Starting phenix.real_space_refine on Wed Mar 4 19:54:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yea_33768/03_2026/7yea_33768.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yea_33768/03_2026/7yea_33768.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yea_33768/03_2026/7yea_33768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yea_33768/03_2026/7yea_33768.map" model { file = "/net/cci-nas-00/data/ceres_data/7yea_33768/03_2026/7yea_33768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yea_33768/03_2026/7yea_33768.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 100 5.16 5 C 10146 2.51 5 N 2810 2.21 5 O 2960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16016 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 8008 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 963} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 8008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1017, 8008 Classifications: {'peptide': 1017} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 52, 'TRANS': 963} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 3.69, per 1000 atoms: 0.23 Number of scatterers: 16016 At special positions: 0 Unit cell: (198.891, 109.347, 128.289, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 100 16.00 O 2960 8.00 N 2810 7.00 C 10146 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.74 Conformation dependent library (CDL) restraints added in 772.4 milliseconds 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3844 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 8 sheets defined 65.5% alpha, 5.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 37 through 51 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 70 through 85 Processing helix chain 'A' and resid 88 through 103 removed outlier: 4.120A pdb=" N TYR A 92 " --> pdb=" O LEU A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 115 Processing helix chain 'A' and resid 123 through 135 removed outlier: 3.528A pdb=" N ILE A 127 " --> pdb=" O ILE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.759A pdb=" N ALA A 169 " --> pdb=" O ASN A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 187 removed outlier: 4.496A pdb=" N ALA A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N CYS A 179 " --> pdb=" O GLU A 175 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU A 181 " --> pdb=" O LYS A 177 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 205 Processing helix chain 'A' and resid 206 through 220 removed outlier: 3.556A pdb=" N ALA A 210 " --> pdb=" O GLU A 206 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N HIS A 212 " --> pdb=" O TRP A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 238 removed outlier: 3.714A pdb=" N ALA A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 253 Processing helix chain 'A' and resid 260 through 273 removed outlier: 3.528A pdb=" N ASN A 264 " --> pdb=" O VAL A 260 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 289 Processing helix chain 'A' and resid 292 through 305 removed outlier: 3.506A pdb=" N TYR A 296 " --> pdb=" O PHE A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 323 Processing helix chain 'A' and resid 326 through 339 Processing helix chain 'A' and resid 342 through 357 Processing helix chain 'A' and resid 360 through 375 Processing helix chain 'A' and resid 377 through 391 Processing helix chain 'A' and resid 394 through 409 removed outlier: 3.588A pdb=" N TYR A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 425 removed outlier: 3.573A pdb=" N LEU A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 444 through 459 Processing helix chain 'A' and resid 462 through 476 removed outlier: 3.661A pdb=" N TYR A 466 " --> pdb=" O PHE A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 481 through 499 Processing helix chain 'A' and resid 507 through 513 removed outlier: 3.741A pdb=" N MET A 511 " --> pdb=" O HIS A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 538 removed outlier: 3.870A pdb=" N VAL A 537 " --> pdb=" O ASP A 533 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU A 538 " --> pdb=" O LYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 570 through 575 Processing helix chain 'A' and resid 576 through 581 removed outlier: 3.538A pdb=" N MET A 580 " --> pdb=" O ILE A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 608 Processing helix chain 'A' and resid 620 through 632 removed outlier: 3.503A pdb=" N ALA A 624 " --> pdb=" O CYS A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 685 through 692 removed outlier: 4.263A pdb=" N GLU A 690 " --> pdb=" O GLU A 687 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR A 692 " --> pdb=" O ALA A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 712 removed outlier: 3.752A pdb=" N MET A 711 " --> pdb=" O ASP A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 717 removed outlier: 3.765A pdb=" N LYS A 717 " --> pdb=" O HIS A 714 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 746 removed outlier: 3.816A pdb=" N ASP A 746 " --> pdb=" O LYS A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 780 through 792 removed outlier: 3.643A pdb=" N ARG A 792 " --> pdb=" O GLU A 788 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 814 Processing helix chain 'A' and resid 814 through 819 removed outlier: 3.823A pdb=" N ALA A 818 " --> pdb=" O ASN A 814 " (cutoff:3.500A) Processing helix chain 'A' and resid 833 through 836 Processing helix chain 'A' and resid 854 through 867 Processing helix chain 'A' and resid 879 through 881 No H-bonds generated for 'chain 'A' and resid 879 through 881' Processing helix chain 'A' and resid 882 through 893 Processing helix chain 'A' and resid 907 through 914 Processing helix chain 'A' and resid 915 through 918 Processing helix chain 'A' and resid 931 through 940 Processing helix chain 'A' and resid 950 through 964 removed outlier: 4.686A pdb=" N ALA A 956 " --> pdb=" O ALA A 952 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA A 957 " --> pdb=" O SER A 953 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N SER A 958 " --> pdb=" O ARG A 954 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN A 959 " --> pdb=" O VAL A 955 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LEU A 960 " --> pdb=" O ALA A 956 " (cutoff:3.500A) Processing helix chain 'A' and resid 965 through 969 Processing helix chain 'A' and resid 972 through 986 Processing helix chain 'A' and resid 986 through 1004 removed outlier: 3.754A pdb=" N ILE A1002 " --> pdb=" O TRP A 998 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A1003 " --> pdb=" O LYS A 999 " (cutoff:3.500A) Processing helix chain 'A' and resid 1008 through 1029 removed outlier: 3.553A pdb=" N ALA A1029 " --> pdb=" O GLU A1025 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 35 Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 55 through 68 Processing helix chain 'B' and resid 70 through 85 Processing helix chain 'B' and resid 88 through 103 removed outlier: 4.119A pdb=" N TYR B 92 " --> pdb=" O LEU B 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 115 Processing helix chain 'B' and resid 123 through 135 removed outlier: 3.529A pdb=" N ILE B 127 " --> pdb=" O ILE B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 153 Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.758A pdb=" N ALA B 169 " --> pdb=" O ASN B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 187 removed outlier: 4.496A pdb=" N ALA B 178 " --> pdb=" O GLU B 174 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N CYS B 179 " --> pdb=" O GLU B 175 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LEU B 181 " --> pdb=" O LYS B 177 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N LYS B 182 " --> pdb=" O ALA B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 205 Processing helix chain 'B' and resid 206 through 220 removed outlier: 3.556A pdb=" N ALA B 210 " --> pdb=" O GLU B 206 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N HIS B 212 " --> pdb=" O TRP B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 225 through 238 removed outlier: 3.714A pdb=" N ALA B 238 " --> pdb=" O VAL B 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 253 Processing helix chain 'B' and resid 260 through 273 removed outlier: 3.528A pdb=" N ASN B 264 " --> pdb=" O VAL B 260 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ALA B 266 " --> pdb=" O HIS B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 289 Processing helix chain 'B' and resid 292 through 305 removed outlier: 3.506A pdb=" N TYR B 296 " --> pdb=" O PHE B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 323 Processing helix chain 'B' and resid 326 through 339 Processing helix chain 'B' and resid 342 through 357 Processing helix chain 'B' and resid 360 through 375 Processing helix chain 'B' and resid 377 through 391 Processing helix chain 'B' and resid 394 through 409 removed outlier: 3.587A pdb=" N TYR B 398 " --> pdb=" O PHE B 394 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 removed outlier: 3.573A pdb=" N LEU B 415 " --> pdb=" O VAL B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 428 through 443 Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 462 through 476 removed outlier: 3.661A pdb=" N TYR B 466 " --> pdb=" O PHE B 462 " (cutoff:3.500A) Processing helix chain 'B' and resid 481 through 499 Processing helix chain 'B' and resid 507 through 513 removed outlier: 3.741A pdb=" N MET B 511 " --> pdb=" O HIS B 508 " (cutoff:3.500A) Processing helix chain 'B' and resid 516 through 538 removed outlier: 3.869A pdb=" N VAL B 537 " --> pdb=" O ASP B 533 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N LEU B 538 " --> pdb=" O LYS B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 576 through 581 removed outlier: 3.539A pdb=" N MET B 580 " --> pdb=" O ILE B 577 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 608 Processing helix chain 'B' and resid 620 through 632 removed outlier: 3.504A pdb=" N ALA B 624 " --> pdb=" O CYS B 620 " (cutoff:3.500A) Processing helix chain 'B' and resid 648 through 653 Processing helix chain 'B' and resid 685 through 692 removed outlier: 4.263A pdb=" N GLU B 690 " --> pdb=" O GLU B 687 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR B 692 " --> pdb=" O ALA B 689 " (cutoff:3.500A) Processing helix chain 'B' and resid 707 through 712 removed outlier: 3.752A pdb=" N MET B 711 " --> pdb=" O ASP B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 713 through 717 removed outlier: 3.764A pdb=" N LYS B 717 " --> pdb=" O HIS B 714 " (cutoff:3.500A) Processing helix chain 'B' and resid 740 through 746 removed outlier: 3.817A pdb=" N ASP B 746 " --> pdb=" O LYS B 742 " (cutoff:3.500A) Processing helix chain 'B' and resid 780 through 792 removed outlier: 3.644A pdb=" N ARG B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 814 Processing helix chain 'B' and resid 814 through 819 removed outlier: 3.823A pdb=" N ALA B 818 " --> pdb=" O ASN B 814 " (cutoff:3.500A) Processing helix chain 'B' and resid 833 through 836 Processing helix chain 'B' and resid 854 through 867 Processing helix chain 'B' and resid 879 through 881 No H-bonds generated for 'chain 'B' and resid 879 through 881' Processing helix chain 'B' and resid 882 through 893 Processing helix chain 'B' and resid 907 through 914 Processing helix chain 'B' and resid 915 through 918 Processing helix chain 'B' and resid 931 through 940 Processing helix chain 'B' and resid 950 through 964 removed outlier: 4.686A pdb=" N ALA B 956 " --> pdb=" O ALA B 952 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ALA B 957 " --> pdb=" O SER B 953 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N SER B 958 " --> pdb=" O ARG B 954 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN B 959 " --> pdb=" O VAL B 955 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU B 960 " --> pdb=" O ALA B 956 " (cutoff:3.500A) Processing helix chain 'B' and resid 965 through 969 Processing helix chain 'B' and resid 972 through 986 Processing helix chain 'B' and resid 986 through 1004 removed outlier: 3.754A pdb=" N ILE B1002 " --> pdb=" O TRP B 998 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B1003 " --> pdb=" O LYS B 999 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1029 removed outlier: 3.553A pdb=" N ALA B1029 " --> pdb=" O GLU B1025 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 612 through 614 removed outlier: 6.231A pdb=" N LEU A 556 " --> pdb=" O GLU A 587 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N PHE A 589 " --> pdb=" O LEU A 556 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL A 558 " --> pdb=" O PHE A 589 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N TYR A 591 " --> pdb=" O VAL A 558 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N TYR A 560 " --> pdb=" O TYR A 591 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG A 557 " --> pdb=" O ILE A 635 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL A 637 " --> pdb=" O ARG A 557 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLY A 559 " --> pdb=" O VAL A 637 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 679 through 680 removed outlier: 7.222A pdb=" N THR A 679 " --> pdb=" O MET A 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 752 through 754 removed outlier: 5.687A pdb=" N ILE A 734 " --> pdb=" O ILE A 721 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 900 through 903 removed outlier: 7.940A pdb=" N ILE A 901 " --> pdb=" O SER A 871 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU A 873 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER A 903 " --> pdb=" O LEU A 873 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU A 875 " --> pdb=" O SER A 903 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ILE A 842 " --> pdb=" O VAL A 872 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TRP A 874 " --> pdb=" O ILE A 842 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N TYR A 844 " --> pdb=" O TRP A 874 " (cutoff:3.500A) removed outlier: 8.981A pdb=" N LEU A 876 " --> pdb=" O TYR A 844 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL A 843 " --> pdb=" O VAL A 920 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 612 through 614 removed outlier: 6.229A pdb=" N LEU B 556 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N PHE B 589 " --> pdb=" O LEU B 556 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL B 558 " --> pdb=" O PHE B 589 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N TYR B 591 " --> pdb=" O VAL B 558 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR B 560 " --> pdb=" O TYR B 591 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG B 557 " --> pdb=" O ILE B 635 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N VAL B 637 " --> pdb=" O ARG B 557 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N GLY B 559 " --> pdb=" O VAL B 637 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 679 through 680 removed outlier: 7.223A pdb=" N THR B 679 " --> pdb=" O MET B 699 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 752 through 754 removed outlier: 5.688A pdb=" N ILE B 734 " --> pdb=" O ILE B 721 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 900 through 903 removed outlier: 7.940A pdb=" N ILE B 901 " --> pdb=" O SER B 871 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N LEU B 873 " --> pdb=" O ILE B 901 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N SER B 903 " --> pdb=" O LEU B 873 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N LEU B 875 " --> pdb=" O SER B 903 " (cutoff:3.500A) removed outlier: 5.824A pdb=" N ILE B 842 " --> pdb=" O VAL B 872 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N TRP B 874 " --> pdb=" O ILE B 842 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N TYR B 844 " --> pdb=" O TRP B 874 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N LEU B 876 " --> pdb=" O TYR B 844 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N VAL B 843 " --> pdb=" O VAL B 920 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 892 hydrogen bonds defined for protein. 2568 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.92 Time building geometry restraints manager: 2.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 5255 1.33 - 1.45: 2369 1.45 - 1.57: 8606 1.57 - 1.69: 0 1.69 - 1.81: 156 Bond restraints: 16386 Sorted by residual: bond pdb=" C LEU A 512 " pdb=" N TYR A 513 " ideal model delta sigma weight residual 1.330 1.236 0.094 1.47e-02 4.63e+03 4.13e+01 bond pdb=" C LEU B 512 " pdb=" N TYR B 513 " ideal model delta sigma weight residual 1.330 1.236 0.094 1.47e-02 4.63e+03 4.11e+01 bond pdb=" CB TRP A 208 " pdb=" CG TRP A 208 " ideal model delta sigma weight residual 1.498 1.425 0.073 3.10e-02 1.04e+03 5.60e+00 bond pdb=" CB TRP B 208 " pdb=" CG TRP B 208 " ideal model delta sigma weight residual 1.498 1.425 0.073 3.10e-02 1.04e+03 5.57e+00 bond pdb=" CB LEU A 197 " pdb=" CG LEU A 197 " ideal model delta sigma weight residual 1.530 1.484 0.046 2.00e-02 2.50e+03 5.33e+00 ... (remaining 16381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 21202 1.72 - 3.45: 848 3.45 - 5.17: 153 5.17 - 6.90: 29 6.90 - 8.62: 12 Bond angle restraints: 22244 Sorted by residual: angle pdb=" C ALA A 217 " pdb=" N VAL A 218 " pdb=" CA VAL A 218 " ideal model delta sigma weight residual 121.84 116.83 5.01 1.13e+00 7.83e-01 1.97e+01 angle pdb=" C ALA B 217 " pdb=" N VAL B 218 " pdb=" CA VAL B 218 " ideal model delta sigma weight residual 121.84 116.84 5.00 1.13e+00 7.83e-01 1.96e+01 angle pdb=" N VAL B 218 " pdb=" CA VAL B 218 " pdb=" C VAL B 218 " ideal model delta sigma weight residual 112.96 109.11 3.85 1.00e+00 1.00e+00 1.48e+01 angle pdb=" N VAL A 218 " pdb=" CA VAL A 218 " pdb=" C VAL A 218 " ideal model delta sigma weight residual 112.96 109.15 3.81 1.00e+00 1.00e+00 1.45e+01 angle pdb=" C VAL A 605 " pdb=" N MET A 606 " pdb=" CA MET A 606 " ideal model delta sigma weight residual 121.58 114.78 6.80 1.95e+00 2.63e-01 1.22e+01 ... (remaining 22239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.41: 8770 16.41 - 32.83: 945 32.83 - 49.24: 159 49.24 - 65.66: 32 65.66 - 82.07: 8 Dihedral angle restraints: 9914 sinusoidal: 3954 harmonic: 5960 Sorted by residual: dihedral pdb=" CA ARG A 239 " pdb=" C ARG A 239 " pdb=" N ILE A 240 " pdb=" CA ILE A 240 " ideal model delta harmonic sigma weight residual 180.00 151.92 28.08 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA ARG B 239 " pdb=" C ARG B 239 " pdb=" N ILE B 240 " pdb=" CA ILE B 240 " ideal model delta harmonic sigma weight residual 180.00 151.95 28.05 0 5.00e+00 4.00e-02 3.15e+01 dihedral pdb=" CA HIS A 545 " pdb=" C HIS A 545 " pdb=" N PRO A 546 " pdb=" CA PRO A 546 " ideal model delta harmonic sigma weight residual -180.00 -152.61 -27.39 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 9911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1604 0.042 - 0.084: 621 0.084 - 0.126: 192 0.126 - 0.167: 19 0.167 - 0.209: 6 Chirality restraints: 2442 Sorted by residual: chirality pdb=" CB ILE A 795 " pdb=" CA ILE A 795 " pdb=" CG1 ILE A 795 " pdb=" CG2 ILE A 795 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE B 795 " pdb=" CA ILE B 795 " pdb=" CG1 ILE B 795 " pdb=" CG2 ILE B 795 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB VAL A 218 " pdb=" CA VAL A 218 " pdb=" CG1 VAL A 218 " pdb=" CG2 VAL A 218 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.34e-01 ... (remaining 2439 not shown) Planarity restraints: 2922 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 861 " -0.027 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP A 861 " 0.073 2.00e-02 2.50e+03 pdb=" CD1 TRP A 861 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP A 861 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 861 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 861 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 861 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 861 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 861 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 861 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 861 " -0.027 2.00e-02 2.50e+03 2.65e-02 1.76e+01 pdb=" CG TRP B 861 " 0.072 2.00e-02 2.50e+03 pdb=" CD1 TRP B 861 " -0.030 2.00e-02 2.50e+03 pdb=" CD2 TRP B 861 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 861 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP B 861 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP B 861 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 861 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 861 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 861 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 224 " -0.029 2.00e-02 2.50e+03 2.46e-02 1.06e+01 pdb=" CG PHE A 224 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 PHE A 224 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE A 224 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 224 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE A 224 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 224 " -0.006 2.00e-02 2.50e+03 ... (remaining 2919 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 419 2.66 - 3.22: 17850 3.22 - 3.78: 26730 3.78 - 4.34: 35203 4.34 - 4.90: 53330 Nonbonded interactions: 133532 Sorted by model distance: nonbonded pdb=" O LYS B 488 " pdb=" OG SER B 491 " model vdw 2.099 3.040 nonbonded pdb=" O LYS A 488 " pdb=" OG SER A 491 " model vdw 2.100 3.040 nonbonded pdb=" O ASN A 434 " pdb=" OG SER A 437 " model vdw 2.127 3.040 nonbonded pdb=" O ASN B 434 " pdb=" OG SER B 437 " model vdw 2.128 3.040 nonbonded pdb=" NH1 ARG A1018 " pdb=" OE1 GLN A1022 " model vdw 2.134 3.120 ... (remaining 133527 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 5.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.230 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 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 : 0.008 0.094 16386 Z= 0.365 Angle : 0.840 8.622 22244 Z= 0.472 Chirality : 0.048 0.209 2442 Planarity : 0.005 0.052 2922 Dihedral : 13.813 82.072 6070 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 22.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.64 % Favored : 92.36 % Rotamer: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.40 (0.19), residues: 2030 helix: -0.42 (0.14), residues: 1236 sheet: -2.24 (0.36), residues: 194 loop : -1.19 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 69 TYR 0.046 0.003 TYR B1020 PHE 0.057 0.003 PHE A 224 TRP 0.073 0.003 TRP A 861 HIS 0.007 0.002 HIS A 212 Details of bonding type rmsd covalent geometry : bond 0.00799 (16386) covalent geometry : angle 0.83990 (22244) hydrogen bonds : bond 0.17721 ( 892) hydrogen bonds : angle 7.80471 ( 2568) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.630 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.5464 (ppp) cc_final: 0.4989 (ppp) REVERT: B 25 MET cc_start: 0.5433 (ppp) cc_final: 0.4972 (ppp) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1085 time to fit residues: 24.1792 Evaluate side-chains 107 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 0.0970 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 GLN A 928 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 97 ASN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 928 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.130708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.113636 restraints weight = 46229.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.109405 restraints weight = 50376.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.106833 restraints weight = 41217.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.106191 restraints weight = 39640.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.104911 restraints weight = 37132.653| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 16386 Z= 0.161 Angle : 0.708 9.640 22244 Z= 0.366 Chirality : 0.044 0.165 2442 Planarity : 0.006 0.071 2922 Dihedral : 5.347 25.816 2210 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 12.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.94 % Allowed : 10.71 % Favored : 88.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.66 (0.19), residues: 2030 helix: 0.21 (0.14), residues: 1240 sheet: -2.06 (0.37), residues: 166 loop : -1.06 (0.29), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 792 TYR 0.023 0.002 TYR A1020 PHE 0.042 0.002 PHE A 66 TRP 0.044 0.002 TRP B 861 HIS 0.007 0.001 HIS B 65 Details of bonding type rmsd covalent geometry : bond 0.00345 (16386) covalent geometry : angle 0.70763 (22244) hydrogen bonds : bond 0.05457 ( 892) hydrogen bonds : angle 5.68875 ( 2568) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 891 GLN cc_start: 0.7668 (OUTLIER) cc_final: 0.7319 (pm20) REVERT: B 891 GLN cc_start: 0.7743 (OUTLIER) cc_final: 0.7352 (pm20) outliers start: 16 outliers final: 4 residues processed: 145 average time/residue: 0.1177 time to fit residues: 26.6662 Evaluate side-chains 128 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 122 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain A residue 1020 TYR Chi-restraints excluded: chain B residue 891 GLN Chi-restraints excluded: chain B residue 983 LEU Chi-restraints excluded: chain B residue 1020 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 7.9990 chunk 105 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 4 optimal weight: 2.9990 chunk 141 optimal weight: 4.9990 chunk 71 optimal weight: 20.0000 chunk 96 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 834 GLN B 29 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.130101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.112022 restraints weight = 46605.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3937 r_free = 0.3937 target = 0.110576 restraints weight = 54350.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.106079 restraints weight = 54975.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.106474 restraints weight = 55905.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.106270 restraints weight = 38905.870| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16386 Z= 0.172 Angle : 0.669 11.167 22244 Z= 0.344 Chirality : 0.043 0.152 2442 Planarity : 0.005 0.048 2922 Dihedral : 5.141 25.134 2210 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 2.05 % Allowed : 13.64 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.19), residues: 2030 helix: 0.43 (0.15), residues: 1236 sheet: -2.28 (0.38), residues: 154 loop : -1.05 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1018 TYR 0.038 0.002 TYR A1020 PHE 0.032 0.002 PHE B 66 TRP 0.027 0.001 TRP B 861 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00386 (16386) covalent geometry : angle 0.66936 (22244) hydrogen bonds : bond 0.04862 ( 892) hydrogen bonds : angle 5.25931 ( 2568) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 131 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9024 (OUTLIER) cc_final: 0.8387 (m-10) REVERT: A 891 GLN cc_start: 0.7667 (OUTLIER) cc_final: 0.7301 (pm20) REVERT: A 893 MET cc_start: 0.7387 (mpp) cc_final: 0.7124 (mmp) REVERT: B 146 TYR cc_start: 0.9029 (OUTLIER) cc_final: 0.8389 (m-10) REVERT: B 891 GLN cc_start: 0.7652 (OUTLIER) cc_final: 0.7278 (pm20) REVERT: B 893 MET cc_start: 0.7368 (mpp) cc_final: 0.7115 (mmp) outliers start: 35 outliers final: 12 residues processed: 159 average time/residue: 0.1002 time to fit residues: 26.0183 Evaluate side-chains 130 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain A residue 927 CYS Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 891 GLN Chi-restraints excluded: chain B residue 927 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 79 optimal weight: 10.0000 chunk 123 optimal weight: 0.5980 chunk 57 optimal weight: 10.0000 chunk 118 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 81 optimal weight: 0.8980 chunk 142 optimal weight: 0.9980 chunk 20 optimal weight: 0.0770 chunk 152 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 814 ASN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 298 ASN ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 814 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.133826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.118415 restraints weight = 49541.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.113654 restraints weight = 56425.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3955 r_free = 0.3955 target = 0.111228 restraints weight = 47960.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.110462 restraints weight = 45644.310| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.109047 restraints weight = 43450.885| |-----------------------------------------------------------------------------| r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7243 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16386 Z= 0.125 Angle : 0.651 12.835 22244 Z= 0.325 Chirality : 0.043 0.389 2442 Planarity : 0.005 0.053 2922 Dihedral : 4.817 23.900 2210 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 1.87 % Allowed : 16.28 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.30 (0.19), residues: 2030 helix: 0.59 (0.15), residues: 1240 sheet: -2.22 (0.38), residues: 154 loop : -1.06 (0.27), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.024 0.001 TYR A1020 PHE 0.039 0.002 PHE A 66 TRP 0.014 0.001 TRP B 861 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00271 (16386) covalent geometry : angle 0.65144 (22244) hydrogen bonds : bond 0.04037 ( 892) hydrogen bonds : angle 4.77710 ( 2568) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.8981 (OUTLIER) cc_final: 0.8456 (m-10) REVERT: A 891 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7266 (pm20) REVERT: B 146 TYR cc_start: 0.8982 (OUTLIER) cc_final: 0.8458 (m-10) REVERT: B 891 GLN cc_start: 0.7602 (OUTLIER) cc_final: 0.7247 (pm20) outliers start: 32 outliers final: 13 residues processed: 145 average time/residue: 0.1092 time to fit residues: 25.1449 Evaluate side-chains 127 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 110 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain A residue 927 CYS Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 891 GLN Chi-restraints excluded: chain B residue 927 CYS Chi-restraints excluded: chain B residue 945 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 26 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 86 optimal weight: 0.9990 chunk 153 optimal weight: 9.9990 chunk 91 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 167 optimal weight: 0.0980 chunk 131 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 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 = 0.4307 r_free = 0.4307 target = 0.133921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.118262 restraints weight = 49908.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.113600 restraints weight = 58355.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.111888 restraints weight = 48426.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.111719 restraints weight = 46964.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.111133 restraints weight = 37659.784| |-----------------------------------------------------------------------------| r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16386 Z= 0.120 Angle : 0.623 10.274 22244 Z= 0.310 Chirality : 0.041 0.176 2442 Planarity : 0.005 0.052 2922 Dihedral : 4.689 22.988 2210 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.05 % Allowed : 16.63 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.00 (0.19), residues: 2030 helix: 0.86 (0.15), residues: 1226 sheet: -2.10 (0.37), residues: 164 loop : -0.95 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 913 TYR 0.023 0.001 TYR B1020 PHE 0.039 0.002 PHE B 66 TRP 0.016 0.001 TRP B 861 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00267 (16386) covalent geometry : angle 0.62312 (22244) hydrogen bonds : bond 0.03815 ( 892) hydrogen bonds : angle 4.63777 ( 2568) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9060 (OUTLIER) cc_final: 0.8536 (m-10) REVERT: A 860 MET cc_start: 0.8004 (mtp) cc_final: 0.7735 (ttm) REVERT: A 891 GLN cc_start: 0.7671 (OUTLIER) cc_final: 0.7362 (pm20) REVERT: B 146 TYR cc_start: 0.9068 (OUTLIER) cc_final: 0.8546 (m-10) REVERT: B 891 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7355 (pm20) outliers start: 35 outliers final: 18 residues processed: 151 average time/residue: 0.1073 time to fit residues: 25.9593 Evaluate side-chains 132 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain A residue 927 CYS Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 891 GLN Chi-restraints excluded: chain B residue 927 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 3 optimal weight: 4.9990 chunk 93 optimal weight: 8.9990 chunk 149 optimal weight: 0.2980 chunk 4 optimal weight: 0.9980 chunk 180 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 120 optimal weight: 0.0970 chunk 124 optimal weight: 0.6980 chunk 122 optimal weight: 1.9990 chunk 146 optimal weight: 0.9980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 272 GLN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 272 GLN ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.132284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.115387 restraints weight = 47684.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.110255 restraints weight = 55842.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.108074 restraints weight = 46076.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.107394 restraints weight = 45876.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.106756 restraints weight = 36744.878| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7231 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16386 Z= 0.116 Angle : 0.631 12.237 22244 Z= 0.310 Chirality : 0.041 0.142 2442 Planarity : 0.005 0.053 2922 Dihedral : 4.541 22.330 2210 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % Rotamer: Outliers : 2.22 % Allowed : 17.80 % Favored : 79.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.19), residues: 2030 helix: 0.98 (0.15), residues: 1228 sheet: -2.01 (0.38), residues: 154 loop : -0.87 (0.27), residues: 648 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 69 TYR 0.018 0.001 TYR A1020 PHE 0.041 0.001 PHE A 66 TRP 0.008 0.001 TRP B 861 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00261 (16386) covalent geometry : angle 0.63149 (22244) hydrogen bonds : bond 0.03620 ( 892) hydrogen bonds : angle 4.51446 ( 2568) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.4105 (ppp) cc_final: 0.3894 (ppp) REVERT: A 146 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8473 (m-10) REVERT: A 891 GLN cc_start: 0.7711 (OUTLIER) cc_final: 0.7425 (pm20) REVERT: A 1016 LEU cc_start: 0.8713 (pp) cc_final: 0.8454 (pp) REVERT: B 146 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8480 (m-10) REVERT: B 891 GLN cc_start: 0.7692 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: B 1016 LEU cc_start: 0.8719 (pp) cc_final: 0.8469 (pp) outliers start: 38 outliers final: 20 residues processed: 159 average time/residue: 0.0975 time to fit residues: 25.2316 Evaluate side-chains 139 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 115 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain A residue 927 CYS Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 891 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 113 optimal weight: 0.9990 chunk 142 optimal weight: 1.9990 chunk 182 optimal weight: 0.2980 chunk 106 optimal weight: 0.9990 chunk 160 optimal weight: 9.9990 chunk 153 optimal weight: 0.4980 chunk 19 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 98 optimal weight: 0.4980 chunk 4 optimal weight: 9.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 HIS ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 581 HIS ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.134704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.119011 restraints weight = 49531.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.114649 restraints weight = 56879.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.112108 restraints weight = 49917.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.111915 restraints weight = 46683.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.111368 restraints weight = 37619.529| |-----------------------------------------------------------------------------| r_work (final): 0.3887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16386 Z= 0.113 Angle : 0.644 10.990 22244 Z= 0.312 Chirality : 0.041 0.232 2442 Planarity : 0.004 0.056 2922 Dihedral : 4.461 21.624 2210 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.75 % Allowed : 18.15 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.25 (0.19), residues: 2030 helix: 1.05 (0.15), residues: 1228 sheet: -2.00 (0.37), residues: 164 loop : -0.83 (0.27), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 913 TYR 0.020 0.001 TYR B 989 PHE 0.040 0.001 PHE B 66 TRP 0.010 0.001 TRP A 861 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00255 (16386) covalent geometry : angle 0.64418 (22244) hydrogen bonds : bond 0.03446 ( 892) hydrogen bonds : angle 4.44531 ( 2568) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 116 time to evaluate : 0.575 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9019 (OUTLIER) cc_final: 0.8478 (m-10) REVERT: A 891 GLN cc_start: 0.7647 (OUTLIER) cc_final: 0.7385 (pm20) REVERT: A 1016 LEU cc_start: 0.8727 (pp) cc_final: 0.8495 (pp) REVERT: A 1023 MET cc_start: 0.6484 (ttp) cc_final: 0.6223 (mtp) REVERT: B 146 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8488 (m-10) REVERT: B 580 MET cc_start: 0.6106 (pmm) cc_final: 0.5794 (pmm) REVERT: B 891 GLN cc_start: 0.7656 (OUTLIER) cc_final: 0.7390 (pm20) REVERT: B 1012 TYR cc_start: 0.8360 (t80) cc_final: 0.8063 (t80) REVERT: B 1016 LEU cc_start: 0.8707 (pp) cc_final: 0.8469 (pp) REVERT: B 1023 MET cc_start: 0.6655 (ttp) cc_final: 0.6272 (mtp) outliers start: 47 outliers final: 26 residues processed: 156 average time/residue: 0.1010 time to fit residues: 25.8131 Evaluate side-chains 145 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 115 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 581 HIS Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain A residue 927 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 891 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 180 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 117 optimal weight: 0.3980 chunk 173 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 132 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 109 optimal weight: 0.0040 chunk 164 optimal weight: 0.0970 chunk 131 optimal weight: 0.9990 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 GLN ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 581 HIS ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 ASN A1000 GLN ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.135172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.119585 restraints weight = 49742.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.115740 restraints weight = 57021.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.113538 restraints weight = 43731.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.113060 restraints weight = 47069.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.112259 restraints weight = 40368.358| |-----------------------------------------------------------------------------| r_work (final): 0.3894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16386 Z= 0.114 Angle : 0.676 13.885 22244 Z= 0.323 Chirality : 0.041 0.162 2442 Planarity : 0.004 0.053 2922 Dihedral : 4.394 21.152 2210 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.87 % Allowed : 19.67 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.19), residues: 2030 helix: 1.09 (0.15), residues: 1230 sheet: -1.95 (0.38), residues: 164 loop : -0.77 (0.28), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 69 TYR 0.017 0.001 TYR A1020 PHE 0.040 0.001 PHE B 66 TRP 0.007 0.001 TRP A 861 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00258 (16386) covalent geometry : angle 0.67615 (22244) hydrogen bonds : bond 0.03431 ( 892) hydrogen bonds : angle 4.45080 ( 2568) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 0.578 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8477 (m-10) REVERT: A 891 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: A 1016 LEU cc_start: 0.8713 (pp) cc_final: 0.8476 (pp) REVERT: A 1023 MET cc_start: 0.6440 (ttp) cc_final: 0.6116 (mtp) REVERT: B 25 MET cc_start: 0.4304 (ppp) cc_final: 0.3812 (ppp) REVERT: B 146 TYR cc_start: 0.9027 (OUTLIER) cc_final: 0.8486 (m-10) REVERT: B 891 GLN cc_start: 0.7670 (OUTLIER) cc_final: 0.7410 (pm20) REVERT: B 1016 LEU cc_start: 0.8745 (pp) cc_final: 0.8531 (pp) REVERT: B 1023 MET cc_start: 0.6671 (ttp) cc_final: 0.6313 (mtp) outliers start: 32 outliers final: 21 residues processed: 146 average time/residue: 0.1031 time to fit residues: 24.4606 Evaluate side-chains 140 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain A residue 927 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 891 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 79 optimal weight: 20.0000 chunk 194 optimal weight: 4.9990 chunk 192 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 186 optimal weight: 0.0040 chunk 80 optimal weight: 0.7980 chunk 125 optimal weight: 0.5980 chunk 199 optimal weight: 7.9990 chunk 71 optimal weight: 5.9990 chunk 143 optimal weight: 0.9980 chunk 118 optimal weight: 0.4980 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN B 84 GLN ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 806 ASN B 834 GLN B1000 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.133275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.115455 restraints weight = 46508.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.110310 restraints weight = 55953.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.108694 restraints weight = 43689.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.108103 restraints weight = 40712.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.107081 restraints weight = 37272.522| |-----------------------------------------------------------------------------| r_work (final): 0.3866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7205 moved from start: 0.3431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16386 Z= 0.118 Angle : 0.687 13.499 22244 Z= 0.329 Chirality : 0.042 0.193 2442 Planarity : 0.004 0.055 2922 Dihedral : 4.381 20.615 2210 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.87 % Allowed : 19.91 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.20), residues: 2030 helix: 1.13 (0.15), residues: 1230 sheet: -1.94 (0.37), residues: 164 loop : -0.67 (0.28), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 69 TYR 0.035 0.001 TYR A 989 PHE 0.043 0.001 PHE B 66 TRP 0.004 0.000 TRP A 479 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00268 (16386) covalent geometry : angle 0.68729 (22244) hydrogen bonds : bond 0.03464 ( 892) hydrogen bonds : angle 4.45751 ( 2568) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 122 time to evaluate : 0.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9023 (OUTLIER) cc_final: 0.8482 (m-10) REVERT: A 580 MET cc_start: 0.5754 (pmm) cc_final: 0.5392 (pmm) REVERT: A 891 GLN cc_start: 0.7717 (OUTLIER) cc_final: 0.7475 (pm20) REVERT: A 1012 TYR cc_start: 0.8407 (t80) cc_final: 0.8069 (t80) REVERT: B 25 MET cc_start: 0.4329 (ppp) cc_final: 0.3871 (ppp) REVERT: B 146 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8485 (m-10) REVERT: B 891 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7471 (pm20) REVERT: B 1012 TYR cc_start: 0.8359 (t80) cc_final: 0.8023 (t80) REVERT: B 1016 LEU cc_start: 0.8789 (pp) cc_final: 0.8495 (pp) REVERT: B 1023 MET cc_start: 0.6696 (ttp) cc_final: 0.6299 (mtp) outliers start: 32 outliers final: 23 residues processed: 151 average time/residue: 0.1109 time to fit residues: 26.1005 Evaluate side-chains 144 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 117 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 720 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain A residue 927 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 891 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 128 optimal weight: 0.8980 chunk 164 optimal weight: 0.4980 chunk 79 optimal weight: 20.0000 chunk 123 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 198 optimal weight: 9.9990 chunk 73 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 70 optimal weight: 30.0000 chunk 155 optimal weight: 0.3980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1000 GLN ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1000 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.134987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.119630 restraints weight = 49494.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.115964 restraints weight = 53633.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.112532 restraints weight = 50268.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.112355 restraints weight = 49017.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.111898 restraints weight = 38419.709| |-----------------------------------------------------------------------------| r_work (final): 0.3901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16386 Z= 0.128 Angle : 0.720 12.758 22244 Z= 0.346 Chirality : 0.044 0.299 2442 Planarity : 0.004 0.055 2922 Dihedral : 4.376 20.319 2210 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.76 % Allowed : 19.96 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.20), residues: 2030 helix: 1.15 (0.15), residues: 1230 sheet: -1.92 (0.38), residues: 164 loop : -0.62 (0.28), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 792 TYR 0.033 0.001 TYR A 989 PHE 0.045 0.001 PHE B 66 TRP 0.007 0.001 TRP A 861 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00298 (16386) covalent geometry : angle 0.71986 (22244) hydrogen bonds : bond 0.03590 ( 892) hydrogen bonds : angle 4.52750 ( 2568) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4060 Ramachandran restraints generated. 2030 Oldfield, 0 Emsley, 2030 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 119 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9050 (OUTLIER) cc_final: 0.8517 (m-10) REVERT: A 580 MET cc_start: 0.5796 (pmm) cc_final: 0.5372 (pmm) REVERT: A 891 GLN cc_start: 0.7749 (OUTLIER) cc_final: 0.7498 (pm20) REVERT: A 1012 TYR cc_start: 0.8349 (t80) cc_final: 0.8031 (t80) REVERT: B 146 TYR cc_start: 0.9045 (OUTLIER) cc_final: 0.8519 (m-10) REVERT: B 891 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7476 (pm20) REVERT: B 1012 TYR cc_start: 0.8275 (t80) cc_final: 0.7955 (t80) REVERT: B 1023 MET cc_start: 0.6727 (ttp) cc_final: 0.6495 (mtp) outliers start: 30 outliers final: 23 residues processed: 145 average time/residue: 0.1075 time to fit residues: 24.7984 Evaluate side-chains 142 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 115 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain A residue 927 CYS Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 510 SER Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 577 ILE Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 891 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 111 optimal weight: 0.6980 chunk 200 optimal weight: 0.9990 chunk 166 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 108 optimal weight: 0.9980 chunk 118 optimal weight: 0.2980 chunk 182 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 chunk 130 optimal weight: 0.5980 chunk 138 optimal weight: 6.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 710 ASN A1000 GLN ** B 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 710 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4304 r_free = 0.4304 target = 0.133635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.115283 restraints weight = 45794.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.110348 restraints weight = 55222.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.109282 restraints weight = 44939.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.108872 restraints weight = 38534.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.107766 restraints weight = 36843.979| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7176 moved from start: 0.3650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16386 Z= 0.121 Angle : 0.718 13.385 22244 Z= 0.345 Chirality : 0.044 0.299 2442 Planarity : 0.005 0.110 2922 Dihedral : 4.386 19.969 2210 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.64 % Allowed : 19.91 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.20), residues: 2030 helix: 1.18 (0.15), residues: 1232 sheet: -1.86 (0.38), residues: 164 loop : -0.64 (0.28), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG B 792 TYR 0.034 0.001 TYR B 989 PHE 0.045 0.001 PHE B 66 TRP 0.006 0.001 TRP B 861 HIS 0.007 0.001 HIS B 111 Details of bonding type rmsd covalent geometry : bond 0.00279 (16386) covalent geometry : angle 0.71780 (22244) hydrogen bonds : bond 0.03525 ( 892) hydrogen bonds : angle 4.49711 ( 2568) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2502.29 seconds wall clock time: 44 minutes 12.06 seconds (2652.06 seconds total)