Starting phenix.real_space_refine on Sat Jun 14 09:30:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yea_33768/06_2025/7yea_33768.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yea_33768/06_2025/7yea_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_33768/06_2025/7yea_33768.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yea_33768/06_2025/7yea_33768.map" model { file = "/net/cci-nas-00/data/ceres_data/7yea_33768/06_2025/7yea_33768.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yea_33768/06_2025/7yea_33768.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 10.06, per 1000 atoms: 0.63 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: 4.51 Conformation dependent library (CDL) restraints added in 2.1 seconds 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: 2.06 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: 6.30 Time building geometry restraints manager: 5.26 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: 0.09 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: 6.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.720 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 40.970 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.410 ------------------------------------------------------------------------------- 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 : 22.75 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (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 TRP 0.073 0.003 TRP A 861 HIS 0.007 0.002 HIS A 212 PHE 0.057 0.003 PHE A 224 TYR 0.046 0.003 TYR B1020 ARG 0.005 0.001 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.17721 ( 892) hydrogen bonds : angle 7.80471 ( 2568) covalent geometry : bond 0.00799 (16386) covalent geometry : angle 0.83990 (22244) *********************** 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 : 1.660 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: 0.2522 time to fit residues: 56.7762 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 : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 8.9990 chunk 153 optimal weight: 8.9990 chunk 84 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 103 optimal weight: 7.9990 chunk 81 optimal weight: 9.9990 chunk 158 optimal weight: 8.9990 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 183 optimal weight: 0.7980 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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 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 859 GLN B 928 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.129749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.111984 restraints weight = 46081.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.109828 restraints weight = 52411.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.106045 restraints weight = 45726.912| |-----------------------------------------------------------------------------| r_work (final): 0.3911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 16386 Z= 0.205 Angle : 0.727 9.633 22244 Z= 0.378 Chirality : 0.045 0.165 2442 Planarity : 0.006 0.079 2922 Dihedral : 5.466 26.325 2210 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 1.05 % Allowed : 11.12 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.19), residues: 2030 helix: 0.10 (0.14), residues: 1238 sheet: -2.13 (0.38), residues: 166 loop : -1.08 (0.29), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP B 861 HIS 0.008 0.001 HIS B 65 PHE 0.041 0.003 PHE A 66 TYR 0.053 0.002 TYR A1020 ARG 0.017 0.001 ARG B 792 Details of bonding type rmsd hydrogen bonds : bond 0.05663 ( 892) hydrogen bonds : angle 5.85847 ( 2568) covalent geometry : bond 0.00461 (16386) covalent geometry : angle 0.72664 (22244) *********************** 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 147 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.817 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 891 GLN cc_start: 0.7732 (OUTLIER) cc_final: 0.7382 (pm20) REVERT: B 891 GLN cc_start: 0.7748 (OUTLIER) cc_final: 0.7357 (pm20) outliers start: 18 outliers final: 9 residues processed: 139 average time/residue: 0.3007 time to fit residues: 66.4843 Evaluate side-chains 127 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1020 TYR Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 858 LEU 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 139 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 57 optimal weight: 8.9990 chunk 3 optimal weight: 0.9980 chunk 173 optimal weight: 20.0000 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 95 optimal weight: 4.9990 chunk 151 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- 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 298 ASN ** A 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 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 298 ASN ** B 581 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4208 r_free = 0.4208 target = 0.128141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.108792 restraints weight = 45890.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.103626 restraints weight = 50395.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.101637 restraints weight = 47762.848| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 16386 Z= 0.293 Angle : 0.749 10.204 22244 Z= 0.390 Chirality : 0.046 0.201 2442 Planarity : 0.005 0.049 2922 Dihedral : 5.531 29.262 2210 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.52 % Favored : 94.48 % Rotamer: Outliers : 1.99 % Allowed : 14.93 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.19), residues: 2030 helix: 0.12 (0.14), residues: 1238 sheet: -2.44 (0.38), residues: 154 loop : -1.24 (0.28), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 861 HIS 0.006 0.001 HIS A 111 PHE 0.041 0.003 PHE A 224 TYR 0.058 0.002 TYR B1020 ARG 0.004 0.000 ARG A1018 Details of bonding type rmsd hydrogen bonds : bond 0.05674 ( 892) hydrogen bonds : angle 5.76640 ( 2568) covalent geometry : bond 0.00667 (16386) covalent geometry : angle 0.74873 (22244) *********************** 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 159 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 125 time to evaluate : 1.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9101 (OUTLIER) cc_final: 0.8747 (m-10) REVERT: A 891 GLN cc_start: 0.7806 (OUTLIER) cc_final: 0.7401 (pm20) REVERT: B 146 TYR cc_start: 0.9105 (OUTLIER) cc_final: 0.8755 (m-10) REVERT: B 891 GLN cc_start: 0.7813 (OUTLIER) cc_final: 0.7412 (pm20) outliers start: 34 outliers final: 15 residues processed: 148 average time/residue: 0.2534 time to fit residues: 60.3655 Evaluate side-chains 138 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 1.706 ------------------------------------------------------------------------------- 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 525 GLU Chi-restraints excluded: chain A residue 637 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 858 LEU Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 525 GLU Chi-restraints excluded: chain B residue 637 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 858 LEU Chi-restraints excluded: chain B residue 891 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 23 optimal weight: 0.9990 chunk 100 optimal weight: 0.3980 chunk 118 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 63 optimal weight: 0.0570 chunk 61 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 160 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 29 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 overall best weight: 0.5098 ------------------------------------------------------------------------------- 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 ** 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 630 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.131295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3995 r_free = 0.3995 target = 0.114249 restraints weight = 47267.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.109473 restraints weight = 53171.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.108026 restraints weight = 45236.238| |-----------------------------------------------------------------------------| r_work (final): 0.3877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16386 Z= 0.121 Angle : 0.659 12.755 22244 Z= 0.327 Chirality : 0.043 0.379 2442 Planarity : 0.005 0.053 2922 Dihedral : 4.933 24.735 2210 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.17 % Allowed : 17.27 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.19), residues: 2030 helix: 0.51 (0.14), residues: 1246 sheet: -2.35 (0.37), residues: 154 loop : -1.13 (0.28), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 861 HIS 0.007 0.001 HIS B 111 PHE 0.037 0.002 PHE A 66 TYR 0.019 0.002 TYR A1020 ARG 0.003 0.000 ARG B 627 Details of bonding type rmsd hydrogen bonds : bond 0.04106 ( 892) hydrogen bonds : angle 4.90025 ( 2568) covalent geometry : bond 0.00261 (16386) covalent geometry : angle 0.65936 (22244) *********************** 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 171 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 1.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9017 (OUTLIER) cc_final: 0.8535 (m-10) REVERT: A 860 MET cc_start: 0.8158 (mtp) cc_final: 0.7727 (ttm) REVERT: A 891 GLN cc_start: 0.7628 (OUTLIER) cc_final: 0.7299 (pm20) REVERT: A 1016 LEU cc_start: 0.8650 (pp) cc_final: 0.8348 (pp) REVERT: B 146 TYR cc_start: 0.9015 (OUTLIER) cc_final: 0.8542 (m-10) REVERT: B 861 TRP cc_start: 0.8440 (m-90) cc_final: 0.7285 (m-90) REVERT: B 891 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7307 (pm20) REVERT: B 1016 LEU cc_start: 0.8623 (pp) cc_final: 0.8310 (pp) outliers start: 37 outliers final: 11 residues processed: 164 average time/residue: 0.2825 time to fit residues: 73.4432 Evaluate side-chains 137 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 2.867 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 891 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 125 optimal weight: 0.7980 chunk 169 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 163 optimal weight: 5.9990 chunk 121 optimal weight: 0.7980 chunk 49 optimal weight: 4.9990 chunk 185 optimal weight: 0.1980 chunk 192 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 ASN ** 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 ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.130763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.113522 restraints weight = 48001.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.110461 restraints weight = 52625.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.106884 restraints weight = 54808.386| |-----------------------------------------------------------------------------| r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2482 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= 0.145 Angle : 0.655 10.865 22244 Z= 0.328 Chirality : 0.042 0.149 2442 Planarity : 0.005 0.053 2922 Dihedral : 4.873 23.993 2210 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 11.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.87 % Allowed : 19.56 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.19), residues: 2030 helix: 0.63 (0.15), residues: 1244 sheet: -2.17 (0.38), residues: 152 loop : -1.13 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 861 HIS 0.007 0.001 HIS B 111 PHE 0.040 0.002 PHE B 66 TYR 0.020 0.001 TYR B1012 ARG 0.004 0.000 ARG A 913 Details of bonding type rmsd hydrogen bonds : bond 0.04181 ( 892) hydrogen bonds : angle 4.85003 ( 2568) covalent geometry : bond 0.00329 (16386) covalent geometry : angle 0.65507 (22244) *********************** 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 164 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 1.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9052 (OUTLIER) cc_final: 0.8592 (m-10) REVERT: A 891 GLN cc_start: 0.7733 (OUTLIER) cc_final: 0.7389 (pm20) REVERT: B 146 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8504 (m-10) REVERT: B 860 MET cc_start: 0.8112 (mtp) cc_final: 0.7848 (ttm) REVERT: B 891 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7389 (pm20) outliers start: 32 outliers final: 16 residues processed: 160 average time/residue: 0.2499 time to fit residues: 63.7061 Evaluate side-chains 137 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.492 ------------------------------------------------------------------------------- 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 245 VAL Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 735 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 B residue 146 TYR Chi-restraints excluded: chain B residue 190 PHE 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 104 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 chunk 58 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 176 optimal weight: 20.0000 chunk 66 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 119 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 ASN ** 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 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.131154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.114423 restraints weight = 47420.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.110652 restraints weight = 54035.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.108291 restraints weight = 44146.668| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.2733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 16386 Z= 0.132 Angle : 0.658 12.188 22244 Z= 0.324 Chirality : 0.042 0.222 2442 Planarity : 0.005 0.057 2922 Dihedral : 4.737 23.121 2210 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 2.22 % Allowed : 20.55 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 2030 helix: 0.78 (0.15), residues: 1232 sheet: -2.15 (0.38), residues: 154 loop : -0.97 (0.27), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 861 HIS 0.007 0.001 HIS B 111 PHE 0.041 0.002 PHE A 66 TYR 0.017 0.001 TYR B 989 ARG 0.003 0.000 ARG A 913 Details of bonding type rmsd hydrogen bonds : bond 0.03870 ( 892) hydrogen bonds : angle 4.71868 ( 2568) covalent geometry : bond 0.00303 (16386) covalent geometry : angle 0.65837 (22244) *********************** 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 : 2.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8544 (m-10) REVERT: A 891 GLN cc_start: 0.7682 (OUTLIER) cc_final: 0.7377 (pm20) REVERT: A 1016 LEU cc_start: 0.8499 (pp) cc_final: 0.8205 (pp) REVERT: B 146 TYR cc_start: 0.9074 (OUTLIER) cc_final: 0.8496 (m-10) REVERT: B 860 MET cc_start: 0.8008 (mtp) cc_final: 0.7674 (ttm) REVERT: B 891 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7365 (pm20) REVERT: B 946 MET cc_start: 0.7904 (ppp) cc_final: 0.7612 (ptp) REVERT: B 1016 LEU cc_start: 0.8582 (pp) cc_final: 0.8361 (pp) outliers start: 38 outliers final: 20 residues processed: 157 average time/residue: 0.2610 time to fit residues: 66.6177 Evaluate side-chains 145 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 2.564 ------------------------------------------------------------------------------- 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 858 LEU Chi-restraints excluded: chain A residue 891 GLN 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 735 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 8.9990 chunk 67 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 44 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 182 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 196 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 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 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.130038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.113624 restraints weight = 47812.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.110011 restraints weight = 51241.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.106147 restraints weight = 53542.085| |-----------------------------------------------------------------------------| r_work (final): 0.3906 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16386 Z= 0.182 Angle : 0.690 11.755 22244 Z= 0.341 Chirality : 0.043 0.276 2442 Planarity : 0.005 0.058 2922 Dihedral : 4.808 23.301 2210 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.93 % Allowed : 20.55 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.19), residues: 2030 helix: 0.75 (0.15), residues: 1240 sheet: -2.16 (0.38), residues: 154 loop : -0.92 (0.28), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 861 HIS 0.006 0.001 HIS B 111 PHE 0.041 0.002 PHE A 66 TYR 0.019 0.001 TYR A 989 ARG 0.003 0.000 ARG B1018 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 892) hydrogen bonds : angle 4.88599 ( 2568) covalent geometry : bond 0.00418 (16386) covalent geometry : angle 0.68966 (22244) *********************** 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 179 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 129 time to evaluate : 1.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9127 (OUTLIER) cc_final: 0.8540 (m-10) REVERT: A 860 MET cc_start: 0.7919 (mmm) cc_final: 0.7657 (ttm) REVERT: A 891 GLN cc_start: 0.7664 (OUTLIER) cc_final: 0.7364 (pm20) REVERT: A 1016 LEU cc_start: 0.8576 (pp) cc_final: 0.8304 (pp) REVERT: B 146 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.8611 (m-10) REVERT: B 891 GLN cc_start: 0.7734 (OUTLIER) cc_final: 0.7414 (pm20) REVERT: B 1016 LEU cc_start: 0.8695 (pp) cc_final: 0.8476 (pp) outliers start: 50 outliers final: 28 residues processed: 175 average time/residue: 0.2190 time to fit residues: 62.5638 Evaluate side-chains 157 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 125 time to evaluate : 1.680 ------------------------------------------------------------------------------- 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 240 ILE 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 782 ILE 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 240 ILE 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 782 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 95 optimal weight: 4.9990 chunk 166 optimal weight: 0.9990 chunk 159 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 171 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 chunk 175 optimal weight: 0.0970 overall best weight: 0.5138 ------------------------------------------------------------------------------- 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 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 814 ASN ** 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 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.131828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.114929 restraints weight = 47442.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.110835 restraints weight = 54460.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.107355 restraints weight = 38849.706| |-----------------------------------------------------------------------------| r_work (final): 0.3862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16386 Z= 0.121 Angle : 0.693 12.733 22244 Z= 0.335 Chirality : 0.043 0.311 2442 Planarity : 0.005 0.060 2922 Dihedral : 4.605 22.276 2210 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 1.99 % Allowed : 21.66 % Favored : 76.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.19), residues: 2030 helix: 0.95 (0.15), residues: 1232 sheet: -2.14 (0.37), residues: 164 loop : -0.85 (0.27), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 48 HIS 0.007 0.001 HIS B 111 PHE 0.043 0.001 PHE A 66 TYR 0.013 0.001 TYR A1020 ARG 0.005 0.000 ARG A 485 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 892) hydrogen bonds : angle 4.64829 ( 2568) covalent geometry : bond 0.00273 (16386) covalent geometry : angle 0.69262 (22244) *********************** 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 164 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 1.699 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9058 (OUTLIER) cc_final: 0.8476 (m-10) REVERT: A 860 MET cc_start: 0.7877 (mmm) cc_final: 0.7669 (ttm) REVERT: A 891 GLN cc_start: 0.7684 (OUTLIER) cc_final: 0.7427 (pm20) REVERT: A 1016 LEU cc_start: 0.8561 (pp) cc_final: 0.8320 (pp) REVERT: B 146 TYR cc_start: 0.9063 (OUTLIER) cc_final: 0.8583 (m-10) REVERT: B 891 GLN cc_start: 0.7685 (OUTLIER) cc_final: 0.7395 (pm20) outliers start: 34 outliers final: 23 residues processed: 160 average time/residue: 0.3180 time to fit residues: 84.1030 Evaluate side-chains 151 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 2.042 ------------------------------------------------------------------------------- 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 776 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 891 GLN 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 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 795 ILE 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 105 optimal weight: 10.0000 chunk 147 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 98 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 150 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 55 optimal weight: 0.0980 chunk 112 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 814 ASN ** 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 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 630 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.130764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.114095 restraints weight = 47477.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.110148 restraints weight = 53478.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.107604 restraints weight = 46669.640| |-----------------------------------------------------------------------------| r_work (final): 0.3927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16386 Z= 0.157 Angle : 0.702 12.687 22244 Z= 0.344 Chirality : 0.044 0.309 2442 Planarity : 0.005 0.059 2922 Dihedral : 4.614 22.172 2210 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.70 % Allowed : 22.42 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.19), residues: 2030 helix: 0.98 (0.15), residues: 1228 sheet: -2.09 (0.37), residues: 164 loop : -0.77 (0.28), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B1024 HIS 0.006 0.001 HIS B 111 PHE 0.043 0.002 PHE A 66 TYR 0.010 0.001 TYR A 32 ARG 0.006 0.000 ARG B1018 Details of bonding type rmsd hydrogen bonds : bond 0.04036 ( 892) hydrogen bonds : angle 4.74756 ( 2568) covalent geometry : bond 0.00363 (16386) covalent geometry : angle 0.70197 (22244) *********************** 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: 29 poor density : 125 time to evaluate : 1.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.4244 (ppp) cc_final: 0.3739 (ppp) REVERT: A 146 TYR cc_start: 0.9107 (OUTLIER) cc_final: 0.8530 (m-10) REVERT: A 891 GLN cc_start: 0.7701 (OUTLIER) cc_final: 0.7432 (pm20) REVERT: A 930 HIS cc_start: 0.8110 (OUTLIER) cc_final: 0.7560 (m90) REVERT: A 1023 MET cc_start: 0.6554 (ttp) cc_final: 0.6122 (mtp) REVERT: B 25 MET cc_start: 0.4185 (ppp) cc_final: 0.3708 (ppp) REVERT: B 146 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8528 (m-10) REVERT: B 891 GLN cc_start: 0.7713 (OUTLIER) cc_final: 0.7444 (pm20) outliers start: 29 outliers final: 23 residues processed: 149 average time/residue: 0.2389 time to fit residues: 57.3949 Evaluate side-chains 149 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 1.868 ------------------------------------------------------------------------------- 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 776 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 795 ILE Chi-restraints excluded: chain A residue 891 GLN Chi-restraints excluded: chain A residue 930 HIS 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 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 795 ILE Chi-restraints excluded: chain B residue 858 LEU 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 105 optimal weight: 10.0000 chunk 51 optimal weight: 0.0010 chunk 30 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 62 optimal weight: 0.9990 chunk 135 optimal weight: 0.8980 chunk 187 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6990 ------------------------------------------------------------------------------- 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 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 GLN ** B 111 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 = 0.4306 r_free = 0.4306 target = 0.133839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.117896 restraints weight = 49822.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.114885 restraints weight = 57789.327| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.112630 restraints weight = 48658.325| |-----------------------------------------------------------------------------| r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7079 moved from start: 0.3246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 16386 Z= 0.129 Angle : 0.716 14.931 22244 Z= 0.346 Chirality : 0.044 0.318 2442 Planarity : 0.005 0.060 2922 Dihedral : 4.528 21.575 2210 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 11.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.93 % Allowed : 22.31 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.19), residues: 2030 helix: 1.03 (0.15), residues: 1232 sheet: -2.09 (0.37), residues: 164 loop : -0.78 (0.28), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B1024 HIS 0.007 0.001 HIS B 111 PHE 0.045 0.002 PHE B 66 TYR 0.035 0.001 TYR B1020 ARG 0.005 0.000 ARG A 792 Details of bonding type rmsd hydrogen bonds : bond 0.03787 ( 892) hydrogen bonds : angle 4.67494 ( 2568) covalent geometry : bond 0.00296 (16386) covalent geometry : angle 0.71613 (22244) ********************** 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 158 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 125 time to evaluate : 2.028 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.4330 (ppp) cc_final: 0.3910 (ppp) REVERT: A 146 TYR cc_start: 0.9084 (OUTLIER) cc_final: 0.8500 (m-10) REVERT: A 891 GLN cc_start: 0.7681 (OUTLIER) cc_final: 0.7458 (pm20) REVERT: A 1023 MET cc_start: 0.6587 (ttp) cc_final: 0.6347 (mtp) REVERT: B 25 MET cc_start: 0.4332 (ppp) cc_final: 0.3915 (ppp) REVERT: B 146 TYR cc_start: 0.9077 (OUTLIER) cc_final: 0.8498 (m-10) REVERT: B 891 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7423 (pm20) REVERT: B 930 HIS cc_start: 0.8131 (OUTLIER) cc_final: 0.7663 (m90) outliers start: 33 outliers final: 22 residues processed: 154 average time/residue: 0.2545 time to fit residues: 62.4091 Evaluate side-chains 151 residues out of total 1710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 1.689 ------------------------------------------------------------------------------- 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 776 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 891 GLN 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 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 795 ILE Chi-restraints excluded: chain B residue 891 GLN Chi-restraints excluded: chain B residue 930 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 6 optimal weight: 0.0070 chunk 12 optimal weight: 0.8980 chunk 198 optimal weight: 0.9980 chunk 137 optimal weight: 0.8980 chunk 155 optimal weight: 4.9990 chunk 4 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 181 optimal weight: 10.0000 chunk 162 optimal weight: 0.8980 chunk 175 optimal weight: 30.0000 overall best weight: 0.7398 ------------------------------------------------------------------------------- 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** ** B 111 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.133998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.117917 restraints weight = 49454.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.114035 restraints weight = 59447.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.111330 restraints weight = 42542.255| |-----------------------------------------------------------------------------| r_work (final): 0.3888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16386 Z= 0.127 Angle : 0.723 13.225 22244 Z= 0.347 Chirality : 0.044 0.315 2442 Planarity : 0.005 0.063 2922 Dihedral : 4.464 21.242 2210 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.87 % Allowed : 22.19 % Favored : 75.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.89 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.20), residues: 2030 helix: 1.08 (0.15), residues: 1232 sheet: -2.04 (0.38), residues: 164 loop : -0.75 (0.28), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1024 HIS 0.007 0.001 HIS A 111 PHE 0.045 0.002 PHE B 66 TYR 0.042 0.001 TYR B1020 ARG 0.020 0.000 ARG B 792 Details of bonding type rmsd hydrogen bonds : bond 0.03702 ( 892) hydrogen bonds : angle 4.66805 ( 2568) covalent geometry : bond 0.00292 (16386) covalent geometry : angle 0.72286 (22244) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5919.69 seconds wall clock time: 107 minutes 26.60 seconds (6446.60 seconds total)