Starting phenix.real_space_refine on Tue Apr 9 10:00:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yea_33768/04_2024/7yea_33768.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yea_33768/04_2024/7yea_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yea_33768/04_2024/7yea_33768.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yea_33768/04_2024/7yea_33768.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yea_33768/04_2024/7yea_33768.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yea_33768/04_2024/7yea_33768.pdb" } 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 Residue "A TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 175": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 447": "OE1" <-> "OE2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A GLU 649": "OE1" <-> "OE2" Residue "A ARG 792": "NH1" <-> "NH2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 910": "OE1" <-> "OE2" Residue "A TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1017": "OE1" <-> "OE2" Residue "B TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 175": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 447": "OE1" <-> "OE2" Residue "B GLU 484": "OE1" <-> "OE2" Residue "B GLU 649": "OE1" <-> "OE2" Residue "B ARG 792": "NH1" <-> "NH2" Residue "B GLU 839": "OE1" <-> "OE2" Residue "B TYR 844": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 910": "OE1" <-> "OE2" Residue "B TYR 976": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1017": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 8.72, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.05 Conformation dependent library (CDL) restraints added in 3.0 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: 2.17 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: 6.16 Time building geometry restraints manager: 7.58 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: 96.68 - 104.17: 292 104.17 - 111.66: 7531 111.66 - 119.14: 5908 119.14 - 126.63: 8280 126.63 - 134.11: 233 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 2.440 nonbonded pdb=" O LYS A 488 " pdb=" OG SER A 491 " model vdw 2.100 2.440 nonbonded pdb=" O ASN A 434 " pdb=" OG SER A 437 " model vdw 2.127 2.440 nonbonded pdb=" O ASN B 434 " pdb=" OG SER B 437 " model vdw 2.128 2.440 nonbonded pdb=" NH1 ARG A1018 " pdb=" OE1 GLN A1022 " model vdw 2.134 2.520 ... (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 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: 4.610 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: 14.140 Check model and map are aligned: 0.260 Set scattering table: 0.160 Process input model: 47.140 Find NCS groups from input model: 0.840 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: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.150 ------------------------------------------------------------------------------- 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= 0.518 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.894 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: 0.2665 time to fit residues: 59.7400 Evaluate side-chains 107 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.929 ------------------------------------------------------------------------------- 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: 7.9990 chunk 153 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 52 optimal weight: 0.0970 chunk 103 optimal weight: 6.9990 chunk 81 optimal weight: 4.9990 chunk 158 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 chunk 183 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- 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 ** 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 859 GLN ** A 928 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 298 ASN ** 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 859 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 16386 Z= 0.390 Angle : 0.743 9.576 22244 Z= 0.390 Chirality : 0.046 0.162 2442 Planarity : 0.005 0.048 2922 Dihedral : 5.655 28.326 2210 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 1.46 % Allowed : 11.48 % Favored : 87.06 % 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: -0.99 (0.19), residues: 2030 helix: -0.04 (0.14), residues: 1238 sheet: -2.28 (0.37), residues: 166 loop : -1.19 (0.29), residues: 626 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP B 861 HIS 0.006 0.001 HIS A 111 PHE 0.042 0.003 PHE A 66 TYR 0.058 0.002 TYR A1020 ARG 0.004 0.000 ARG B 792 *********************** 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 fitting. rotamer outliers: 25 poor density : 122 time to evaluate : 1.922 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9056 (OUTLIER) cc_final: 0.8507 (m-10) REVERT: A 408 MET cc_start: 0.7639 (ppp) cc_final: 0.7012 (ppp) REVERT: B 146 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8503 (m-10) REVERT: B 408 MET cc_start: 0.7618 (ppp) cc_final: 0.6989 (ppp) outliers start: 25 outliers final: 16 residues processed: 135 average time/residue: 0.2581 time to fit residues: 55.2865 Evaluate side-chains 132 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 114 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 328 ASP Chi-restraints excluded: chain A residue 637 VAL Chi-restraints excluded: chain A residue 674 MET Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 983 LEU Chi-restraints excluded: chain A residue 1020 TYR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 637 VAL Chi-restraints excluded: chain B residue 674 MET Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 858 LEU 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 101 optimal weight: 20.0000 chunk 56 optimal weight: 10.0000 chunk 152 optimal weight: 10.0000 chunk 124 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 183 optimal weight: 0.9980 chunk 198 optimal weight: 0.9980 chunk 163 optimal weight: 7.9990 chunk 182 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 147 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- 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 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 29 HIS ** 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 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 863 ASN ** B 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7039 moved from start: 0.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16386 Z= 0.251 Angle : 0.649 10.253 22244 Z= 0.337 Chirality : 0.043 0.153 2442 Planarity : 0.005 0.046 2922 Dihedral : 5.269 25.843 2210 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.81 % Allowed : 15.75 % Favored : 82.44 % 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: -0.60 (0.19), residues: 2030 helix: 0.35 (0.14), residues: 1242 sheet: -2.25 (0.36), residues: 166 loop : -1.18 (0.28), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 861 HIS 0.006 0.001 HIS A 111 PHE 0.034 0.002 PHE B 66 TYR 0.057 0.002 TYR A1020 ARG 0.002 0.000 ARG B 501 *********************** 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 165 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 134 time to evaluate : 1.848 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 674 MET cc_start: 0.7065 (OUTLIER) cc_final: 0.6863 (mmm) REVERT: B 893 MET cc_start: 0.6983 (mpp) cc_final: 0.6767 (mmp) outliers start: 31 outliers final: 12 residues processed: 155 average time/residue: 0.2507 time to fit residues: 62.2135 Evaluate side-chains 129 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 116 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 674 MET 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 858 LEU Chi-restraints excluded: chain B residue 190 PHE 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 9.9990 chunk 138 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 87 optimal weight: 0.2980 chunk 123 optimal weight: 0.7980 chunk 184 optimal weight: 6.9990 chunk 195 optimal weight: 5.9990 chunk 96 optimal weight: 0.9990 chunk 174 optimal weight: 2.9990 chunk 52 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 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 ** 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 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16386 Z= 0.181 Angle : 0.650 14.175 22244 Z= 0.319 Chirality : 0.043 0.372 2442 Planarity : 0.005 0.050 2922 Dihedral : 4.941 25.058 2210 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.28 % Allowed : 17.39 % Favored : 80.33 % 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 (0.19), residues: 2030 helix: 0.63 (0.15), residues: 1246 sheet: -2.34 (0.36), residues: 164 loop : -1.15 (0.28), residues: 620 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 0.039 0.002 PHE B 66 TYR 0.019 0.001 TYR A1020 ARG 0.003 0.000 ARG B 627 *********************** 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 167 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 128 time to evaluate : 1.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.8472 (m-10) REVERT: A 691 GLN cc_start: 0.6943 (OUTLIER) cc_final: 0.6679 (pt0) REVERT: B 146 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.8470 (m-10) REVERT: B 691 GLN cc_start: 0.6839 (OUTLIER) cc_final: 0.6562 (pt0) REVERT: B 891 GLN cc_start: 0.7653 (OUTLIER) cc_final: 0.7253 (pm20) outliers start: 39 outliers final: 14 residues processed: 161 average time/residue: 0.2436 time to fit residues: 63.0127 Evaluate side-chains 135 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 116 time to evaluate : 1.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 691 GLN 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 858 LEU Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 691 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 145 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 166 optimal weight: 0.9990 chunk 134 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 99 optimal weight: 9.9990 chunk 175 optimal weight: 0.0000 chunk 49 optimal weight: 6.9990 overall best weight: 1.1790 ------------------------------------------------------------------------------- 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 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 863 ASN ** A 928 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 814 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6992 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16386 Z= 0.217 Angle : 0.646 12.207 22244 Z= 0.321 Chirality : 0.041 0.144 2442 Planarity : 0.004 0.049 2922 Dihedral : 4.827 24.441 2210 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.48 % Favored : 95.52 % Rotamer: Outliers : 2.34 % Allowed : 19.91 % Favored : 77.75 % 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: -0.14 (0.19), residues: 2030 helix: 0.79 (0.15), residues: 1242 sheet: -2.32 (0.36), residues: 164 loop : -1.10 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 861 HIS 0.007 0.001 HIS B 111 PHE 0.042 0.002 PHE A 66 TYR 0.017 0.001 TYR A1020 ARG 0.004 0.000 ARG B 69 *********************** 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 161 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 121 time to evaluate : 1.759 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.8581 (m-10) REVERT: A 691 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6673 (pt0) REVERT: B 146 TYR cc_start: 0.9065 (OUTLIER) cc_final: 0.8583 (m-10) REVERT: B 691 GLN cc_start: 0.6845 (OUTLIER) cc_final: 0.6582 (pt0) REVERT: B 891 GLN cc_start: 0.7608 (OUTLIER) cc_final: 0.7264 (pm20) outliers start: 40 outliers final: 23 residues processed: 154 average time/residue: 0.2301 time to fit residues: 57.5394 Evaluate side-chains 147 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 119 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 245 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 691 GLN Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 927 CYS Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 735 VAL Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 891 GLN Chi-restraints excluded: chain B residue 927 CYS Chi-restraints excluded: chain B residue 945 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 0.0970 chunk 175 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 114 optimal weight: 0.2980 chunk 48 optimal weight: 0.8980 chunk 195 optimal weight: 4.9990 chunk 162 optimal weight: 0.9990 chunk 90 optimal weight: 5.9990 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 791 ASN A 814 ASN ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** 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 791 ASN B 814 ASN ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16386 Z= 0.168 Angle : 0.623 12.940 22244 Z= 0.309 Chirality : 0.041 0.149 2442 Planarity : 0.004 0.051 2922 Dihedral : 4.640 23.571 2210 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.63 % Allowed : 19.44 % Favored : 77.93 % 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: 0.96 (0.15), residues: 1242 sheet: -2.26 (0.36), residues: 164 loop : -1.03 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 861 HIS 0.007 0.001 HIS B 111 PHE 0.042 0.002 PHE A 66 TYR 0.015 0.001 TYR A1020 ARG 0.005 0.000 ARG A 69 *********************** 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 172 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 127 time to evaluate : 1.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9042 (OUTLIER) cc_final: 0.8479 (m-10) REVERT: A 1016 LEU cc_start: 0.8278 (pp) cc_final: 0.8011 (pp) REVERT: B 146 TYR cc_start: 0.9041 (OUTLIER) cc_final: 0.8476 (m-10) REVERT: B 691 GLN cc_start: 0.6783 (OUTLIER) cc_final: 0.6571 (pt0) REVERT: B 860 MET cc_start: 0.7451 (mtp) cc_final: 0.7065 (ttm) REVERT: B 1016 LEU cc_start: 0.8261 (pp) cc_final: 0.8006 (pp) outliers start: 45 outliers final: 28 residues processed: 166 average time/residue: 0.2384 time to fit residues: 64.3146 Evaluate side-chains 148 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 117 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 155 ASP Chi-restraints excluded: chain A residue 190 PHE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 927 CYS Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 155 ASP Chi-restraints excluded: chain B residue 190 PHE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 328 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 720 VAL 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 858 LEU Chi-restraints excluded: chain B residue 927 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 111 optimal weight: 0.9990 chunk 142 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 164 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 194 optimal weight: 0.7980 chunk 121 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6949 moved from start: 0.2731 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= 0.178 Angle : 0.634 11.463 22244 Z= 0.314 Chirality : 0.041 0.205 2442 Planarity : 0.004 0.050 2922 Dihedral : 4.610 23.346 2210 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 2.40 % Allowed : 20.67 % Favored : 76.93 % 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: 0.17 (0.20), residues: 2030 helix: 1.04 (0.15), residues: 1242 sheet: -2.18 (0.36), residues: 164 loop : -0.99 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 861 HIS 0.007 0.001 HIS B 111 PHE 0.042 0.002 PHE B 66 TYR 0.019 0.001 TYR A 989 ARG 0.006 0.000 ARG A 69 *********************** 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 166 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 125 time to evaluate : 1.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 146 TYR cc_start: 0.9106 (OUTLIER) cc_final: 0.8532 (m-10) REVERT: A 930 HIS cc_start: 0.7884 (OUTLIER) cc_final: 0.7410 (m90) REVERT: B 146 TYR cc_start: 0.9098 (OUTLIER) cc_final: 0.8523 (m-10) REVERT: B 691 GLN cc_start: 0.6786 (OUTLIER) cc_final: 0.6581 (pt0) REVERT: B 860 MET cc_start: 0.7438 (mtp) cc_final: 0.7142 (ttm) REVERT: B 930 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7417 (m90) outliers start: 41 outliers final: 28 residues processed: 163 average time/residue: 0.2393 time to fit residues: 63.7200 Evaluate side-chains 148 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 115 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 155 ASP 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 328 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 735 VAL Chi-restraints excluded: chain A residue 741 LEU Chi-restraints excluded: chain A residue 745 LEU Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 788 GLU Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 155 ASP 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 328 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 691 GLN Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 927 CYS Chi-restraints excluded: chain B residue 930 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 0.8980 chunk 77 optimal weight: 20.0000 chunk 116 optimal weight: 0.7980 chunk 58 optimal weight: 4.9990 chunk 38 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 123 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 153 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 887 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.2881 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= 0.184 Angle : 0.657 13.582 22244 Z= 0.320 Chirality : 0.041 0.185 2442 Planarity : 0.004 0.052 2922 Dihedral : 4.530 22.777 2210 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.58 % Allowed : 21.19 % Favored : 76.23 % 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: 0.21 (0.19), residues: 2030 helix: 1.08 (0.15), residues: 1242 sheet: -2.06 (0.37), residues: 164 loop : -1.04 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 48 HIS 0.007 0.001 HIS A 111 PHE 0.042 0.001 PHE B 66 TYR 0.019 0.001 TYR A1012 ARG 0.007 0.000 ARG A 69 *********************** 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 169 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 125 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.4401 (ppp) cc_final: 0.3900 (ppp) REVERT: A 146 TYR cc_start: 0.9088 (OUTLIER) cc_final: 0.8512 (m-10) REVERT: A 930 HIS cc_start: 0.7895 (OUTLIER) cc_final: 0.7477 (m90) REVERT: A 1016 LEU cc_start: 0.8141 (pp) cc_final: 0.7840 (pp) REVERT: B 25 MET cc_start: 0.4451 (ppp) cc_final: 0.3980 (ppp) REVERT: B 146 TYR cc_start: 0.9081 (OUTLIER) cc_final: 0.8495 (m-10) REVERT: B 860 MET cc_start: 0.7413 (mtp) cc_final: 0.7130 (ttm) REVERT: B 930 HIS cc_start: 0.7899 (OUTLIER) cc_final: 0.7475 (m90) REVERT: B 1016 LEU cc_start: 0.8178 (pp) cc_final: 0.7892 (pp) outliers start: 44 outliers final: 26 residues processed: 159 average time/residue: 0.2387 time to fit residues: 60.9028 Evaluate side-chains 146 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 116 time to evaluate : 1.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 155 ASP 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 328 ASP Chi-restraints excluded: chain A residue 396 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 930 HIS Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 155 ASP 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 328 ASP Chi-restraints excluded: chain B residue 396 ASP Chi-restraints excluded: chain B residue 533 ASP Chi-restraints excluded: chain B residue 653 LEU Chi-restraints excluded: chain B residue 720 VAL Chi-restraints excluded: chain B residue 741 LEU Chi-restraints excluded: chain B residue 745 LEU Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 788 GLU Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 930 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 4.9990 chunk 186 optimal weight: 0.0870 chunk 170 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 142 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 163 optimal weight: 7.9990 chunk 171 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 GLN ** 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 332 ASN ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 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 332 ASN ** B 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 887 GLN ** B 891 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 897 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 16386 Z= 0.363 Angle : 0.743 13.982 22244 Z= 0.371 Chirality : 0.045 0.193 2442 Planarity : 0.005 0.047 2922 Dihedral : 4.860 25.161 2210 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.40 % Allowed : 21.66 % 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: 0.04 (0.20), residues: 2030 helix: 0.85 (0.15), residues: 1238 sheet: -1.98 (0.39), residues: 152 loop : -0.95 (0.28), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 48 HIS 0.006 0.001 HIS B 111 PHE 0.042 0.002 PHE B 66 TYR 0.033 0.002 TYR A 989 ARG 0.007 0.000 ARG B 69 *********************** 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 163 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 122 time to evaluate : 1.821 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.4475 (ppp) cc_final: 0.4115 (ppp) REVERT: A 146 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8732 (m-10) REVERT: A 860 MET cc_start: 0.7452 (mtp) cc_final: 0.7252 (ttm) REVERT: A 930 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7497 (m90) REVERT: A 1016 LEU cc_start: 0.8205 (pp) cc_final: 0.7926 (pp) REVERT: B 25 MET cc_start: 0.4488 (ppp) cc_final: 0.4119 (ppp) REVERT: B 146 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.8733 (m-10) REVERT: B 860 MET cc_start: 0.7560 (mtp) cc_final: 0.7248 (ttm) REVERT: B 930 HIS cc_start: 0.7993 (OUTLIER) cc_final: 0.7462 (m90) REVERT: B 1016 LEU cc_start: 0.8232 (pp) cc_final: 0.7958 (pp) outliers start: 41 outliers final: 33 residues processed: 157 average time/residue: 0.2372 time to fit residues: 60.5313 Evaluate side-chains 160 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 1.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 TYR Chi-restraints excluded: chain A residue 155 ASP 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 328 ASP Chi-restraints excluded: chain A residue 396 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 811 THR Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 930 HIS Chi-restraints excluded: chain A residue 945 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 155 ASP 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 328 ASP Chi-restraints excluded: chain B residue 396 ASP 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 811 THR Chi-restraints excluded: chain B residue 858 LEU Chi-restraints excluded: chain B residue 930 HIS Chi-restraints excluded: chain B residue 943 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 0.5980 chunk 191 optimal weight: 0.0050 chunk 117 optimal weight: 0.6980 chunk 91 optimal weight: 3.9990 chunk 133 optimal weight: 7.9990 chunk 201 optimal weight: 2.9990 chunk 185 optimal weight: 0.0270 chunk 160 optimal weight: 10.0000 chunk 16 optimal weight: 0.5980 chunk 123 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 overall best weight: 0.3852 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 GLN ** 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 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.3085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16386 Z= 0.172 Angle : 0.707 14.254 22244 Z= 0.336 Chirality : 0.043 0.334 2442 Planarity : 0.004 0.052 2922 Dihedral : 4.559 22.605 2210 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 14.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 1.81 % Allowed : 22.31 % 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: 0.24 (0.20), residues: 2030 helix: 1.04 (0.15), residues: 1240 sheet: -1.79 (0.39), residues: 152 loop : -0.99 (0.28), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 194 HIS 0.007 0.001 HIS B 111 PHE 0.045 0.001 PHE B 66 TYR 0.011 0.001 TYR B 418 ARG 0.008 0.000 ARG A 69 ********************** 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 157 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 126 time to evaluate : 1.990 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 25 MET cc_start: 0.4498 (ppp) cc_final: 0.4151 (ppp) REVERT: A 146 TYR cc_start: 0.9051 (OUTLIER) cc_final: 0.8539 (m-10) REVERT: A 1016 LEU cc_start: 0.8238 (pp) cc_final: 0.8003 (pp) REVERT: B 25 MET cc_start: 0.4623 (ppp) cc_final: 0.4289 (ppp) REVERT: B 146 TYR cc_start: 0.9055 (OUTLIER) cc_final: 0.8550 (m-10) REVERT: B 860 MET cc_start: 0.7464 (mtp) cc_final: 0.7236 (ttm) REVERT: B 1014 MET cc_start: 0.7403 (ppp) cc_final: 0.7146 (ppp) REVERT: B 1016 LEU cc_start: 0.8244 (pp) cc_final: 0.7975 (pp) outliers start: 31 outliers final: 25 residues processed: 156 average time/residue: 0.2463 time to fit residues: 61.7126 Evaluate side-chains 146 residues out of total 1710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 119 time to evaluate : 1.997 ------------------------------------------------------------------------------- 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 155 ASP 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 328 ASP Chi-restraints excluded: chain A residue 396 ASP Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 741 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 945 THR Chi-restraints excluded: chain B residue 55 THR Chi-restraints excluded: chain B residue 146 TYR Chi-restraints excluded: chain B residue 155 ASP 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 328 ASP Chi-restraints excluded: chain B residue 396 ASP 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 776 VAL Chi-restraints excluded: chain B residue 788 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 160 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 164 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 29 optimal weight: 0.0020 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 629 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 928 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 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 834 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 846 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 848 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 928 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 = 0.4275 r_free = 0.4275 target = 0.132269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.115443 restraints weight = 47465.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.111697 restraints weight = 53060.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.108973 restraints weight = 43556.016| |-----------------------------------------------------------------------------| r_work (final): 0.3898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3214 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= 0.182 Angle : 0.702 13.171 22244 Z= 0.334 Chirality : 0.043 0.315 2442 Planarity : 0.004 0.051 2922 Dihedral : 4.461 22.000 2210 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 1.99 % Allowed : 22.31 % Favored : 75.70 % 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: 1244 sheet: -1.76 (0.40), residues: 152 loop : -0.90 (0.28), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 48 HIS 0.007 0.001 HIS B 111 PHE 0.045 0.002 PHE B 66 TYR 0.034 0.001 TYR A 989 ARG 0.003 0.000 ARG B 69 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3072.27 seconds wall clock time: 57 minutes 9.36 seconds (3429.36 seconds total)