)) selection = (chain 'B' and (resid 76 through 216 or (resid 217 and (name N or name CA or nam \ e C or name O or name CB )) or resid 218 through 610 or (resid 611 and (name N o \ r name CA or name C or name O or name CB )) or resid 612 through 885 or (resid 8 \ 86 and (name N or name CA or name C or name O or name CB )) or resid 887 through \ 1190 or resid 1405 through 1406)) } 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.420 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 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 : 0.003 0.038 15238 Z= 0.174 Angle : 0.668 10.340 20820 Z= 0.321 Chirality : 0.043 0.276 2599 Planarity : 0.004 0.039 2529 Dihedral : 20.467 124.474 5924 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.19), residues: 1935 helix: 1.21 (0.14), residues: 1357 sheet: 1.70 (0.52), residues: 105 loop : -0.77 (0.27), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 573 TYR 0.022 0.001 TYR B 309 PHE 0.010 0.001 PHE B1080 TRP 0.022 0.001 TRP B 635 HIS 0.002 0.001 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 (15238) covalent geometry : angle 0.66769 / 0.32 (20820) hydrogen bonds : bond 0.10752 / 7.10 ( 1067) hydrogen bonds : angle 4.59147 / 3.48 ( 3171) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8200 (tmm) cc_final: 0.7832 (tmm) REVERT: A 277 LEU cc_start: 0.8755 (tp) cc_final: 0.8453 (mm) REVERT: A 383 MET cc_start: 0.6424 (ttt) cc_final: 0.6069 (tpp) REVERT: A 397 ILE cc_start: 0.9255 (pt) cc_final: 0.8986 (pt) REVERT: A 398 ILE cc_start: 0.8954 (pt) cc_final: 0.8749 (pt) REVERT: A 503 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7749 (tm-30) REVERT: A 926 GLU cc_start: 0.8294 (mp0) cc_final: 0.7493 (mp0) REVERT: B 231 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7574 (mt-10) REVERT: B 397 ILE cc_start: 0.9299 (pt) cc_final: 0.9025 (pt) REVERT: B 398 ILE cc_start: 0.8979 (pt) cc_final: 0.8776 (pt) REVERT: B 503 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7718 (tm-30) REVERT: B 938 MET cc_start: 0.8589 (tpp) cc_final: 0.8034 (tpp) outliers start: 0 outliers final: 0 residues processed: 249 average time/residue: 0.1041 time to fit residues: 41.1117 Evaluate side-chains 175 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 175 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 50.0000 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.0000 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 187 ASN A 270 GLN A 900 GLN B 900 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4095 r_free = 0.4095 target = 0.152623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.104154 restraints weight = 29694.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.101583 restraints weight = 20419.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.102110 restraints weight = 16032.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.102616 restraints weight = 14083.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.102794 restraints weight = 13086.982| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15238 Z= 0.123 Angle : 0.714 10.017 20820 Z= 0.319 Chirality : 0.042 0.267 2599 Planarity : 0.003 0.035 2529 Dihedral : 15.736 103.837 2956 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.99 % Allowed : 14.00 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.81 (0.19), residues: 1935 helix: 1.79 (0.14), residues: 1376 sheet: 1.58 (0.51), residues: 107 loop : -0.68 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 585 TYR 0.021 0.001 TYR A 309 PHE 0.018 0.001 PHE A 386 TRP 0.037 0.001 TRP B1091 HIS 0.002 0.001 HIS B 869 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.12 (15238) covalent geometry : angle 0.71417 / 0.32 (20820) hydrogen bonds : bond 0.04347 / 2.93 ( 1067) hydrogen bonds : angle 3.83493 / 2.91 ( 3171) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 202 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8354 (tmm) cc_final: 0.7902 (tmm) REVERT: A 277 LEU cc_start: 0.8857 (tp) cc_final: 0.8542 (mm) REVERT: A 503 GLU cc_start: 0.8307 (tm-30) cc_final: 0.8058 (tm-30) REVERT: A 926 GLU cc_start: 0.8476 (mp0) cc_final: 0.7600 (mp0) REVERT: A 1187 PHE cc_start: 0.8666 (t80) cc_final: 0.8454 (t80) REVERT: B 187 ASN cc_start: 0.7653 (m-40) cc_final: 0.7212 (m-40) REVERT: B 195 PHE cc_start: 0.8256 (t80) cc_final: 0.7864 (t80) REVERT: B 206 SER cc_start: 0.8624 (t) cc_final: 0.8392 (t) REVERT: B 388 LEU cc_start: 0.9441 (OUTLIER) cc_final: 0.9212 (tt) REVERT: B 389 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9099 (mp) REVERT: B 503 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 678 MET cc_start: 0.6511 (ppp) cc_final: 0.6152 (ppp) REVERT: B 823 LEU cc_start: 0.9303 (mt) cc_final: 0.9007 (pp) REVERT: B 938 MET cc_start: 0.8459 (tpp) cc_final: 0.7835 (tpp) outliers start: 28 outliers final: 6 residues processed: 224 average time/residue: 0.0944 time to fit residues: 34.8855 Evaluate side-chains 187 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 179 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 1006 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 121 optimal weight: 0.0370 chunk 118 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 104 optimal weight: 0.6980 chunk 111 optimal weight: 9.9990 chunk 109 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.151434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101495 restraints weight = 30347.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099710 restraints weight = 19200.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.100794 restraints weight = 14957.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101498 restraints weight = 12950.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.101509 restraints weight = 11332.386| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15238 Z= 0.131 Angle : 0.670 10.781 20820 Z= 0.303 Chirality : 0.041 0.290 2599 Planarity : 0.003 0.032 2529 Dihedral : 11.811 107.964 2956 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.91 % Allowed : 15.00 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.10 (0.19), residues: 1935 helix: 2.02 (0.14), residues: 1371 sheet: 1.61 (0.50), residues: 107 loop : -0.61 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 573 TYR 0.021 0.001 TYR B 309 PHE 0.012 0.001 PHE A 352 TRP 0.027 0.001 TRP A1091 HIS 0.003 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (15238) covalent geometry : angle 0.66968 / 0.30 (20820) hydrogen bonds : bond 0.04388 / 2.96 ( 1067) hydrogen bonds : angle 3.75278 / 2.84 ( 3171) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8396 (tmm) cc_final: 0.8067 (tmm) REVERT: A 277 LEU cc_start: 0.8863 (tp) cc_final: 0.8512 (mm) REVERT: A 397 ILE cc_start: 0.9489 (pt) cc_final: 0.9234 (pt) REVERT: A 494 MET cc_start: 0.8773 (tpp) cc_final: 0.8253 (tpp) REVERT: A 503 GLU cc_start: 0.8353 (tm-30) cc_final: 0.8088 (tm-30) REVERT: A 926 GLU cc_start: 0.8528 (mp0) cc_final: 0.7584 (mp0) REVERT: B 187 ASN cc_start: 0.7684 (m-40) cc_final: 0.7418 (m-40) REVERT: B 199 MET cc_start: 0.8571 (tpp) cc_final: 0.8145 (tpt) REVERT: B 388 LEU cc_start: 0.9491 (OUTLIER) cc_final: 0.9277 (tt) REVERT: B 389 ILE cc_start: 0.9366 (OUTLIER) cc_final: 0.9143 (mp) REVERT: B 483 MET cc_start: 0.7677 (ptm) cc_final: 0.7465 (ptm) REVERT: B 494 MET cc_start: 0.8805 (tpp) cc_final: 0.8283 (tpp) REVERT: B 503 GLU cc_start: 0.8275 (tm-30) cc_final: 0.8009 (tm-30) REVERT: B 624 GLN cc_start: 0.8547 (tp-100) cc_final: 0.8214 (pm20) REVERT: B 823 LEU cc_start: 0.9283 (mt) cc_final: 0.9043 (pp) outliers start: 41 outliers final: 17 residues processed: 215 average time/residue: 0.0937 time to fit residues: 33.5291 Evaluate side-chains 187 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 390 ILE Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 1006 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 133 optimal weight: 0.9990 chunk 170 optimal weight: 1.9990 chunk 172 optimal weight: 8.9990 chunk 164 optimal weight: 5.9990 chunk 91 optimal weight: 0.0870 chunk 48 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 21 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 30 optimal weight: 6.9990 overall best weight: 1.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.150630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.105052 restraints weight = 29967.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.102504 restraints weight = 23304.594| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.101915 restraints weight = 21483.030| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102611 restraints weight = 18908.438| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.103267 restraints weight = 15272.093| |-----------------------------------------------------------------------------| r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15238 Z= 0.124 Angle : 0.629 9.440 20820 Z= 0.293 Chirality : 0.040 0.268 2599 Planarity : 0.003 0.031 2529 Dihedral : 9.654 110.666 2956 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.49 % Allowed : 16.84 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.19), residues: 1935 helix: 2.06 (0.14), residues: 1369 sheet: 1.60 (0.50), residues: 107 loop : -0.57 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 585 TYR 0.020 0.001 TYR B 309 PHE 0.012 0.001 PHE A 352 TRP 0.052 0.001 TRP A1091 HIS 0.005 0.000 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15238) covalent geometry : angle 0.62872 / 0.29 (20820) hydrogen bonds : bond 0.04336 / 2.91 ( 1067) hydrogen bonds : angle 3.67518 / 2.78 ( 3171) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 188 time to evaluate : 0.557 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8351 (tmm) cc_final: 0.8030 (tmm) REVERT: A 277 LEU cc_start: 0.8901 (tp) cc_final: 0.8562 (mm) REVERT: A 354 GLU cc_start: 0.7612 (mm-30) cc_final: 0.7337 (mp0) REVERT: A 494 MET cc_start: 0.8679 (tpp) cc_final: 0.8192 (tpp) REVERT: A 926 GLU cc_start: 0.8502 (mp0) cc_final: 0.7585 (mp0) REVERT: B 187 ASN cc_start: 0.7448 (m-40) cc_final: 0.7195 (m-40) REVERT: B 388 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9291 (tt) REVERT: B 389 ILE cc_start: 0.9292 (OUTLIER) cc_final: 0.9073 (mp) REVERT: B 494 MET cc_start: 0.8664 (tpp) cc_final: 0.8162 (tpp) REVERT: B 503 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7924 (tm-30) REVERT: B 624 GLN cc_start: 0.8505 (tp-100) cc_final: 0.8183 (pm20) REVERT: B 823 LEU cc_start: 0.9235 (mt) cc_final: 0.9030 (pp) outliers start: 35 outliers final: 22 residues processed: 216 average time/residue: 0.0930 time to fit residues: 33.6086 Evaluate side-chains 197 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 1006 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 43 optimal weight: 0.9990 chunk 82 optimal weight: 30.0000 chunk 190 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 194 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 152 optimal weight: 0.2980 chunk 146 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.148183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.102093 restraints weight = 29944.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098719 restraints weight = 22362.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.099879 restraints weight = 18703.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.100248 restraints weight = 14749.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.100388 restraints weight = 14268.144| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15238 Z= 0.185 Angle : 0.666 10.059 20820 Z= 0.316 Chirality : 0.040 0.196 2599 Planarity : 0.003 0.032 2529 Dihedral : 9.337 109.003 2956 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.48 % Allowed : 17.56 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.19), residues: 1935 helix: 1.99 (0.14), residues: 1378 sheet: 1.59 (0.50), residues: 107 loop : -0.51 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 940 TYR 0.024 0.001 TYR B 309 PHE 0.021 0.001 PHE A 195 TRP 0.031 0.002 TRP A1091 HIS 0.006 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.19 (15238) covalent geometry : angle 0.66634 / 0.32 (20820) hydrogen bonds : bond 0.04933 / 3.34 ( 1067) hydrogen bonds : angle 3.79727 / 2.87 ( 3171) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 184 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7656 (m110) cc_final: 0.7410 (m110) REVERT: A 249 MET cc_start: 0.8387 (tmm) cc_final: 0.8006 (tmm) REVERT: A 354 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7502 (mp0) REVERT: A 494 MET cc_start: 0.8623 (tpp) cc_final: 0.8126 (tpp) REVERT: A 926 GLU cc_start: 0.8534 (mp0) cc_final: 0.7617 (mp0) REVERT: B 187 ASN cc_start: 0.7489 (m-40) cc_final: 0.7138 (m110) REVERT: B 388 LEU cc_start: 0.9575 (OUTLIER) cc_final: 0.9327 (tt) REVERT: B 389 ILE cc_start: 0.9416 (OUTLIER) cc_final: 0.9153 (mp) REVERT: B 494 MET cc_start: 0.8623 (tpp) cc_final: 0.8103 (tpp) REVERT: B 503 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 649 GLU cc_start: 0.7863 (tp30) cc_final: 0.7288 (tp30) REVERT: B 848 GLU cc_start: 0.8176 (tp30) cc_final: 0.7959 (tp30) outliers start: 49 outliers final: 31 residues processed: 222 average time/residue: 0.0943 time to fit residues: 35.1313 Evaluate side-chains 211 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 242 ILE Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 477 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 858 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 90 optimal weight: 9.9990 chunk 134 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 115 optimal weight: 5.9990 chunk 136 optimal weight: 0.7980 chunk 180 optimal weight: 8.9990 chunk 172 optimal weight: 0.0870 chunk 132 optimal weight: 0.8980 chunk 65 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 overall best weight: 0.9360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 165 GLN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4072 r_free = 0.4072 target = 0.150916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.102968 restraints weight = 29845.104| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.102108 restraints weight = 20032.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.102397 restraints weight = 18096.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102926 restraints weight = 14109.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.103006 restraints weight = 12510.569| |-----------------------------------------------------------------------------| r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15238 Z= 0.119 Angle : 0.641 13.901 20820 Z= 0.298 Chirality : 0.039 0.210 2599 Planarity : 0.003 0.031 2529 Dihedral : 8.846 103.705 2956 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.91 % Allowed : 18.76 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.19), residues: 1935 helix: 2.10 (0.14), residues: 1372 sheet: 1.58 (0.50), residues: 107 loop : -0.51 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 940 TYR 0.020 0.001 TYR B 309 PHE 0.009 0.001 PHE B 352 TRP 0.030 0.001 TRP B 635 HIS 0.004 0.000 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (15238) covalent geometry : angle 0.64079 / 0.30 (20820) hydrogen bonds : bond 0.04372 / 2.95 ( 1067) hydrogen bonds : angle 3.61724 / 2.74 ( 3171) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 184 time to evaluate : 0.581 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7495 (m110) cc_final: 0.7246 (m-40) REVERT: A 249 MET cc_start: 0.8382 (tmm) cc_final: 0.8036 (tmm) REVERT: A 277 LEU cc_start: 0.8869 (tp) cc_final: 0.8488 (mm) REVERT: A 494 MET cc_start: 0.8679 (tpp) cc_final: 0.8152 (tpp) REVERT: A 926 GLU cc_start: 0.8534 (mp0) cc_final: 0.7538 (mp0) REVERT: B 187 ASN cc_start: 0.7469 (m-40) cc_final: 0.7200 (m-40) REVERT: B 388 LEU cc_start: 0.9507 (OUTLIER) cc_final: 0.9263 (tt) REVERT: B 389 ILE cc_start: 0.9385 (OUTLIER) cc_final: 0.9155 (mp) REVERT: B 494 MET cc_start: 0.8637 (tpp) cc_final: 0.8090 (tpp) REVERT: B 503 GLU cc_start: 0.8202 (tm-30) cc_final: 0.7965 (tm-30) REVERT: B 649 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7329 (tp30) outliers start: 41 outliers final: 30 residues processed: 215 average time/residue: 0.0935 time to fit residues: 33.5739 Evaluate side-chains 205 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 858 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 62 optimal weight: 0.4980 chunk 137 optimal weight: 0.5980 chunk 48 optimal weight: 5.9990 chunk 157 optimal weight: 30.0000 chunk 121 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 172 optimal weight: 0.0170 chunk 171 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 141 optimal weight: 0.2980 chunk 97 optimal weight: 2.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 900 GLN B 900 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.151865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.113963 restraints weight = 29587.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.110315 restraints weight = 32580.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.111322 restraints weight = 22036.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.111939 restraints weight = 14906.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.112756 restraints weight = 13615.144| |-----------------------------------------------------------------------------| r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 15238 Z= 0.113 Angle : 0.634 13.073 20820 Z= 0.295 Chirality : 0.039 0.220 2599 Planarity : 0.003 0.032 2529 Dihedral : 8.392 97.902 2956 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.49 % Allowed : 19.97 % Favored : 77.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.23 (0.19), residues: 1935 helix: 2.10 (0.14), residues: 1372 sheet: 1.59 (0.49), residues: 107 loop : -0.47 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 573 TYR 0.018 0.001 TYR A 309 PHE 0.025 0.001 PHE A 195 TRP 0.069 0.002 TRP A1091 HIS 0.004 0.000 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (15238) covalent geometry : angle 0.63444 / 0.29 (20820) hydrogen bonds : bond 0.04005 / 2.70 ( 1067) hydrogen bonds : angle 3.56721 / 2.70 ( 3171) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.567 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7513 (m110) cc_final: 0.7305 (m-40) REVERT: A 249 MET cc_start: 0.8227 (tmm) cc_final: 0.7951 (tmm) REVERT: A 277 LEU cc_start: 0.8832 (tp) cc_final: 0.8459 (mm) REVERT: A 494 MET cc_start: 0.8504 (tpp) cc_final: 0.7999 (tpp) REVERT: A 926 GLU cc_start: 0.8467 (mp0) cc_final: 0.7633 (mp0) REVERT: B 388 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9241 (tt) REVERT: B 389 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9023 (mp) REVERT: B 494 MET cc_start: 0.8501 (tpp) cc_final: 0.7967 (tpp) outliers start: 35 outliers final: 26 residues processed: 209 average time/residue: 0.0914 time to fit residues: 32.2062 Evaluate side-chains 200 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 172 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 858 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 86 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 59 optimal weight: 0.0060 chunk 116 optimal weight: 3.9990 chunk 174 optimal weight: 30.0000 chunk 165 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 177 optimal weight: 5.9990 chunk 118 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.5200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 900 GLN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.151394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.103831 restraints weight = 29841.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.101500 restraints weight = 23744.187| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.101306 restraints weight = 20332.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.102467 restraints weight = 16370.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.102654 restraints weight = 14004.628| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15238 Z= 0.129 Angle : 0.643 13.004 20820 Z= 0.302 Chirality : 0.039 0.218 2599 Planarity : 0.003 0.030 2529 Dihedral : 8.316 92.645 2956 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.42 % Allowed : 20.61 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.19), residues: 1935 helix: 2.09 (0.14), residues: 1373 sheet: 1.57 (0.49), residues: 107 loop : -0.47 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 573 TYR 0.021 0.001 TYR A 309 PHE 0.025 0.001 PHE A 195 TRP 0.069 0.002 TRP B1091 HIS 0.005 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.13 (15238) covalent geometry : angle 0.64305 / 0.30 (20820) hydrogen bonds : bond 0.04225 / 2.85 ( 1067) hydrogen bonds : angle 3.59199 / 2.72 ( 3171) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.564 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8341 (tmm) cc_final: 0.8012 (tmm) REVERT: A 277 LEU cc_start: 0.8899 (tp) cc_final: 0.8507 (mm) REVERT: A 354 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: A 494 MET cc_start: 0.8694 (tpp) cc_final: 0.8168 (tpp) REVERT: A 926 GLU cc_start: 0.8594 (mp0) cc_final: 0.7662 (mp0) REVERT: B 389 ILE cc_start: 0.9383 (OUTLIER) cc_final: 0.9163 (mp) REVERT: B 494 MET cc_start: 0.8657 (tpp) cc_final: 0.8098 (tpp) outliers start: 34 outliers final: 28 residues processed: 199 average time/residue: 0.0940 time to fit residues: 31.4389 Evaluate side-chains 201 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 649 GLU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 858 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 25 optimal weight: 3.9990 chunk 52 optimal weight: 0.0170 chunk 29 optimal weight: 2.9990 chunk 167 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 149 optimal weight: 0.0770 chunk 182 optimal weight: 50.0000 chunk 35 optimal weight: 0.0870 chunk 41 optimal weight: 0.0870 chunk 43 optimal weight: 2.9990 overall best weight: 0.4534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 900 GLN B 900 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.153856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.115475 restraints weight = 29912.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.114433 restraints weight = 40024.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.115701 restraints weight = 23253.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.116649 restraints weight = 15367.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117492 restraints weight = 13516.270| |-----------------------------------------------------------------------------| r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 15238 Z= 0.110 Angle : 0.636 13.275 20820 Z= 0.296 Chirality : 0.039 0.227 2599 Planarity : 0.003 0.032 2529 Dihedral : 7.702 77.091 2956 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 1.99 % Allowed : 21.04 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.28 (0.19), residues: 1935 helix: 2.13 (0.14), residues: 1373 sheet: 1.57 (0.49), residues: 107 loop : -0.42 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 573 TYR 0.016 0.001 TYR A 309 PHE 0.022 0.001 PHE A 386 TRP 0.070 0.002 TRP B1091 HIS 0.003 0.000 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 (15238) covalent geometry : angle 0.63561 / 0.30 (20820) hydrogen bonds : bond 0.03707 / 2.49 ( 1067) hydrogen bonds : angle 3.51523 / 2.67 ( 3171) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 0.531 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8117 (tmm) cc_final: 0.7806 (tmm) REVERT: A 277 LEU cc_start: 0.8826 (tp) cc_final: 0.8472 (mm) REVERT: A 354 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: A 494 MET cc_start: 0.8495 (tpp) cc_final: 0.7923 (tpp) REVERT: A 926 GLU cc_start: 0.8481 (mp0) cc_final: 0.7498 (mp0) REVERT: B 388 LEU cc_start: 0.9475 (OUTLIER) cc_final: 0.9231 (tt) REVERT: B 389 ILE cc_start: 0.9258 (OUTLIER) cc_final: 0.9039 (mp) REVERT: B 494 MET cc_start: 0.8547 (tpp) cc_final: 0.7956 (tpp) REVERT: B 678 MET cc_start: 0.6269 (ppp) cc_final: 0.5282 (pmm) outliers start: 28 outliers final: 22 residues processed: 207 average time/residue: 0.0982 time to fit residues: 33.3679 Evaluate side-chains 196 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 858 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 55 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 161 optimal weight: 2.9990 chunk 45 optimal weight: 5.9990 chunk 117 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 122 optimal weight: 0.9980 chunk 99 optimal weight: 0.0270 chunk 169 optimal weight: 2.9990 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 187 ASN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 900 GLN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.151122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.104429 restraints weight = 29985.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.101798 restraints weight = 21458.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.102084 restraints weight = 18515.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.102760 restraints weight = 15656.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.102971 restraints weight = 13956.736| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15238 Z= 0.125 Angle : 0.671 14.583 20820 Z= 0.312 Chirality : 0.040 0.226 2599 Planarity : 0.003 0.031 2529 Dihedral : 7.409 62.233 2956 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.20 % Allowed : 21.46 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.30 (0.19), residues: 1935 helix: 2.12 (0.14), residues: 1383 sheet: 1.57 (0.49), residues: 107 loop : -0.39 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 583 TYR 0.031 0.001 TYR A 387 PHE 0.031 0.001 PHE B 195 TRP 0.068 0.002 TRP A1091 HIS 0.004 0.001 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 (15238) covalent geometry : angle 0.67076 / 0.31 (20820) hydrogen bonds : bond 0.04029 / 2.71 ( 1067) hydrogen bonds : angle 3.59156 / 2.72 ( 3171) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3870 Ramachandran restraints generated. 1935 Oldfield, 0 Emsley, 1935 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8163 (tmm) cc_final: 0.7847 (tmm) REVERT: A 277 LEU cc_start: 0.8881 (tp) cc_final: 0.8502 (mm) REVERT: A 354 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7002 (mp0) REVERT: A 494 MET cc_start: 0.8615 (tpp) cc_final: 0.8038 (tpp) REVERT: A 926 GLU cc_start: 0.8551 (mp0) cc_final: 0.7566 (mp0) REVERT: B 354 GLU cc_start: 0.7153 (mp0) cc_final: 0.6922 (mp0) REVERT: B 388 LEU cc_start: 0.9485 (OUTLIER) cc_final: 0.9251 (tt) REVERT: B 389 ILE cc_start: 0.9360 (OUTLIER) cc_final: 0.9134 (mp) REVERT: B 494 MET cc_start: 0.8628 (tpp) cc_final: 0.8039 (tpp) REVERT: B 678 MET cc_start: 0.6463 (ppp) cc_final: 0.5593 (pmm) outliers start: 31 outliers final: 26 residues processed: 200 average time/residue: 0.0935 time to fit residues: 31.4161 Evaluate side-chains 201 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 107 LEU Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 477 LEU Chi-restraints excluded: chain A residue 587 LEU Chi-restraints excluded: chain A residue 844 ILE Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 MET Chi-restraints excluded: chain B residue 162 SER Chi-restraints excluded: chain B residue 277 LEU Chi-restraints excluded: chain B residue 310 LEU Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 464 VAL Chi-restraints excluded: chain B residue 587 LEU Chi-restraints excluded: chain B residue 822 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 858 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 43 optimal weight: 0.9980 chunk 174 optimal weight: 20.0000 chunk 128 optimal weight: 0.9990 chunk 108 optimal weight: 0.9990 chunk 116 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 188 optimal weight: 30.0000 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 176 optimal weight: 40.0000 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN A 900 GLN ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.151760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.114482 restraints weight = 29845.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.109676 restraints weight = 32444.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.110539 restraints weight = 22540.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.111077 restraints weight = 15422.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.111862 restraints weight = 14093.905| |-----------------------------------------------------------------------------| r_work (final): 0.3504 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15238 Z= 0.118 Angle : 0.677 14.058 20820 Z= 0.316 Chirality : 0.040 0.309 2599 Planarity : 0.003 0.031 2529 Dihedral : 7.131 62.128 2956 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.56 % Allowed : 21.18 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.32 (0.19), residues: 1935 helix: 2.13 (0.14), residues: 1386 sheet: 1.57 (0.49), residues: 107 loop : -0.37 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 573 TYR 0.019 0.001 TYR A 309 PHE 0.017 0.001 PHE A 386 TRP 0.067 0.002 TRP A1091 HIS 0.004 0.000 HIS A 889 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (15238) covalent geometry : angle 0.67696 / 0.32 (20820) hydrogen bonds : bond 0.03986 / 2.69 ( 1067) hydrogen bonds : angle 3.58979 / 2.71 ( 3171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2390.28 seconds wall clock time: 42 minutes 14.56 seconds (2534.56 seconds total)