Starting phenix.real_space_refine on Fri Jun 13 10:28:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u7o_41987/06_2025/8u7o_41987.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u7o_41987/06_2025/8u7o_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8u7o_41987/06_2025/8u7o_41987.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u7o_41987/06_2025/8u7o_41987.map" model { file = "/net/cci-nas-00/data/ceres_data/8u7o_41987/06_2025/8u7o_41987.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u7o_41987/06_2025/8u7o_41987.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.017 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLN:plan1': 4, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 4, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 16, 'ARG:plan': 13} 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: {'GLN:plan1': 3, 'HIS:plan': 4, 'TYR:plan': 3, 'ASN:plan1': 5, 'ASP:plan': 6, 'PHE:plan': 9, 'GLU:plan': 17, 'ARG:plan': 13} 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: {'RNA': 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: {'RNA': 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: 8.84, per 1000 atoms: 0.59 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: 4.63 Conformation dependent library (CDL) restraints added in 2.4 seconds 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: 1.89 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: 6.83 Time building geometry restraints manager: 5.05 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 - 2.06: 20463 2.06 - 4.13: 291 4.13 - 6.19: 49 6.19 - 8.26: 12 8.26 - 10.32: 5 Bond angle restraints: 20820 Sorted by residual: 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=" C PHE B 294 " pdb=" N ASN B 295 " pdb=" CA ASN B 295 " ideal model delta sigma weight residual 121.54 127.23 -5.69 1.91e+00 2.74e-01 8.88e+00 angle pdb=" C PHE A 294 " pdb=" N ASN A 295 " pdb=" CA ASN A 295 " ideal model delta sigma weight residual 121.54 127.21 -5.67 1.91e+00 2.74e-01 8.81e+00 angle pdb=" CA LEU B 979 " pdb=" CB LEU B 979 " pdb=" CG LEU B 979 " ideal model delta sigma weight residual 116.30 126.62 -10.32 3.50e+00 8.16e-02 8.70e+00 ... (remaining 20815 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.19: 9076 26.19 - 52.37: 359 52.37 - 78.56: 53 78.56 - 104.74: 35 104.74 - 130.93: 91 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 - 0.048: 2015 0.048 - 0.097: 494 0.097 - 0.145: 75 0.145 - 0.194: 6 0.194 - 0.242: 9 Chirality restraints: 2599 Sorted by residual: 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 chirality pdb=" C10 AJP B1403 " pdb=" C08 AJP B1403 " pdb=" C11 AJP B1403 " pdb=" O82 AJP B1403 " both_signs ideal model delta sigma weight residual False 2.61 2.38 0.23 2.00e-01 2.50e+01 1.31e+00 chirality pdb=" C10 AJP B1404 " pdb=" C08 AJP B1404 " pdb=" C11 AJP B1404 " pdb=" O82 AJP B1404 " both_signs ideal model delta sigma weight residual False 2.61 2.38 0.23 2.00e-01 2.50e+01 1.31e+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: 20.250 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: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 37.670 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 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= 0.173 Angle : 0.646 10.323 20820 Z= 0.319 Chirality : 0.043 0.242 2599 Planarity : 0.004 0.039 2529 Dihedral : 20.602 130.930 5924 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.49 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.022 0.001 TRP B 635 HIS 0.002 0.001 HIS A 908 PHE 0.010 0.001 PHE B1080 TYR 0.022 0.001 TYR B 309 ARG 0.002 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.10752 ( 1067) hydrogen bonds : angle 4.59147 ( 3171) covalent geometry : bond 0.00317 (15238) covalent geometry : angle 0.64576 (20820) *********************** 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 : 1.650 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: 0.9254 (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: 0.2624 time to fit residues: 102.1448 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 : 1.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 164 optimal weight: 0.9980 chunk 147 optimal weight: 2.9990 chunk 82 optimal weight: 40.0000 chunk 50 optimal weight: 1.9990 chunk 99 optimal weight: 8.9990 chunk 78 optimal weight: 9.9990 chunk 152 optimal weight: 20.0000 chunk 59 optimal weight: 0.4980 chunk 92 optimal weight: 50.0000 chunk 113 optimal weight: 0.9990 chunk 177 optimal weight: 30.0000 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN A 270 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.150492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.109949 restraints weight = 29620.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.108871 restraints weight = 37305.398| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.110086 restraints weight = 23963.996| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15238 Z= 0.143 Angle : 0.711 9.786 20820 Z= 0.325 Chirality : 0.042 0.252 2599 Planarity : 0.003 0.037 2529 Dihedral : 16.692 136.430 2956 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.85 % Allowed : 14.29 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.19), residues: 1935 helix: 1.79 (0.14), residues: 1377 sheet: 1.58 (0.51), residues: 107 loop : -0.69 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B1091 HIS 0.003 0.001 HIS A 132 PHE 0.020 0.001 PHE A 386 TYR 0.022 0.001 TYR A 309 ARG 0.003 0.000 ARG B 585 Details of bonding type rmsd hydrogen bonds : bond 0.04633 ( 1067) hydrogen bonds : angle 3.90540 ( 3171) covalent geometry : bond 0.00302 (15238) covalent geometry : angle 0.71123 (20820) *********************** 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 223 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8227 (tmm) cc_final: 0.7922 (tmm) REVERT: A 277 LEU cc_start: 0.8865 (tp) cc_final: 0.8526 (mm) REVERT: A 926 GLU cc_start: 0.8470 (mp0) cc_final: 0.7611 (mp0) REVERT: B 187 ASN cc_start: 0.7602 (m-40) cc_final: 0.7207 (m-40) REVERT: B 195 PHE cc_start: 0.8256 (t80) cc_final: 0.7929 (t80) REVERT: B 388 LEU cc_start: 0.9533 (OUTLIER) cc_final: 0.9310 (tt) REVERT: B 389 ILE cc_start: 0.9176 (OUTLIER) cc_final: 0.8892 (mp) REVERT: B 823 LEU cc_start: 0.9154 (mt) cc_final: 0.8949 (pp) REVERT: B 938 MET cc_start: 0.8411 (tpp) cc_final: 0.7933 (tpp) outliers start: 26 outliers final: 6 residues processed: 218 average time/residue: 0.2070 time to fit residues: 73.4907 Evaluate side-chains 181 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 173 time to evaluate : 1.574 ------------------------------------------------------------------------------- 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 277 LEU Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 389 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 136 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 157 optimal weight: 50.0000 chunk 183 optimal weight: 50.0000 chunk 107 optimal weight: 1.9990 chunk 190 optimal weight: 50.0000 chunk 185 optimal weight: 7.9990 chunk 189 optimal weight: 50.0000 chunk 112 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4071 r_free = 0.4071 target = 0.150245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.103113 restraints weight = 29532.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100884 restraints weight = 21262.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.101574 restraints weight = 16632.177| |-----------------------------------------------------------------------------| r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 15238 Z= 0.134 Angle : 0.671 11.139 20820 Z= 0.307 Chirality : 0.041 0.285 2599 Planarity : 0.003 0.032 2529 Dihedral : 12.715 135.399 2956 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 3.27 % Allowed : 14.93 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.19), residues: 1935 helix: 2.02 (0.14), residues: 1369 sheet: 1.56 (0.50), residues: 107 loop : -0.60 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A1091 HIS 0.003 0.001 HIS A 889 PHE 0.012 0.001 PHE A 352 TYR 0.021 0.001 TYR B 309 ARG 0.004 0.000 ARG B 573 Details of bonding type rmsd hydrogen bonds : bond 0.04527 ( 1067) hydrogen bonds : angle 3.76809 ( 3171) covalent geometry : bond 0.00289 (15238) covalent geometry : angle 0.67079 (20820) *********************** 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 229 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 1.473 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: 0.8412 (tmm) cc_final: 0.8093 (tmm) REVERT: A 277 LEU cc_start: 0.8868 (tp) cc_final: 0.8525 (mm) REVERT: A 354 GLU cc_start: 0.7634 (OUTLIER) cc_final: 0.7434 (mm-30) REVERT: A 383 MET cc_start: 0.8124 (tpp) cc_final: 0.7886 (ttt) REVERT: A 397 ILE cc_start: 0.9437 (pt) cc_final: 0.9155 (pt) REVERT: A 494 MET cc_start: 0.8704 (tpp) cc_final: 0.8212 (tpp) REVERT: A 926 GLU cc_start: 0.8502 (mp0) cc_final: 0.7632 (mp0) REVERT: B 187 ASN cc_start: 0.7594 (m-40) cc_final: 0.7368 (m-40) REVERT: B 199 MET cc_start: 0.8527 (tpp) cc_final: 0.8262 (tpt) REVERT: B 388 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9315 (tt) REVERT: B 389 ILE cc_start: 0.9347 (OUTLIER) cc_final: 0.9114 (mp) REVERT: B 494 MET cc_start: 0.8675 (tpp) cc_final: 0.8166 (tpp) REVERT: B 624 GLN cc_start: 0.8538 (tp-100) cc_final: 0.8220 (pm20) REVERT: B 649 GLU cc_start: 0.8042 (tp30) cc_final: 0.7795 (tp30) REVERT: B 823 LEU cc_start: 0.9283 (mt) cc_final: 0.9064 (pp) REVERT: B 938 MET cc_start: 0.8537 (tpp) cc_final: 0.8056 (tpp) outliers start: 46 outliers final: 21 residues processed: 217 average time/residue: 0.1950 time to fit residues: 69.7201 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 : 1.783 ------------------------------------------------------------------------------- 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 354 GLU Chi-restraints excluded: chain A residue 402 VAL Chi-restraints excluded: chain A residue 464 VAL 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 107 LEU 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 89 optimal weight: 0.0470 chunk 184 optimal weight: 20.0000 chunk 123 optimal weight: 6.9990 chunk 104 optimal weight: 0.6980 chunk 180 optimal weight: 8.9990 chunk 172 optimal weight: 9.9990 chunk 66 optimal weight: 2.9990 chunk 149 optimal weight: 0.0470 chunk 21 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 161 optimal weight: 4.9990 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4074 r_free = 0.4074 target = 0.150391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.105864 restraints weight = 29773.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.104498 restraints weight = 28444.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.105230 restraints weight = 19845.330| |-----------------------------------------------------------------------------| r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15238 Z= 0.127 Angle : 0.626 9.083 20820 Z= 0.296 Chirality : 0.040 0.320 2599 Planarity : 0.003 0.033 2529 Dihedral : 10.797 135.367 2956 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.70 % Allowed : 17.20 % Favored : 80.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.19), residues: 1935 helix: 2.08 (0.14), residues: 1369 sheet: 1.56 (0.50), residues: 107 loop : -0.59 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP A1091 HIS 0.003 0.000 HIS A 889 PHE 0.011 0.001 PHE A 352 TYR 0.020 0.001 TYR B 309 ARG 0.004 0.000 ARG B 940 Details of bonding type rmsd hydrogen bonds : bond 0.04393 ( 1067) hydrogen bonds : angle 3.69005 ( 3171) covalent geometry : bond 0.00273 (15238) covalent geometry : angle 0.62632 (20820) *********************** 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 218 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 1.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8321 (tmm) cc_final: 0.8032 (tmm) REVERT: A 277 LEU cc_start: 0.8854 (tp) cc_final: 0.8498 (mm) REVERT: A 354 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7476 (mm-30) REVERT: A 494 MET cc_start: 0.8615 (tpp) cc_final: 0.8144 (tpp) REVERT: A 926 GLU cc_start: 0.8479 (mp0) cc_final: 0.7600 (mp0) REVERT: B 187 ASN cc_start: 0.7452 (m-40) cc_final: 0.7192 (m-40) REVERT: B 199 MET cc_start: 0.8357 (tpp) cc_final: 0.8064 (tpt) REVERT: B 388 LEU cc_start: 0.9524 (OUTLIER) cc_final: 0.9313 (tt) REVERT: B 389 ILE cc_start: 0.9241 (OUTLIER) cc_final: 0.9012 (mp) REVERT: B 494 MET cc_start: 0.8612 (tpp) cc_final: 0.8135 (tpp) outliers start: 38 outliers final: 24 residues processed: 208 average time/residue: 0.1952 time to fit residues: 67.1382 Evaluate side-chains 193 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 354 GLU 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 84 SER Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 133 MET 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 390 ILE Chi-restraints excluded: chain B residue 402 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 29 optimal weight: 0.9980 chunk 89 optimal weight: 0.0370 chunk 105 optimal weight: 4.9990 chunk 6 optimal weight: 0.0980 chunk 30 optimal weight: 0.3980 chunk 59 optimal weight: 10.0000 chunk 124 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 113 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 overall best weight: 0.4658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.151877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.104887 restraints weight = 29807.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.102402 restraints weight = 21605.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.102795 restraints weight = 18027.392| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.1740 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= 0.113 Angle : 0.618 13.263 20820 Z= 0.290 Chirality : 0.039 0.202 2599 Planarity : 0.003 0.033 2529 Dihedral : 9.790 135.121 2956 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.42 % Allowed : 18.19 % Favored : 79.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.19), residues: 1935 helix: 2.11 (0.14), residues: 1368 sheet: 1.59 (0.50), residues: 107 loop : -0.58 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A1091 HIS 0.001 0.000 HIS A 889 PHE 0.026 0.001 PHE A 195 TYR 0.018 0.001 TYR A 309 ARG 0.007 0.000 ARG A 940 Details of bonding type rmsd hydrogen bonds : bond 0.04003 ( 1067) hydrogen bonds : angle 3.59184 ( 3171) covalent geometry : bond 0.00222 (15238) covalent geometry : angle 0.61810 (20820) *********************** 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 217 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 1.655 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: 0.7427 (m110) cc_final: 0.7161 (m-40) REVERT: A 199 MET cc_start: 0.8401 (tpp) cc_final: 0.8188 (tpp) REVERT: A 249 MET cc_start: 0.8332 (tmm) cc_final: 0.8057 (tmm) REVERT: A 277 LEU cc_start: 0.8860 (tp) cc_final: 0.8546 (mm) REVERT: A 354 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7499 (mm-30) REVERT: A 494 MET cc_start: 0.8701 (tpp) cc_final: 0.8184 (tpp) REVERT: A 926 GLU cc_start: 0.8535 (mp0) cc_final: 0.7571 (mp0) REVERT: B 187 ASN cc_start: 0.7343 (m-40) cc_final: 0.7094 (m-40) REVERT: B 388 LEU cc_start: 0.9492 (OUTLIER) cc_final: 0.9266 (tt) REVERT: B 389 ILE cc_start: 0.9349 (OUTLIER) cc_final: 0.9136 (mp) REVERT: B 494 MET cc_start: 0.8697 (tpp) cc_final: 0.8152 (tpp) REVERT: B 678 MET cc_start: 0.6297 (ppp) cc_final: 0.5963 (ppp) outliers start: 34 outliers final: 19 residues processed: 206 average time/residue: 0.2041 time to fit residues: 69.0026 Evaluate side-chains 191 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 169 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 310 LEU Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 VAL 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 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 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 822 ILE Chi-restraints excluded: chain B residue 844 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 7 optimal weight: 0.7980 chunk 99 optimal weight: 2.9990 chunk 45 optimal weight: 0.0170 chunk 169 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 190 optimal weight: 20.0000 chunk 8 optimal weight: 2.9990 chunk 156 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 21 optimal weight: 6.9990 chunk 148 optimal weight: 8.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4086 r_free = 0.4086 target = 0.151499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.105244 restraints weight = 29892.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.102048 restraints weight = 20314.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.102847 restraints weight = 17708.143| |-----------------------------------------------------------------------------| r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 15238 Z= 0.116 Angle : 0.613 12.189 20820 Z= 0.291 Chirality : 0.039 0.211 2599 Planarity : 0.003 0.030 2529 Dihedral : 9.383 134.907 2956 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.56 % Allowed : 18.91 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.27 (0.19), residues: 1935 helix: 2.16 (0.14), residues: 1367 sheet: 1.57 (0.50), residues: 107 loop : -0.52 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 635 HIS 0.002 0.000 HIS A 889 PHE 0.009 0.001 PHE A 352 TYR 0.019 0.001 TYR A 309 ARG 0.001 0.000 ARG A 585 Details of bonding type rmsd hydrogen bonds : bond 0.04026 ( 1067) hydrogen bonds : angle 3.56526 ( 3171) covalent geometry : bond 0.00246 (15238) covalent geometry : angle 0.61328 (20820) *********************** 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 213 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 177 time to evaluate : 1.661 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: 0.7514 (m110) cc_final: 0.7282 (m-40) REVERT: A 249 MET cc_start: 0.8351 (tmm) cc_final: 0.8061 (tmm) REVERT: A 277 LEU cc_start: 0.8902 (tp) cc_final: 0.8584 (mm) REVERT: A 354 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7570 (mm-30) REVERT: A 494 MET cc_start: 0.8661 (tpp) cc_final: 0.8138 (tpp) REVERT: A 926 GLU cc_start: 0.8541 (mp0) cc_final: 0.7558 (mp0) REVERT: B 187 ASN cc_start: 0.7666 (m-40) cc_final: 0.7369 (m-40) REVERT: B 195 PHE cc_start: 0.8171 (t80) cc_final: 0.7901 (t80) REVERT: B 388 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9259 (tt) REVERT: B 389 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9141 (mp) REVERT: B 494 MET cc_start: 0.8675 (tpp) cc_final: 0.8141 (tpp) outliers start: 36 outliers final: 27 residues processed: 205 average time/residue: 0.2085 time to fit residues: 70.8035 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 : 1.642 ------------------------------------------------------------------------------- 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 354 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 481 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 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 481 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 189 optimal weight: 20.0000 chunk 130 optimal weight: 4.9990 chunk 166 optimal weight: 6.9990 chunk 91 optimal weight: 50.0000 chunk 44 optimal weight: 0.6980 chunk 133 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 2 optimal weight: 6.9990 chunk 159 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 19 optimal weight: 5.9990 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4039 r_free = 0.4039 target = 0.148234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097872 restraints weight = 29959.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.095188 restraints weight = 18495.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.096318 restraints weight = 15327.443| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15238 Z= 0.192 Angle : 0.686 11.743 20820 Z= 0.329 Chirality : 0.040 0.209 2599 Planarity : 0.003 0.031 2529 Dihedral : 9.762 134.983 2956 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 3.13 % Allowed : 19.33 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.19), residues: 1935 helix: 2.05 (0.14), residues: 1376 sheet: 1.64 (0.50), residues: 102 loop : -0.49 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 635 HIS 0.004 0.001 HIS B 502 PHE 0.023 0.002 PHE A 195 TYR 0.026 0.001 TYR B 309 ARG 0.002 0.000 ARG A 940 Details of bonding type rmsd hydrogen bonds : bond 0.05112 ( 1067) hydrogen bonds : angle 3.77012 ( 3171) covalent geometry : bond 0.00445 (15238) covalent geometry : angle 0.68566 (20820) *********************** 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 223 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 179 time to evaluate : 1.948 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: 0.7678 (m110) cc_final: 0.7458 (m-40) REVERT: A 249 MET cc_start: 0.8433 (tmm) cc_final: 0.8052 (tmm) REVERT: A 354 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7749 (mm-30) REVERT: A 383 MET cc_start: 0.6633 (ttt) cc_final: 0.6106 (tpp) REVERT: A 387 TYR cc_start: 0.8343 (m-10) cc_final: 0.8070 (m-80) REVERT: A 494 MET cc_start: 0.8689 (tpp) cc_final: 0.8183 (tpp) REVERT: A 926 GLU cc_start: 0.8605 (mp0) cc_final: 0.7586 (mp0) REVERT: B 187 ASN cc_start: 0.7585 (m-40) cc_final: 0.7301 (m-40) REVERT: B 389 ILE cc_start: 0.9411 (OUTLIER) cc_final: 0.9182 (mp) REVERT: B 494 MET cc_start: 0.8699 (tpp) cc_final: 0.8169 (tpp) REVERT: B 649 GLU cc_start: 0.8140 (tp30) cc_final: 0.7367 (tp30) outliers start: 44 outliers final: 31 residues processed: 212 average time/residue: 0.2129 time to fit residues: 74.5360 Evaluate side-chains 206 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 173 time to evaluate : 1.587 ------------------------------------------------------------------------------- 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 341 ILE Chi-restraints excluded: chain A residue 354 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 402 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 389 ILE Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 472 THR Chi-restraints excluded: chain B residue 477 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 36 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 chunk 150 optimal weight: 3.9990 chunk 176 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 170 optimal weight: 0.9990 chunk 153 optimal weight: 7.9990 chunk 182 optimal weight: 40.0000 chunk 0 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.148619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.110893 restraints weight = 29677.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.105275 restraints weight = 30479.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.106085 restraints weight = 23005.808| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 15238 Z= 0.151 Angle : 0.662 16.820 20820 Z= 0.316 Chirality : 0.039 0.219 2599 Planarity : 0.003 0.029 2529 Dihedral : 9.578 134.960 2956 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.84 % Allowed : 19.97 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.19), residues: 1935 helix: 2.12 (0.14), residues: 1374 sheet: 1.53 (0.49), residues: 107 loop : -0.56 (0.29), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP A 962 HIS 0.002 0.000 HIS A 889 PHE 0.012 0.001 PHE A 352 TYR 0.022 0.001 TYR B 309 ARG 0.002 0.000 ARG A 875 Details of bonding type rmsd hydrogen bonds : bond 0.04797 ( 1067) hydrogen bonds : angle 3.67915 ( 3171) covalent geometry : bond 0.00342 (15238) covalent geometry : angle 0.66249 (20820) *********************** 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 219 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 179 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 ASN cc_start: 0.7601 (m110) cc_final: 0.7388 (m-40) REVERT: A 249 MET cc_start: 0.8324 (tmm) cc_final: 0.7976 (tmm) REVERT: A 354 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7485 (mm-30) REVERT: A 387 TYR cc_start: 0.8225 (m-10) cc_final: 0.7626 (m-10) REVERT: A 494 MET cc_start: 0.8600 (tpp) cc_final: 0.8109 (tpp) REVERT: A 926 GLU cc_start: 0.8518 (mp0) cc_final: 0.7591 (mp0) REVERT: B 187 ASN cc_start: 0.7498 (m-40) cc_final: 0.7218 (m-40) REVERT: B 388 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9288 (tt) REVERT: B 389 ILE cc_start: 0.9337 (OUTLIER) cc_final: 0.9072 (mp) REVERT: B 494 MET cc_start: 0.8545 (tpp) cc_final: 0.8039 (tpp) REVERT: B 649 GLU cc_start: 0.8188 (OUTLIER) cc_final: 0.7390 (tp30) outliers start: 40 outliers final: 30 residues processed: 206 average time/residue: 0.2012 time to fit residues: 68.2168 Evaluate side-chains 205 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 171 time to evaluate : 1.531 ------------------------------------------------------------------------------- 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 354 GLU Chi-restraints excluded: chain A residue 368 VAL 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 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 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 89 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 79 optimal weight: 40.0000 chunk 147 optimal weight: 4.9990 chunk 192 optimal weight: 30.0000 chunk 116 optimal weight: 1.9990 chunk 149 optimal weight: 0.1980 overall best weight: 3.0388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 900 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4032 r_free = 0.4032 target = 0.147280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.110650 restraints weight = 29352.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.104421 restraints weight = 33604.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.105336 restraints weight = 24279.894| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15238 Z= 0.196 Angle : 0.714 14.521 20820 Z= 0.342 Chirality : 0.041 0.226 2599 Planarity : 0.003 0.029 2529 Dihedral : 9.710 134.945 2956 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.84 % Allowed : 20.04 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.19), residues: 1935 helix: 1.99 (0.14), residues: 1383 sheet: 1.71 (0.50), residues: 100 loop : -0.53 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.002 TRP B1091 HIS 0.005 0.001 HIS B 981 PHE 0.025 0.002 PHE A 195 TYR 0.024 0.001 TYR B 309 ARG 0.002 0.000 ARG B 910 Details of bonding type rmsd hydrogen bonds : bond 0.05150 ( 1067) hydrogen bonds : angle 3.82484 ( 3171) covalent geometry : bond 0.00454 (15238) covalent geometry : angle 0.71429 (20820) *********************** 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: 40 poor density : 173 time to evaluate : 1.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 249 MET cc_start: 0.8364 (tmm) cc_final: 0.8007 (tmm) REVERT: A 354 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7521 (mm-30) REVERT: A 494 MET cc_start: 0.8527 (tpp) cc_final: 0.8032 (tpp) REVERT: A 926 GLU cc_start: 0.8528 (mp0) cc_final: 0.7631 (mp0) REVERT: B 187 ASN cc_start: 0.7543 (m-40) cc_final: 0.7278 (m-40) REVERT: B 388 LEU cc_start: 0.9613 (OUTLIER) cc_final: 0.9340 (tt) REVERT: B 389 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9029 (mp) REVERT: B 494 MET cc_start: 0.8516 (tpp) cc_final: 0.8016 (tpp) REVERT: B 649 GLU cc_start: 0.8036 (OUTLIER) cc_final: 0.7365 (tp30) outliers start: 40 outliers final: 32 residues processed: 202 average time/residue: 0.1908 time to fit residues: 63.7970 Evaluate side-chains 203 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 1.461 ------------------------------------------------------------------------------- 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 354 GLU Chi-restraints excluded: chain A residue 368 VAL 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 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 77 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 117 optimal weight: 0.3980 chunk 81 optimal weight: 7.9990 chunk 132 optimal weight: 0.9990 chunk 68 optimal weight: 0.9990 chunk 166 optimal weight: 3.9990 chunk 171 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 193 optimal weight: 7.9990 chunk 177 optimal weight: 5.9990 chunk 94 optimal weight: 40.0000 chunk 27 optimal weight: 0.6980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 187 ASN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.150525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.099570 restraints weight = 29879.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.099302 restraints weight = 19780.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.099350 restraints weight = 14862.855| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2111 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= 0.126 Angle : 0.679 14.168 20820 Z= 0.322 Chirality : 0.040 0.236 2599 Planarity : 0.003 0.031 2529 Dihedral : 9.308 134.935 2956 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.20 % Allowed : 20.82 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.25 (0.19), residues: 1935 helix: 2.12 (0.14), residues: 1377 sheet: 1.54 (0.48), residues: 107 loop : -0.49 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP A1091 HIS 0.002 0.000 HIS A 889 PHE 0.032 0.001 PHE B 195 TYR 0.023 0.001 TYR A1088 ARG 0.005 0.000 ARG A 399 Details of bonding type rmsd hydrogen bonds : bond 0.04505 ( 1067) hydrogen bonds : angle 3.67028 ( 3171) covalent geometry : bond 0.00256 (15238) covalent geometry : angle 0.67898 (20820) ********************** 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 206 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 175 time to evaluate : 1.634 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: 0.8450 (tmm) cc_final: 0.8095 (tmm) REVERT: A 277 LEU cc_start: 0.8883 (tp) cc_final: 0.8486 (mm) REVERT: A 354 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7483 (mm-30) REVERT: A 494 MET cc_start: 0.8700 (tpp) cc_final: 0.8127 (tpp) REVERT: A 926 GLU cc_start: 0.8613 (mp0) cc_final: 0.7690 (mp0) REVERT: B 187 ASN cc_start: 0.7511 (m-40) cc_final: 0.7303 (m-40) REVERT: B 388 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9205 (tt) REVERT: B 389 ILE cc_start: 0.9395 (OUTLIER) cc_final: 0.9161 (mp) REVERT: B 494 MET cc_start: 0.8711 (tpp) cc_final: 0.8118 (tpp) REVERT: B 649 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7629 (tp30) outliers start: 31 outliers final: 27 residues processed: 200 average time/residue: 0.1901 time to fit residues: 62.7690 Evaluate side-chains 203 residues out of total 1682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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 354 GLU Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 464 VAL 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 161 optimal weight: 7.9990 chunk 190 optimal weight: 20.0000 chunk 178 optimal weight: 20.0000 chunk 180 optimal weight: 40.0000 chunk 79 optimal weight: 0.2980 chunk 105 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 77 optimal weight: 20.0000 chunk 51 optimal weight: 8.9990 chunk 24 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 overall best weight: 4.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 764 ASN ** A 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 900 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.145982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099274 restraints weight = 29704.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.095890 restraints weight = 22852.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.096901 restraints weight = 18810.637| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 15238 Z= 0.247 Angle : 0.770 13.267 20820 Z= 0.372 Chirality : 0.043 0.282 2599 Planarity : 0.003 0.034 2529 Dihedral : 9.798 134.973 2956 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 2.99 % Allowed : 20.18 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.01 (0.19), residues: 1935 helix: 1.89 (0.14), residues: 1387 sheet: 1.68 (0.49), residues: 100 loop : -0.46 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.003 TRP A1091 HIS 0.004 0.001 HIS B 132 PHE 0.027 0.002 PHE A 195 TYR 0.026 0.001 TYR B 309 ARG 0.008 0.000 ARG A 573 Details of bonding type rmsd hydrogen bonds : bond 0.05558 ( 1067) hydrogen bonds : angle 3.99243 ( 3171) covalent geometry : bond 0.00576 (15238) covalent geometry : angle 0.76985 (20820) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4452.79 seconds wall clock time: 78 minutes 41.37 seconds (4721.37 seconds total)