Starting phenix.real_space_refine on Thu Nov 20 06:38:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5w9m_8788/11_2025/5w9m_8788.cif Found real_map, /net/cci-nas-00/data/ceres_data/5w9m_8788/11_2025/5w9m_8788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5w9m_8788/11_2025/5w9m_8788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5w9m_8788/11_2025/5w9m_8788.map" model { file = "/net/cci-nas-00/data/ceres_data/5w9m_8788/11_2025/5w9m_8788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5w9m_8788/11_2025/5w9m_8788.cif" } resolution = 4.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 171 5.16 5 C 19751 2.51 5 N 5166 2.21 5 O 6038 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31126 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "B" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 3496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3496 Classifications: {'peptide': 457} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 431} Chain breaks: 2 Chain: "G" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 22, 'TRANS': 437} Chain breaks: 1 Chain: "H" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 948 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "I" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 835 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "E" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 3, 'PTRANS': 36, 'TRANS': 686} Chain: "F" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Chain: "J" Number of atoms: 5658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 726, 5658 Classifications: {'peptide': 726} Link IDs: {'CIS': 5, 'PTRANS': 36, 'TRANS': 684} Time building chain proxies: 7.46, per 1000 atoms: 0.24 Number of scatterers: 31126 At special positions: 0 Unit cell: (155.04, 154.02, 217.26, 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 171 16.00 O 6038 8.00 N 5166 7.00 C 19751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=55, symmetry=0 Simple disulfide: pdb=" SG CYS A 806 " - pdb=" SG CYS A 828 " distance=1.88 Simple disulfide: pdb=" SG CYS A 811 " - pdb=" SG CYS A 817 " distance=2.02 Simple disulfide: pdb=" SG CYS A 912 " - pdb=" SG CYS A 925 " distance=2.11 Simple disulfide: pdb=" SG CYS A1106 " - pdb=" SG CYS A1117 " distance=2.03 Simple disulfide: pdb=" SG CYS A1156 " - pdb=" SG CYS A1164 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 92 " distance=2.05 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.02 Simple disulfide: pdb=" SG CYS D 806 " - pdb=" SG CYS D 828 " distance=2.03 Simple disulfide: pdb=" SG CYS D 811 " - pdb=" SG CYS D 817 " distance=2.03 Simple disulfide: pdb=" SG CYS D 912 " - pdb=" SG CYS D 925 " distance=2.11 Simple disulfide: pdb=" SG CYS D1106 " - pdb=" SG CYS D1117 " distance=2.03 Simple disulfide: pdb=" SG CYS D1156 " - pdb=" SG CYS D1164 " distance=2.00 Simple disulfide: pdb=" SG CYS G 806 " - pdb=" SG CYS G 828 " distance=2.02 Simple disulfide: pdb=" SG CYS G 811 " - pdb=" SG CYS G 817 " distance=2.03 Simple disulfide: pdb=" SG CYS G 912 " - pdb=" SG CYS G 925 " distance=2.05 Simple disulfide: pdb=" SG CYS G1106 " - pdb=" SG CYS G1117 " distance=2.13 Simple disulfide: pdb=" SG CYS G1156 " - pdb=" SG CYS G1164 " distance=2.14 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.05 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 88 " distance=1.98 Simple disulfide: pdb=" SG CYS E 30 " - pdb=" SG CYS E 195 " distance=2.06 Simple disulfide: pdb=" SG CYS E 176 " - pdb=" SG CYS E 214 " distance=2.04 Simple disulfide: pdb=" SG CYS E 185 " - pdb=" SG CYS E 237 " distance=2.07 Simple disulfide: pdb=" SG CYS E 339 " - pdb=" SG CYS E 349 " distance=2.07 Simple disulfide: pdb=" SG CYS E 383 " - pdb=" SG CYS E 407 " distance=2.86 Simple disulfide: pdb=" SG CYS E 425 " - pdb=" SG CYS E 478 " distance=2.00 Simple disulfide: pdb=" SG CYS E 437 " - pdb=" SG CYS E 585 " distance=2.11 Simple disulfide: pdb=" SG CYS E 503 " - pdb=" SG CYS E 526 " distance=2.02 Simple disulfide: pdb=" SG CYS E 603 " - pdb=" SG CYS E 654 " distance=1.76 Simple disulfide: pdb=" SG CYS E 620 " - pdb=" SG CYS E 650 " distance=1.71 Simple disulfide: pdb=" SG CYS E 679 " - pdb=" SG CYS E 713 " distance=2.03 Simple disulfide: pdb=" SG CYS E 727 " - pdb=" SG CYS E 736 " distance=2.02 Simple disulfide: pdb=" SG CYS F 30 " - pdb=" SG CYS F 195 " distance=2.06 Simple disulfide: pdb=" SG CYS F 176 " - pdb=" SG CYS F 214 " distance=2.09 Simple disulfide: pdb=" SG CYS F 185 " - pdb=" SG CYS F 237 " distance=2.04 Simple disulfide: pdb=" SG CYS F 339 " - pdb=" SG CYS F 349 " distance=2.04 Simple disulfide: pdb=" SG CYS F 383 " - pdb=" SG CYS F 407 " distance=2.17 Simple disulfide: pdb=" SG CYS F 425 " - pdb=" SG CYS F 478 " distance=2.04 Simple disulfide: pdb=" SG CYS F 437 " - pdb=" SG CYS F 585 " distance=2.14 Simple disulfide: pdb=" SG CYS F 503 " - pdb=" SG CYS F 526 " distance=2.02 Simple disulfide: pdb=" SG CYS F 603 " - pdb=" SG CYS F 654 " distance=2.10 Simple disulfide: pdb=" SG CYS F 620 " - pdb=" SG CYS F 650 " distance=2.05 Simple disulfide: pdb=" SG CYS F 679 " - pdb=" SG CYS F 713 " distance=2.03 Simple disulfide: pdb=" SG CYS F 727 " - pdb=" SG CYS F 736 " distance=2.02 Simple disulfide: pdb=" SG CYS J 30 " - pdb=" SG CYS J 195 " distance=2.05 Simple disulfide: pdb=" SG CYS J 176 " - pdb=" SG CYS J 214 " distance=2.08 Simple disulfide: pdb=" SG CYS J 185 " - pdb=" SG CYS J 237 " distance=2.07 Simple disulfide: pdb=" SG CYS J 339 " - pdb=" SG CYS J 349 " distance=2.04 Simple disulfide: pdb=" SG CYS J 383 " - pdb=" SG CYS J 407 " distance=2.07 Simple disulfide: pdb=" SG CYS J 425 " - pdb=" SG CYS J 478 " distance=2.38 Simple disulfide: pdb=" SG CYS J 437 " - pdb=" SG CYS J 585 " distance=2.09 Simple disulfide: pdb=" SG CYS J 503 " - pdb=" SG CYS J 526 " distance=2.02 Simple disulfide: pdb=" SG CYS J 603 " - pdb=" SG CYS J 654 " distance=2.23 Simple disulfide: pdb=" SG CYS J 620 " - pdb=" SG CYS J 650 " distance=2.13 Simple disulfide: pdb=" SG CYS J 679 " - pdb=" SG CYS J 713 " distance=2.07 Simple disulfide: pdb=" SG CYS J 727 " - pdb=" SG CYS J 736 " distance=1.78 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.93 Conformation dependent library (CDL) restraints added in 1.3 seconds 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7470 Finding SS restraints... Secondary structure from input PDB file: 99 helices and 69 sheets defined 23.6% alpha, 25.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.61 Creating SS restraints... Processing helix chain 'A' and resid 816 through 821 Processing helix chain 'A' and resid 824 through 854 removed outlier: 3.688A pdb=" N SER A 852 " --> pdb=" O ASN A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 888 through 898 Processing helix chain 'A' and resid 907 through 912 Processing helix chain 'A' and resid 922 through 931 removed outlier: 3.559A pdb=" N ALA A 926 " --> pdb=" O ASP A 922 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N TYR A 928 " --> pdb=" O ILE A 924 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 929 " --> pdb=" O CYS A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 940 through 953 Processing helix chain 'A' and resid 971 through 982 Processing helix chain 'A' and resid 986 through 993 Processing helix chain 'A' and resid 993 through 1007 Processing helix chain 'A' and resid 1008 through 1010 No H-bonds generated for 'chain 'A' and resid 1008 through 1010' Processing helix chain 'A' and resid 1016 through 1040 removed outlier: 3.506A pdb=" N LEU A1040 " --> pdb=" O LEU A1036 " (cutoff:3.500A) Processing helix chain 'A' and resid 1050 through 1058 Processing helix chain 'A' and resid 1059 through 1104 removed outlier: 4.810A pdb=" N ALA A1065 " --> pdb=" O PRO A1061 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLN A1066 " --> pdb=" O GLU A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1198 through 1200 No H-bonds generated for 'chain 'A' and resid 1198 through 1200' Processing helix chain 'B' and resid 61 through 64 Processing helix chain 'B' and resid 83 through 87 Processing helix chain 'C' and resid 79 through 83 Processing helix chain 'D' and resid 814 through 821 Processing helix chain 'D' and resid 824 through 854 removed outlier: 3.536A pdb=" N CYS D 828 " --> pdb=" O TYR D 824 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N SER D 852 " --> pdb=" O ASN D 848 " (cutoff:3.500A) Processing helix chain 'D' and resid 888 through 898 Processing helix chain 'D' and resid 907 through 912 Processing helix chain 'D' and resid 922 through 931 removed outlier: 5.390A pdb=" N TYR D 928 " --> pdb=" O ILE D 924 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N VAL D 929 " --> pdb=" O CYS D 925 " (cutoff:3.500A) Processing helix chain 'D' and resid 940 through 953 Processing helix chain 'D' and resid 971 through 982 Processing helix chain 'D' and resid 986 through 993 Processing helix chain 'D' and resid 993 through 1007 Processing helix chain 'D' and resid 1008 through 1011 Processing helix chain 'D' and resid 1016 through 1041 removed outlier: 3.528A pdb=" N LEU D1036 " --> pdb=" O ALA D1032 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N SER D1041 " --> pdb=" O ALA D1037 " (cutoff:3.500A) Processing helix chain 'D' and resid 1050 through 1058 Processing helix chain 'D' and resid 1059 through 1104 Processing helix chain 'D' and resid 1198 through 1200 No H-bonds generated for 'chain 'D' and resid 1198 through 1200' Processing helix chain 'G' and resid 814 through 821 Processing helix chain 'G' and resid 824 through 854 Processing helix chain 'G' and resid 888 through 898 Processing helix chain 'G' and resid 922 through 931 removed outlier: 3.525A pdb=" N ALA G 926 " --> pdb=" O ASP G 922 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN G 927 " --> pdb=" O LEU G 923 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N TYR G 928 " --> pdb=" O ILE G 924 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N VAL G 929 " --> pdb=" O CYS G 925 " (cutoff:3.500A) Processing helix chain 'G' and resid 940 through 953 Processing helix chain 'G' and resid 971 through 982 Processing helix chain 'G' and resid 986 through 993 Processing helix chain 'G' and resid 993 through 1007 Processing helix chain 'G' and resid 1008 through 1011 Processing helix chain 'G' and resid 1016 through 1040 Processing helix chain 'G' and resid 1050 through 1058 Processing helix chain 'G' and resid 1059 through 1104 removed outlier: 4.326A pdb=" N ALA G1065 " --> pdb=" O PRO G1061 " (cutoff:3.500A) Processing helix chain 'G' and resid 1198 through 1200 No H-bonds generated for 'chain 'G' and resid 1198 through 1200' Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.702A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 83 through 87 Processing helix chain 'I' and resid 79 through 83 Processing helix chain 'E' and resid 37 through 41 Processing helix chain 'E' and resid 49 through 53 Processing helix chain 'E' and resid 104 through 108 Processing helix chain 'E' and resid 133 through 137 Processing helix chain 'E' and resid 222 through 230 Processing helix chain 'E' and resid 303 through 307 Processing helix chain 'E' and resid 342 through 351 Processing helix chain 'E' and resid 385 through 390 removed outlier: 3.516A pdb=" N SER E 390 " --> pdb=" O PRO E 387 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 399 removed outlier: 3.716A pdb=" N PHE E 399 " --> pdb=" O VAL E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 410 through 415 Processing helix chain 'E' and resid 416 through 418 No H-bonds generated for 'chain 'E' and resid 416 through 418' Processing helix chain 'E' and resid 429 through 436 removed outlier: 3.961A pdb=" N ALA E 434 " --> pdb=" O PRO E 430 " (cutoff:3.500A) Processing helix chain 'E' and resid 449 through 456 removed outlier: 4.957A pdb=" N SER E 454 " --> pdb=" O SER E 451 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 Processing helix chain 'E' and resid 524 through 529 Processing helix chain 'E' and resid 546 through 550 Processing helix chain 'E' and resid 675 through 678 removed outlier: 3.680A pdb=" N ALA E 678 " --> pdb=" O GLY E 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 675 through 678' Processing helix chain 'E' and resid 694 through 702 removed outlier: 3.615A pdb=" N LYS E 698 " --> pdb=" O ARG E 694 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N ARG E 700 " --> pdb=" O MET E 696 " (cutoff:3.500A) Processing helix chain 'F' and resid 37 through 41 removed outlier: 4.156A pdb=" N ASP F 41 " --> pdb=" O THR F 38 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 53 Processing helix chain 'F' and resid 104 through 108 Processing helix chain 'F' and resid 133 through 137 Processing helix chain 'F' and resid 222 through 230 Processing helix chain 'F' and resid 303 through 307 removed outlier: 3.911A pdb=" N ARG F 307 " --> pdb=" O GLN F 304 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 351 Processing helix chain 'F' and resid 385 through 390 removed outlier: 3.624A pdb=" N SER F 390 " --> pdb=" O PRO F 387 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 399 removed outlier: 4.212A pdb=" N PHE F 399 " --> pdb=" O VAL F 396 " (cutoff:3.500A) Processing helix chain 'F' and resid 410 through 416 removed outlier: 3.621A pdb=" N LEU F 414 " --> pdb=" O ASN F 410 " (cutoff:3.500A) Processing helix chain 'F' and resid 431 through 436 Processing helix chain 'F' and resid 449 through 456 removed outlier: 5.168A pdb=" N SER F 454 " --> pdb=" O SER F 451 " (cutoff:3.500A) Processing helix chain 'F' and resid 462 through 468 Processing helix chain 'F' and resid 524 through 529 Processing helix chain 'F' and resid 675 through 678 removed outlier: 4.221A pdb=" N ALA F 678 " --> pdb=" O GLY F 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 675 through 678' Processing helix chain 'F' and resid 694 through 702 removed outlier: 4.887A pdb=" N ARG F 700 " --> pdb=" O MET F 696 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 41 Processing helix chain 'J' and resid 49 through 53 Processing helix chain 'J' and resid 104 through 107 Processing helix chain 'J' and resid 133 through 137 Processing helix chain 'J' and resid 222 through 230 Processing helix chain 'J' and resid 303 through 307 removed outlier: 3.944A pdb=" N ARG J 307 " --> pdb=" O GLN J 304 " (cutoff:3.500A) Processing helix chain 'J' and resid 342 through 351 Processing helix chain 'J' and resid 385 through 389 Processing helix chain 'J' and resid 410 through 416 removed outlier: 4.072A pdb=" N LEU J 414 " --> pdb=" O ASN J 410 " (cutoff:3.500A) Processing helix chain 'J' and resid 429 through 436 removed outlier: 3.644A pdb=" N ALA J 434 " --> pdb=" O PRO J 430 " (cutoff:3.500A) Processing helix chain 'J' and resid 449 through 456 removed outlier: 4.621A pdb=" N SER J 454 " --> pdb=" O SER J 451 " (cutoff:3.500A) Processing helix chain 'J' and resid 462 through 468 Processing helix chain 'J' and resid 524 through 529 Processing helix chain 'J' and resid 546 through 550 Processing helix chain 'J' and resid 675 through 678 removed outlier: 4.437A pdb=" N ALA J 678 " --> pdb=" O GLY J 675 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 675 through 678' Processing helix chain 'J' and resid 694 through 702 removed outlier: 4.837A pdb=" N ARG J 700 " --> pdb=" O MET J 696 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 719 through 724 removed outlier: 7.468A pdb=" N LEU A 759 " --> pdb=" O SER E 720 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LEU E 722 " --> pdb=" O LEU A 759 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 768 through 769 removed outlier: 5.691A pdb=" N ILE A 768 " --> pdb=" O SER D 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 777 through 782 removed outlier: 5.908A pdb=" N VAL A1150 " --> pdb=" O LYS A1174 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N PHE A1172 " --> pdb=" O ALA A1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 785 through 796 Processing sheet with id=AA5, first strand: chain 'A' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'A' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'A' and resid 1202 through 1204 removed outlier: 6.178A pdb=" N CYS A1156 " --> pdb=" O ILE A1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 6 removed outlier: 3.887A pdb=" N ALA B 78 " --> pdb=" O CYS B 22 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 57 through 59 removed outlier: 6.418A pdb=" N SER B 44 " --> pdb=" O SER B 40 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL B 50 " --> pdb=" O ILE B 34 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE B 34 " --> pdb=" O VAL B 50 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 96 through 99 removed outlier: 5.485A pdb=" N TYR B 97 " --> pdb=" O ALA B 100D" (cutoff:3.500A) removed outlier: 7.376A pdb=" N ALA B 100D" --> pdb=" O TYR B 97 " (cutoff:3.500A) removed outlier: 4.523A pdb=" N VAL B 99 " --> pdb=" O VAL B 100B" (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 10 through 13 removed outlier: 7.011A pdb=" N MET C 33 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER C 49 " --> pdb=" O MET C 33 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N TRP C 35 " --> pdb=" O LEU C 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 19 through 22 Processing sheet with id=AB4, first strand: chain 'F' and resid 719 through 724 removed outlier: 7.116A pdb=" N LEU D 759 " --> pdb=" O SER F 720 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N LEU F 722 " --> pdb=" O LEU D 759 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 768 through 769 removed outlier: 5.754A pdb=" N ILE D 768 " --> pdb=" O SER G 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'D' and resid 777 through 782 removed outlier: 5.734A pdb=" N VAL D1150 " --> pdb=" O LYS D1174 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N PHE D1172 " --> pdb=" O ALA D1152 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 785 through 796 Processing sheet with id=AB8, first strand: chain 'D' and resid 802 through 804 Processing sheet with id=AB9, first strand: chain 'D' and resid 1202 through 1204 removed outlier: 6.543A pdb=" N CYS D1156 " --> pdb=" O ILE D1214 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 719 through 724 removed outlier: 7.222A pdb=" N LEU G 759 " --> pdb=" O SER J 720 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N LEU J 722 " --> pdb=" O LEU G 759 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLY J 732 " --> pdb=" O LEU J 735 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ALA J 737 " --> pdb=" O PRO J 730 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 777 through 782 removed outlier: 5.917A pdb=" N VAL G1150 " --> pdb=" O LYS G1174 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N PHE G1172 " --> pdb=" O ALA G1152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 785 through 796 removed outlier: 3.763A pdb=" N VAL G1139 " --> pdb=" O VAL G1124 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N VAL G1124 " --> pdb=" O VAL G1139 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 802 through 804 Processing sheet with id=AC5, first strand: chain 'G' and resid 1165 through 1167 Processing sheet with id=AC6, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AC7, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.372A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N VAL H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'H' and resid 96 through 99 removed outlier: 5.306A pdb=" N TYR H 97 " --> pdb=" O ALA H 100D" (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA H 100D" --> pdb=" O TYR H 97 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N VAL H 99 " --> pdb=" O VAL H 100B" (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 10 through 13 removed outlier: 6.757A pdb=" N MET I 33 " --> pdb=" O SER I 49 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N SER I 49 " --> pdb=" O MET I 33 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N TRP I 35 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'I' and resid 17 through 24 removed outlier: 5.706A pdb=" N GLN I 17 " --> pdb=" O PRO I 77 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE I 71 " --> pdb=" O CYS I 23 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'E' and resid 33 through 35 removed outlier: 6.118A pdb=" N ASP E 34 " --> pdb=" O VAL E 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'E' and resid 68 through 76 removed outlier: 6.514A pdb=" N SER E 267 " --> pdb=" O GLN E 280 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N GLN E 280 " --> pdb=" O SER E 267 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'E' and resid 83 through 85 removed outlier: 3.626A pdb=" N ARG E 335 " --> pdb=" O ASP E 326 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'E' and resid 88 through 89 removed outlier: 7.646A pdb=" N SER E 88 " --> pdb=" O ILE E 300 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'E' and resid 92 through 93 Processing sheet with id=AD7, first strand: chain 'E' and resid 110 through 111 removed outlier: 4.516A pdb=" N ALA E 146 " --> pdb=" O ILE E 296 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N LEU E 180 " --> pdb=" O TYR E 241 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N TYR E 241 " --> pdb=" O LEU E 180 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ALA E 182 " --> pdb=" O PHE E 239 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE E 239 " --> pdb=" O ALA E 182 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N TYR E 184 " --> pdb=" O CYS E 237 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N CYS E 237 " --> pdb=" O TYR E 184 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'E' and resid 126 through 127 removed outlier: 4.124A pdb=" N SER E 126 " --> pdb=" O ILE E 140 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ALA E 309 " --> pdb=" O THR E 139 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AE1, first strand: chain 'E' and resid 359 through 366 removed outlier: 4.114A pdb=" N VAL E 659 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER E 365 " --> pdb=" O VAL E 657 " (cutoff:3.500A) removed outlier: 5.905A pdb=" N VAL E 657 " --> pdb=" O SER E 365 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 374 through 376 Processing sheet with id=AE3, first strand: chain 'E' and resid 400 through 404 removed outlier: 6.649A pdb=" N THR E 483 " --> pdb=" O VAL E 420 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N VAL E 420 " --> pdb=" O THR E 483 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'E' and resid 513 through 515 removed outlier: 5.410A pdb=" N SER E 498 " --> pdb=" O VAL E 561 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL E 561 " --> pdb=" O SER E 498 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N ILE E 500 " --> pdb=" O SER E 559 " (cutoff:3.500A) removed outlier: 6.168A pdb=" N SER E 559 " --> pdb=" O ILE E 500 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 617 through 619 removed outlier: 4.840A pdb=" N VAL E 639 " --> pdb=" O LEU E 651 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL E 631 " --> pdb=" O VAL E 639 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'F' and resid 33 through 35 removed outlier: 5.903A pdb=" N ASP F 34 " --> pdb=" O VAL F 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'F' and resid 69 through 76 removed outlier: 6.475A pdb=" N SER F 267 " --> pdb=" O GLN F 280 " (cutoff:3.500A) removed outlier: 5.444A pdb=" N GLN F 280 " --> pdb=" O SER F 267 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'F' and resid 83 through 85 removed outlier: 3.669A pdb=" N ARG F 335 " --> pdb=" O ASP F 326 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'F' and resid 88 through 89 removed outlier: 7.571A pdb=" N SER F 88 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'F' and resid 92 through 93 Processing sheet with id=AF2, first strand: chain 'F' and resid 110 through 111 removed outlier: 4.476A pdb=" N ALA F 146 " --> pdb=" O ILE F 296 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N ILE F 186 " --> pdb=" O CYS F 237 " (cutoff:3.500A) removed outlier: 6.055A pdb=" N CYS F 237 " --> pdb=" O ILE F 186 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N GLU F 188 " --> pdb=" O ARG F 235 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ARG F 235 " --> pdb=" O GLU F 188 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'F' and resid 126 through 127 removed outlier: 4.390A pdb=" N SER F 126 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ALA F 309 " --> pdb=" O THR F 139 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AF5, first strand: chain 'F' and resid 359 through 366 removed outlier: 3.997A pdb=" N VAL F 659 " --> pdb=" O VAL F 363 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N SER F 365 " --> pdb=" O VAL F 657 " (cutoff:3.500A) removed outlier: 5.916A pdb=" N VAL F 657 " --> pdb=" O SER F 365 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 374 through 375 Processing sheet with id=AF7, first strand: chain 'F' and resid 381 through 382 removed outlier: 6.373A pdb=" N VAL F 381 " --> pdb=" O ASN F 408 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N CYS F 407 " --> pdb=" O CYS F 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'F' and resid 400 through 404 removed outlier: 3.692A pdb=" N LYS F 400 " --> pdb=" O TYR F 445 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N THR F 483 " --> pdb=" O VAL F 420 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N VAL F 420 " --> pdb=" O THR F 483 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 513 through 515 removed outlier: 5.363A pdb=" N SER F 498 " --> pdb=" O VAL F 561 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL F 561 " --> pdb=" O SER F 498 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N ILE F 500 " --> pdb=" O SER F 559 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N SER F 559 " --> pdb=" O ILE F 500 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 617 through 618 removed outlier: 5.353A pdb=" N VAL F 639 " --> pdb=" O LEU F 651 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL F 631 " --> pdb=" O VAL F 639 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 33 through 35 Processing sheet with id=AG3, first strand: chain 'J' and resid 68 through 76 removed outlier: 6.475A pdb=" N SER J 267 " --> pdb=" O GLN J 280 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N GLN J 280 " --> pdb=" O SER J 267 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'J' and resid 83 through 85 removed outlier: 3.696A pdb=" N ARG J 335 " --> pdb=" O ASP J 326 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'J' and resid 88 through 89 removed outlier: 7.607A pdb=" N SER J 88 " --> pdb=" O ILE J 300 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'J' and resid 92 through 93 Processing sheet with id=AG7, first strand: chain 'J' and resid 109 through 111 removed outlier: 4.437A pdb=" N ALA J 146 " --> pdb=" O ILE J 296 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N LEU J 180 " --> pdb=" O THR J 242 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N THR J 242 " --> pdb=" O LEU J 180 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ALA J 182 " --> pdb=" O MET J 240 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N MET J 240 " --> pdb=" O ALA J 182 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N TYR J 184 " --> pdb=" O THR J 238 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ILE J 186 " --> pdb=" O ASN J 236 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N ASN J 236 " --> pdb=" O ILE J 186 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLU J 188 " --> pdb=" O LEU J 234 " (cutoff:3.500A) removed outlier: 5.572A pdb=" N LEU J 234 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'J' and resid 126 through 127 removed outlier: 4.100A pdb=" N SER J 126 " --> pdb=" O ILE J 140 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA J 309 " --> pdb=" O THR J 139 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'J' and resid 153 through 154 Processing sheet with id=AH1, first strand: chain 'J' and resid 359 through 366 removed outlier: 4.282A pdb=" N VAL J 659 " --> pdb=" O VAL J 363 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N SER J 365 " --> pdb=" O VAL J 657 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL J 657 " --> pdb=" O SER J 365 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'J' and resid 371 through 375 removed outlier: 7.349A pdb=" N SER J 371 " --> pdb=" O GLU J 605 " (cutoff:3.500A) removed outlier: 9.490A pdb=" N SER J 607 " --> pdb=" O SER J 371 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N SER J 373 " --> pdb=" O SER J 607 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'J' and resid 381 through 382 removed outlier: 6.329A pdb=" N VAL J 381 " --> pdb=" O ASN J 408 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N CYS J 407 " --> pdb=" O CYS J 585 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'J' and resid 400 through 404 removed outlier: 7.007A pdb=" N THR J 477 " --> pdb=" O CYS J 425 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N CYS J 425 " --> pdb=" O THR J 477 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU J 479 " --> pdb=" O PHE J 423 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N PHE J 423 " --> pdb=" O LEU J 479 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N LEU J 481 " --> pdb=" O ASN J 421 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'J' and resid 513 through 515 removed outlier: 5.454A pdb=" N SER J 498 " --> pdb=" O VAL J 561 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL J 561 " --> pdb=" O SER J 498 " (cutoff:3.500A) removed outlier: 5.459A pdb=" N ILE J 500 " --> pdb=" O SER J 559 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N SER J 559 " --> pdb=" O ILE J 500 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'J' and resid 617 through 619 removed outlier: 5.487A pdb=" N VAL J 639 " --> pdb=" O LEU J 651 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL J 631 " --> pdb=" O VAL J 639 " (cutoff:3.500A) 1176 hydrogen bonds defined for protein. 3027 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: 8.18 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 6819 1.32 - 1.46: 10617 1.46 - 1.60: 14192 1.60 - 1.73: 1 1.73 - 1.87: 232 Bond restraints: 31861 Sorted by residual: bond pdb=" C CYS J 185 " pdb=" O CYS J 185 " ideal model delta sigma weight residual 1.233 1.301 -0.067 1.17e-02 7.31e+03 3.32e+01 bond pdb=" CA LYS A 807 " pdb=" C LYS A 807 " ideal model delta sigma weight residual 1.521 1.468 0.053 9.90e-03 1.02e+04 2.86e+01 bond pdb=" CA PRO G1219 " pdb=" C PRO G1219 " ideal model delta sigma weight residual 1.517 1.567 -0.050 9.30e-03 1.16e+04 2.85e+01 bond pdb=" N CYS J 185 " pdb=" CA CYS J 185 " ideal model delta sigma weight residual 1.456 1.395 0.061 1.16e-02 7.43e+03 2.79e+01 bond pdb=" C ASN J 236 " pdb=" N CYS J 237 " ideal model delta sigma weight residual 1.331 1.403 -0.072 1.37e-02 5.33e+03 2.76e+01 ... (remaining 31856 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 39402 2.88 - 5.76: 3381 5.76 - 8.65: 477 8.65 - 11.53: 68 11.53 - 14.41: 8 Bond angle restraints: 43336 Sorted by residual: angle pdb=" N PRO G1220 " pdb=" CA PRO G1220 " pdb=" C PRO G1220 " ideal model delta sigma weight residual 110.70 125.11 -14.41 1.22e+00 6.72e-01 1.39e+02 angle pdb=" N PRO G1219 " pdb=" CA PRO G1219 " pdb=" C PRO G1219 " ideal model delta sigma weight residual 110.70 124.99 -14.29 1.22e+00 6.72e-01 1.37e+02 angle pdb=" C GLN I 42 " pdb=" N PRO I 43 " pdb=" CA PRO I 43 " ideal model delta sigma weight residual 119.66 127.44 -7.78 7.20e-01 1.93e+00 1.17e+02 angle pdb=" C GLN C 42 " pdb=" N PRO C 43 " pdb=" CA PRO C 43 " ideal model delta sigma weight residual 119.66 127.54 -7.88 7.30e-01 1.88e+00 1.17e+02 angle pdb=" C LEU A 935 " pdb=" N PRO A 936 " pdb=" CA PRO A 936 " ideal model delta sigma weight residual 119.66 126.83 -7.17 7.20e-01 1.93e+00 9.93e+01 ... (remaining 43331 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 18336 17.98 - 35.97: 448 35.97 - 53.95: 156 53.95 - 71.93: 65 71.93 - 89.92: 21 Dihedral angle restraints: 19026 sinusoidal: 7317 harmonic: 11709 Sorted by residual: dihedral pdb=" CB CYS I 23 " pdb=" SG CYS I 23 " pdb=" SG CYS I 88 " pdb=" CB CYS I 88 " ideal model delta sinusoidal sigma weight residual 93.00 166.83 -73.83 1 1.00e+01 1.00e-02 6.93e+01 dihedral pdb=" CB CYS C 23 " pdb=" SG CYS C 23 " pdb=" SG CYS C 88 " pdb=" CB CYS C 88 " ideal model delta sinusoidal sigma weight residual 93.00 163.88 -70.88 1 1.00e+01 1.00e-02 6.46e+01 dihedral pdb=" CB CYS D1106 " pdb=" SG CYS D1106 " pdb=" SG CYS D1117 " pdb=" CB CYS D1117 " ideal model delta sinusoidal sigma weight residual 93.00 158.22 -65.22 1 1.00e+01 1.00e-02 5.58e+01 ... (remaining 19023 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2962 0.073 - 0.146: 1470 0.146 - 0.219: 325 0.219 - 0.292: 50 0.292 - 0.366: 9 Chirality restraints: 4816 Sorted by residual: chirality pdb=" CA CYS J 727 " pdb=" N CYS J 727 " pdb=" C CYS J 727 " pdb=" CB CYS J 727 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.34e+00 chirality pdb=" CA GLN J 688 " pdb=" N GLN J 688 " pdb=" C GLN J 688 " pdb=" CB GLN J 688 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.89e+00 chirality pdb=" CA LEU F 717 " pdb=" N LEU F 717 " pdb=" C LEU F 717 " pdb=" CB LEU F 717 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.44e+00 ... (remaining 4813 not shown) Planarity restraints: 5634 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " 0.089 2.00e-02 2.50e+03 4.51e-02 5.09e+01 pdb=" CG TRP H 47 " -0.024 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " -0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " -0.013 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " -0.012 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " -0.064 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " 0.040 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 932 " -0.081 2.00e-02 2.50e+03 4.59e-02 4.22e+01 pdb=" CG TYR G 932 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR G 932 " 0.034 2.00e-02 2.50e+03 pdb=" CD2 TYR G 932 " 0.034 2.00e-02 2.50e+03 pdb=" CE1 TYR G 932 " 0.028 2.00e-02 2.50e+03 pdb=" CE2 TYR G 932 " 0.028 2.00e-02 2.50e+03 pdb=" CZ TYR G 932 " 0.010 2.00e-02 2.50e+03 pdb=" OH TYR G 932 " -0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS F 603 " -0.029 2.00e-02 2.50e+03 5.90e-02 3.48e+01 pdb=" C CYS F 603 " 0.102 2.00e-02 2.50e+03 pdb=" O CYS F 603 " -0.041 2.00e-02 2.50e+03 pdb=" N VAL F 604 " -0.032 2.00e-02 2.50e+03 ... (remaining 5631 not shown) Histogram of nonbonded interaction distances: 1.31 - 2.02: 14 2.02 - 2.74: 4099 2.74 - 3.46: 43257 3.46 - 4.18: 77162 4.18 - 4.90: 129736 Nonbonded interactions: 254268 Sorted by model distance: nonbonded pdb=" OH TYR A 905 " pdb=" CA PRO A 936 " model vdw 1.306 3.470 nonbonded pdb=" OH TYR G 905 " pdb=" O VAL G 934 " model vdw 1.598 3.040 nonbonded pdb=" CG1 VAL E 381 " pdb=" N ASN E 408 " model vdw 1.617 3.540 nonbonded pdb=" OH TYR D 905 " pdb=" N PRO D 936 " model vdw 1.702 3.120 nonbonded pdb=" CE2 PHE F 506 " pdb=" CG2 VAL F 555 " model vdw 1.741 3.760 ... (remaining 254263 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 753 through 1176 or resid 1183 through 1223)) selection = chain 'D' selection = (chain 'G' and (resid 753 through 1176 or resid 1183 through 1223)) } ncs_group { reference = chain 'B' selection = chain 'H' } ncs_group { reference = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'J' } 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: 2.310 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: 0.040 Extract box with map and model: 0.520 Check model and map are aligned: 0.110 Set scattering table: 0.100 Process input model: 32.030 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 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 : 0.015 0.825 31917 Z= 0.924 Angle : 1.795 46.426 43446 Z= 1.216 Chirality : 0.085 0.366 4816 Planarity : 0.012 0.121 5634 Dihedral : 10.414 89.917 11391 Min Nonbonded Distance : 1.306 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.55 % Allowed : 3.36 % Favored : 96.09 % Rotamer: Outliers : 0.09 % Allowed : 0.41 % Favored : 99.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.65 (0.13), residues: 3993 helix: -0.34 (0.17), residues: 658 sheet: 0.79 (0.16), residues: 871 loop : 1.91 (0.13), residues: 2464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 841 TYR 0.081 0.007 TYR G 932 PHE 0.036 0.005 PHE I 98 TRP 0.089 0.010 TRP H 47 HIS 0.010 0.002 HIS C 76 Details of bonding type rmsd covalent geometry : bond 0.01363 (31861) covalent geometry : angle 1.75175 (43336) SS BOND : bond 0.14836 ( 55) SS BOND : angle 8.02236 ( 110) hydrogen bonds : bond 0.19880 ( 1176) hydrogen bonds : angle 8.14551 ( 3027) Misc. bond : bond 0.04507 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 612 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 609 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1104 ASN cc_start: 0.8838 (m-40) cc_final: 0.7938 (t0) REVERT: B 2 VAL cc_start: 0.7807 (t) cc_final: 0.7333 (t) REVERT: B 28 THR cc_start: 0.8504 (m) cc_final: 0.8207 (p) REVERT: B 32 TYR cc_start: 0.7747 (p90) cc_final: 0.6725 (p90) REVERT: B 35 HIS cc_start: 0.9182 (m-70) cc_final: 0.8828 (m-70) REVERT: B 36 TRP cc_start: 0.8516 (m100) cc_final: 0.7199 (m100) REVERT: B 45 LEU cc_start: 0.9315 (mp) cc_final: 0.9050 (mp) REVERT: B 46 GLU cc_start: 0.8318 (pt0) cc_final: 0.7982 (pt0) REVERT: B 56 ASN cc_start: 0.8594 (m-40) cc_final: 0.8066 (t0) REVERT: B 80 MET cc_start: 0.9355 (tmm) cc_final: 0.9086 (tmm) REVERT: B 82 LEU cc_start: 0.8246 (tt) cc_final: 0.7771 (tt) REVERT: C 33 MET cc_start: 0.7907 (tpp) cc_final: 0.7704 (mmm) REVERT: C 36 PHE cc_start: 0.9221 (m-80) cc_final: 0.8934 (m-80) REVERT: C 85 MET cc_start: 0.9298 (mmm) cc_final: 0.8683 (mmm) REVERT: C 89 GLN cc_start: 0.6940 (tm-30) cc_final: 0.6327 (tm-30) REVERT: D 757 MET cc_start: 0.9174 (mmp) cc_final: 0.8968 (mmm) REVERT: D 780 LEU cc_start: 0.9393 (tp) cc_final: 0.9151 (tt) REVERT: D 793 GLU cc_start: 0.8698 (pt0) cc_final: 0.8482 (pm20) REVERT: D 850 PHE cc_start: 0.8293 (m-10) cc_final: 0.8013 (m-10) REVERT: D 943 MET cc_start: 0.8624 (mtp) cc_final: 0.8422 (ttm) REVERT: D 977 PHE cc_start: 0.9060 (m-80) cc_final: 0.8660 (m-10) REVERT: D 1001 PHE cc_start: 0.9251 (t80) cc_final: 0.8374 (t80) REVERT: D 1136 PHE cc_start: 0.8910 (m-80) cc_final: 0.8372 (m-10) REVERT: D 1190 SER cc_start: 0.8257 (t) cc_final: 0.7804 (t) REVERT: G 874 LEU cc_start: 0.9132 (mt) cc_final: 0.8677 (pp) REVERT: G 875 GLU cc_start: 0.9283 (pm20) cc_final: 0.8114 (pp20) REVERT: G 890 ILE cc_start: 0.9470 (mt) cc_final: 0.9155 (tp) REVERT: G 943 MET cc_start: 0.9305 (mtp) cc_final: 0.8881 (mmm) REVERT: G 944 GLU cc_start: 0.9417 (mt-10) cc_final: 0.9206 (mt-10) REVERT: G 1042 ASN cc_start: 0.9292 (t0) cc_final: 0.8940 (t0) REVERT: G 1075 LEU cc_start: 0.9349 (tp) cc_final: 0.8899 (pp) REVERT: G 1084 GLN cc_start: 0.9550 (tp40) cc_final: 0.9153 (tm-30) REVERT: G 1171 TYR cc_start: 0.8858 (m-80) cc_final: 0.8625 (m-10) REVERT: H 2 VAL cc_start: 0.8980 (t) cc_final: 0.8488 (t) REVERT: H 51 PHE cc_start: 0.8567 (t80) cc_final: 0.8275 (t80) REVERT: H 56 ASN cc_start: 0.8406 (m-40) cc_final: 0.7994 (m110) REVERT: H 80 MET cc_start: 0.8942 (ttp) cc_final: 0.8655 (tpp) REVERT: H 101 ASP cc_start: 0.8312 (t0) cc_final: 0.7381 (t0) REVERT: I 27 ASP cc_start: 0.9115 (m-30) cc_final: 0.8654 (t0) REVERT: I 38 GLN cc_start: 0.8934 (tt0) cc_final: 0.8338 (tt0) REVERT: I 75 ILE cc_start: 0.9326 (mt) cc_final: 0.8879 (tt) REVERT: I 78 VAL cc_start: 0.9234 (t) cc_final: 0.8987 (t) REVERT: I 85 MET cc_start: 0.9124 (mpp) cc_final: 0.8740 (mpp) REVERT: E 56 ILE cc_start: 0.9386 (mm) cc_final: 0.9127 (mm) REVERT: E 367 GLU cc_start: 0.8638 (pt0) cc_final: 0.8398 (tm-30) REVERT: E 382 GLU cc_start: 0.6462 (tp30) cc_final: 0.6229 (mt-10) REVERT: E 638 LEU cc_start: 0.9128 (tp) cc_final: 0.8823 (tp) REVERT: E 662 ILE cc_start: 0.9598 (mp) cc_final: 0.9325 (pt) REVERT: F 49 ASP cc_start: 0.7121 (t0) cc_final: 0.6743 (t0) REVERT: F 278 MET cc_start: 0.8550 (mtm) cc_final: 0.8080 (mtm) REVERT: F 284 LEU cc_start: 0.9525 (mt) cc_final: 0.9302 (tp) REVERT: F 343 ASP cc_start: 0.9260 (m-30) cc_final: 0.8432 (p0) REVERT: F 356 VAL cc_start: 0.8448 (t) cc_final: 0.8237 (m) REVERT: F 686 MET cc_start: 0.7442 (mmm) cc_final: 0.5919 (mmm) REVERT: F 700 ARG cc_start: 0.6552 (mtt90) cc_final: 0.6248 (mmm160) REVERT: J 239 PHE cc_start: 0.8749 (m-80) cc_final: 0.8545 (m-80) REVERT: J 240 MET cc_start: 0.8809 (ppp) cc_final: 0.8597 (ppp) REVERT: J 278 MET cc_start: 0.8101 (mmm) cc_final: 0.7707 (mmm) REVERT: J 284 LEU cc_start: 0.9132 (mt) cc_final: 0.8824 (mp) REVERT: J 333 ILE cc_start: 0.9245 (mt) cc_final: 0.8960 (mm) REVERT: J 346 GLN cc_start: 0.9445 (tp40) cc_final: 0.9203 (mm110) REVERT: J 356 VAL cc_start: 0.8579 (t) cc_final: 0.8374 (t) REVERT: J 529 ILE cc_start: 0.6568 (tp) cc_final: 0.5247 (pt) REVERT: J 576 GLN cc_start: 0.8682 (tp40) cc_final: 0.8277 (tt0) REVERT: J 717 LEU cc_start: 0.8994 (mt) cc_final: 0.8568 (tp) outliers start: 3 outliers final: 0 residues processed: 612 average time/residue: 0.2035 time to fit residues: 198.2976 Evaluate side-chains 293 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 0.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 0.8980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 HIS A1122 HIS A1217 ASN B 58 ASN C 76 HIS D1104 ASN G 808 GLN ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 637 ASN E 688 GLN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 HIS J 406 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.070618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053780 restraints weight = 217091.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.055609 restraints weight = 145553.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.055881 restraints weight = 98533.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.056650 restraints weight = 76044.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.057100 restraints weight = 59362.545| |-----------------------------------------------------------------------------| r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 31917 Z= 0.162 Angle : 0.705 13.486 43446 Z= 0.394 Chirality : 0.045 0.236 4816 Planarity : 0.007 0.077 5634 Dihedral : 5.570 32.139 4371 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.35 % Allowed : 3.18 % Favored : 96.47 % Rotamer: Outliers : 0.12 % Allowed : 1.33 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.08 % Cis-general : 0.50 % Twisted Proline : 0.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.13), residues: 3993 helix: 1.17 (0.20), residues: 640 sheet: 0.57 (0.15), residues: 938 loop : 1.03 (0.13), residues: 2415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 841 TYR 0.035 0.002 TYR A 905 PHE 0.042 0.002 PHE A 850 TRP 0.020 0.002 TRP E 553 HIS 0.006 0.001 HIS D1122 Details of bonding type rmsd covalent geometry : bond 0.00326 (31861) covalent geometry : angle 0.69849 (43336) SS BOND : bond 0.00552 ( 55) SS BOND : angle 1.97890 ( 110) hydrogen bonds : bond 0.06415 ( 1176) hydrogen bonds : angle 6.46290 ( 3027) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 408 time to evaluate : 1.228 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 809 TYR cc_start: 0.9040 (t80) cc_final: 0.8512 (t80) REVERT: A 1001 PHE cc_start: 0.8870 (t80) cc_final: 0.8646 (t80) REVERT: A 1036 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9033 (mp) REVERT: B 28 THR cc_start: 0.8441 (m) cc_final: 0.7987 (p) REVERT: B 35 HIS cc_start: 0.9064 (m-70) cc_final: 0.8639 (m-70) REVERT: B 36 TRP cc_start: 0.8020 (m100) cc_final: 0.7202 (m100) REVERT: B 56 ASN cc_start: 0.8591 (m-40) cc_final: 0.8374 (t0) REVERT: C 33 MET cc_start: 0.8398 (tpp) cc_final: 0.7662 (mmm) REVERT: C 36 PHE cc_start: 0.9217 (m-80) cc_final: 0.8675 (m-80) REVERT: C 62 PHE cc_start: 0.8508 (m-80) cc_final: 0.8293 (m-80) REVERT: C 85 MET cc_start: 0.9058 (mmm) cc_final: 0.8618 (mmm) REVERT: D 850 PHE cc_start: 0.7729 (m-10) cc_final: 0.7515 (m-10) REVERT: D 943 MET cc_start: 0.8300 (mtp) cc_final: 0.7913 (ttm) REVERT: D 990 LEU cc_start: 0.9382 (mt) cc_final: 0.9029 (mt) REVERT: D 1001 PHE cc_start: 0.9113 (t80) cc_final: 0.8808 (t80) REVERT: D 1137 MET cc_start: 0.8019 (mpp) cc_final: 0.7608 (mpp) REVERT: G 757 MET cc_start: 0.8559 (mmt) cc_final: 0.8285 (tpp) REVERT: G 943 MET cc_start: 0.9352 (mtp) cc_final: 0.8762 (mmm) REVERT: G 1075 LEU cc_start: 0.8939 (tp) cc_final: 0.8627 (pp) REVERT: G 1107 VAL cc_start: 0.9655 (t) cc_final: 0.9360 (t) REVERT: G 1127 VAL cc_start: 0.9028 (p) cc_final: 0.8818 (m) REVERT: G 1136 PHE cc_start: 0.9145 (m-10) cc_final: 0.8660 (m-10) REVERT: G 1171 TYR cc_start: 0.8320 (m-80) cc_final: 0.8008 (m-10) REVERT: G 1218 LEU cc_start: 0.8942 (tp) cc_final: 0.8636 (mt) REVERT: H 31 ASP cc_start: 0.8718 (m-30) cc_final: 0.8360 (m-30) REVERT: H 51 PHE cc_start: 0.8420 (t80) cc_final: 0.7976 (t80) REVERT: H 56 ASN cc_start: 0.8600 (m-40) cc_final: 0.8272 (m110) REVERT: H 80 MET cc_start: 0.8815 (ttp) cc_final: 0.8552 (ttp) REVERT: H 101 ASP cc_start: 0.8086 (t0) cc_final: 0.7095 (t0) REVERT: I 27 ASP cc_start: 0.8869 (m-30) cc_final: 0.8538 (t0) REVERT: I 33 MET cc_start: 0.9033 (tpp) cc_final: 0.8745 (tpp) REVERT: I 46 LEU cc_start: 0.9018 (mp) cc_final: 0.8815 (mp) REVERT: E 117 VAL cc_start: 0.9064 (m) cc_final: 0.8644 (p) REVERT: E 638 LEU cc_start: 0.8867 (tp) cc_final: 0.8416 (tp) REVERT: E 662 ILE cc_start: 0.9590 (mp) cc_final: 0.9323 (pt) REVERT: E 677 VAL cc_start: 0.9353 (p) cc_final: 0.8951 (p) REVERT: F 49 ASP cc_start: 0.7296 (t0) cc_final: 0.6894 (t0) REVERT: F 324 LEU cc_start: 0.9238 (mt) cc_final: 0.8969 (mt) REVERT: F 343 ASP cc_start: 0.8460 (m-30) cc_final: 0.8248 (p0) REVERT: F 406 ASN cc_start: 0.8289 (m110) cc_final: 0.8019 (m110) REVERT: F 441 LEU cc_start: 0.8831 (tp) cc_final: 0.8338 (mp) REVERT: F 589 GLU cc_start: 0.7057 (mt-10) cc_final: 0.6593 (pm20) REVERT: F 686 MET cc_start: 0.6300 (mmm) cc_final: 0.5540 (mmm) REVERT: J 218 ASN cc_start: 0.9203 (t0) cc_final: 0.8754 (p0) REVERT: J 278 MET cc_start: 0.8382 (mmm) cc_final: 0.6958 (mmm) REVERT: J 284 LEU cc_start: 0.9215 (mt) cc_final: 0.8845 (mp) REVERT: J 333 ILE cc_start: 0.9130 (mt) cc_final: 0.8846 (mm) REVERT: J 401 ARG cc_start: 0.8062 (ttm170) cc_final: 0.7172 (mpt-90) REVERT: J 686 MET cc_start: 0.6832 (mmt) cc_final: 0.6537 (mmm) REVERT: J 717 LEU cc_start: 0.8939 (mt) cc_final: 0.8693 (tp) outliers start: 4 outliers final: 0 residues processed: 410 average time/residue: 0.1945 time to fit residues: 131.1200 Evaluate side-chains 251 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 250 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 2 optimal weight: 1.9990 chunk 317 optimal weight: 7.9990 chunk 358 optimal weight: 7.9990 chunk 356 optimal weight: 0.0770 chunk 122 optimal weight: 9.9990 chunk 229 optimal weight: 40.0000 chunk 285 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 121 optimal weight: 1.9990 chunk 258 optimal weight: 10.0000 chunk 311 optimal weight: 7.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 836 HIS ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN B 61 GLN C 34 ASN D1104 ASN G 792 GLN ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 836 HIS ** G1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 466 GLN E 475 ASN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 HIS J 319 GLN J 346 GLN J 406 ASN J 628 GLN J 637 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.068540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.051738 restraints weight = 221647.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053496 restraints weight = 145990.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.054071 restraints weight = 96687.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.054546 restraints weight = 75489.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.054699 restraints weight = 61483.720| |-----------------------------------------------------------------------------| r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 31917 Z= 0.184 Angle : 0.660 11.705 43446 Z= 0.365 Chirality : 0.044 0.216 4816 Planarity : 0.006 0.075 5634 Dihedral : 5.235 28.977 4371 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.86 % Favored : 95.87 % Rotamer: Outliers : 0.09 % Allowed : 2.20 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.13), residues: 3993 helix: 1.39 (0.20), residues: 649 sheet: 0.31 (0.16), residues: 918 loop : 0.69 (0.13), residues: 2426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 626 TYR 0.030 0.002 TYR A 905 PHE 0.034 0.002 PHE A 850 TRP 0.031 0.002 TRP E 553 HIS 0.006 0.001 HIS E 670 Details of bonding type rmsd covalent geometry : bond 0.00391 (31861) covalent geometry : angle 0.65529 (43336) SS BOND : bond 0.00482 ( 55) SS BOND : angle 1.74301 ( 110) hydrogen bonds : bond 0.05510 ( 1176) hydrogen bonds : angle 6.11208 ( 3027) Misc. bond : bond 0.02306 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 322 time to evaluate : 1.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 939 MET cc_start: 0.8081 (tpt) cc_final: 0.7870 (tpt) REVERT: A 1192 TYR cc_start: 0.8782 (t80) cc_final: 0.8579 (t80) REVERT: B 28 THR cc_start: 0.8200 (m) cc_final: 0.7499 (p) REVERT: B 35 HIS cc_start: 0.9091 (m-70) cc_final: 0.8604 (m-70) REVERT: B 36 TRP cc_start: 0.8529 (m100) cc_final: 0.8167 (m100) REVERT: B 56 ASN cc_start: 0.8820 (m-40) cc_final: 0.8572 (t0) REVERT: C 33 MET cc_start: 0.8509 (tpp) cc_final: 0.7830 (mmm) REVERT: C 36 PHE cc_start: 0.9179 (m-80) cc_final: 0.8908 (m-80) REVERT: C 62 PHE cc_start: 0.8635 (m-80) cc_final: 0.8267 (m-80) REVERT: C 85 MET cc_start: 0.8946 (mmm) cc_final: 0.8513 (mmm) REVERT: D 977 PHE cc_start: 0.8541 (m-80) cc_final: 0.7360 (m-10) REVERT: D 990 LEU cc_start: 0.9437 (mt) cc_final: 0.8651 (mt) REVERT: D 1001 PHE cc_start: 0.9152 (t80) cc_final: 0.8772 (t80) REVERT: D 1005 LEU cc_start: 0.8956 (mt) cc_final: 0.8754 (mt) REVERT: D 1067 ILE cc_start: 0.9603 (mt) cc_final: 0.9253 (tt) REVERT: D 1136 PHE cc_start: 0.8466 (m-80) cc_final: 0.8068 (m-10) REVERT: D 1137 MET cc_start: 0.8074 (mpp) cc_final: 0.7613 (mpp) REVERT: G 757 MET cc_start: 0.8580 (mmt) cc_final: 0.8170 (tpp) REVERT: G 843 ASP cc_start: 0.9366 (p0) cc_final: 0.9138 (p0) REVERT: G 932 TYR cc_start: 0.7184 (t80) cc_final: 0.6910 (t80) REVERT: G 939 MET cc_start: 0.7867 (tpt) cc_final: 0.7664 (tpt) REVERT: G 943 MET cc_start: 0.9304 (mtp) cc_final: 0.8837 (mmm) REVERT: G 1171 TYR cc_start: 0.8470 (m-80) cc_final: 0.8207 (m-10) REVERT: H 31 ASP cc_start: 0.8603 (m-30) cc_final: 0.8252 (m-30) REVERT: H 51 PHE cc_start: 0.8502 (t80) cc_final: 0.7890 (t80) REVERT: H 56 ASN cc_start: 0.8675 (m-40) cc_final: 0.8465 (m-40) REVERT: H 101 ASP cc_start: 0.8354 (t0) cc_final: 0.7637 (t0) REVERT: I 27 VAL cc_start: 0.8251 (m) cc_final: 0.7994 (m) REVERT: I 33 MET cc_start: 0.9149 (tpp) cc_final: 0.8755 (tpp) REVERT: I 38 GLN cc_start: 0.8685 (tt0) cc_final: 0.8098 (tt0) REVERT: I 45 LYS cc_start: 0.9224 (mmpt) cc_final: 0.8967 (mmmt) REVERT: I 73 LEU cc_start: 0.9263 (tt) cc_final: 0.8506 (tp) REVERT: I 75 ILE cc_start: 0.9397 (mp) cc_final: 0.8830 (tt) REVERT: I 85 MET cc_start: 0.8953 (mpp) cc_final: 0.7868 (mpp) REVERT: I 103 LYS cc_start: 0.8419 (pttm) cc_final: 0.8003 (tptp) REVERT: E 117 VAL cc_start: 0.9098 (m) cc_final: 0.8791 (p) REVERT: E 638 LEU cc_start: 0.8996 (tp) cc_final: 0.8624 (tp) REVERT: E 662 ILE cc_start: 0.9636 (mp) cc_final: 0.9370 (pt) REVERT: F 49 ASP cc_start: 0.7165 (t0) cc_final: 0.6699 (t0) REVERT: F 256 ILE cc_start: 0.8634 (mm) cc_final: 0.8192 (mm) REVERT: F 284 LEU cc_start: 0.8418 (tp) cc_final: 0.8119 (tp) REVERT: F 324 LEU cc_start: 0.9243 (mt) cc_final: 0.9033 (mt) REVERT: F 343 ASP cc_start: 0.8508 (m-30) cc_final: 0.8299 (p0) REVERT: F 406 ASN cc_start: 0.8232 (m110) cc_final: 0.7991 (m110) REVERT: F 441 LEU cc_start: 0.8692 (tp) cc_final: 0.8155 (mt) REVERT: F 479 LEU cc_start: 0.7861 (mt) cc_final: 0.7520 (tp) REVERT: F 589 GLU cc_start: 0.7094 (mt-10) cc_final: 0.6643 (pm20) REVERT: F 686 MET cc_start: 0.6533 (mmm) cc_final: 0.5835 (mmm) REVERT: J 148 MET cc_start: 0.9159 (ttm) cc_final: 0.8820 (tpp) REVERT: J 168 THR cc_start: 0.8648 (p) cc_final: 0.7682 (p) REVERT: J 278 MET cc_start: 0.8621 (mmm) cc_final: 0.7254 (mmm) REVERT: J 284 LEU cc_start: 0.9096 (mt) cc_final: 0.8707 (mp) REVERT: J 333 ILE cc_start: 0.9157 (mt) cc_final: 0.8931 (mm) REVERT: J 686 MET cc_start: 0.7064 (mmt) cc_final: 0.6778 (mmm) REVERT: J 717 LEU cc_start: 0.8914 (mt) cc_final: 0.8643 (tp) outliers start: 3 outliers final: 1 residues processed: 325 average time/residue: 0.1870 time to fit residues: 101.3695 Evaluate side-chains 235 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 234 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 65 optimal weight: 20.0000 chunk 289 optimal weight: 0.7980 chunk 203 optimal weight: 10.0000 chunk 265 optimal weight: 6.9990 chunk 327 optimal weight: 0.0170 chunk 256 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 132 optimal weight: 9.9990 chunk 79 optimal weight: 0.0370 chunk 186 optimal weight: 9.9990 chunk 364 optimal weight: 8.9990 overall best weight: 1.3098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 993 ASN ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1084 GLN E 466 GLN ** F 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 406 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.069528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.052483 restraints weight = 218708.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.053828 restraints weight = 132722.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.054758 restraints weight = 93459.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.055413 restraints weight = 73110.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.055823 restraints weight = 61399.981| |-----------------------------------------------------------------------------| r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.3542 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 31917 Z= 0.119 Angle : 0.590 10.957 43446 Z= 0.318 Chirality : 0.043 0.211 4816 Planarity : 0.005 0.062 5634 Dihedral : 4.896 29.047 4371 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.28 % Allowed : 3.88 % Favored : 95.84 % Rotamer: Outliers : 0.03 % Allowed : 1.53 % Favored : 98.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.13), residues: 3993 helix: 1.57 (0.20), residues: 659 sheet: 0.36 (0.16), residues: 946 loop : 0.56 (0.13), residues: 2388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 626 TYR 0.023 0.001 TYR E 287 PHE 0.022 0.001 PHE A 850 TRP 0.037 0.001 TRP E 553 HIS 0.007 0.001 HIS D1122 Details of bonding type rmsd covalent geometry : bond 0.00243 (31861) covalent geometry : angle 0.58598 (43336) SS BOND : bond 0.00858 ( 55) SS BOND : angle 1.54475 ( 110) hydrogen bonds : bond 0.04809 ( 1176) hydrogen bonds : angle 5.72426 ( 3027) Misc. bond : bond 0.00192 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 331 time to evaluate : 1.240 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 809 TYR cc_start: 0.9009 (t80) cc_final: 0.8134 (t80) REVERT: A 839 ASN cc_start: 0.9089 (m110) cc_final: 0.8796 (m-40) REVERT: A 939 MET cc_start: 0.8110 (tpt) cc_final: 0.7825 (tpt) REVERT: A 976 ILE cc_start: 0.9627 (mm) cc_final: 0.9400 (mm) REVERT: A 1036 LEU cc_start: 0.9700 (tp) cc_final: 0.9480 (tp) REVERT: A 1063 GLN cc_start: 0.8585 (tt0) cc_final: 0.8305 (tt0) REVERT: A 1129 ASN cc_start: 0.9191 (t0) cc_final: 0.8964 (t0) REVERT: B 3 GLN cc_start: 0.8956 (pt0) cc_final: 0.8578 (pm20) REVERT: B 28 THR cc_start: 0.8211 (m) cc_final: 0.7508 (p) REVERT: B 35 HIS cc_start: 0.8999 (m-70) cc_final: 0.8621 (m-70) REVERT: B 80 MET cc_start: 0.8634 (ttm) cc_final: 0.8240 (tmm) REVERT: C 33 MET cc_start: 0.8555 (tpp) cc_final: 0.7753 (mmm) REVERT: C 36 PHE cc_start: 0.9198 (m-80) cc_final: 0.8815 (m-80) REVERT: C 62 PHE cc_start: 0.8311 (m-80) cc_final: 0.8100 (m-80) REVERT: C 85 MET cc_start: 0.8989 (mmm) cc_final: 0.8571 (mmm) REVERT: D 835 LEU cc_start: 0.9505 (mm) cc_final: 0.9197 (tp) REVERT: D 939 MET cc_start: 0.6235 (tpt) cc_final: 0.6024 (mmm) REVERT: D 977 PHE cc_start: 0.8488 (m-80) cc_final: 0.7385 (m-10) REVERT: D 990 LEU cc_start: 0.9426 (mt) cc_final: 0.8729 (mt) REVERT: D 1001 PHE cc_start: 0.8985 (t80) cc_final: 0.8462 (t80) REVERT: D 1027 ASN cc_start: 0.9231 (m-40) cc_final: 0.9024 (m110) REVERT: D 1067 ILE cc_start: 0.9560 (mt) cc_final: 0.9163 (tt) REVERT: D 1136 PHE cc_start: 0.8337 (m-80) cc_final: 0.7933 (m-10) REVERT: D 1137 MET cc_start: 0.7867 (mpp) cc_final: 0.7592 (mpp) REVERT: G 757 MET cc_start: 0.8480 (mmt) cc_final: 0.8015 (tpp) REVERT: G 943 MET cc_start: 0.9305 (mtp) cc_final: 0.8535 (mmm) REVERT: G 1039 GLU cc_start: 0.9255 (mm-30) cc_final: 0.8975 (tp30) REVERT: G 1042 ASN cc_start: 0.8961 (t0) cc_final: 0.8657 (t0) REVERT: G 1171 TYR cc_start: 0.8370 (m-80) cc_final: 0.8148 (m-10) REVERT: H 31 ASP cc_start: 0.8560 (m-30) cc_final: 0.8210 (m-30) REVERT: H 38 LYS cc_start: 0.9304 (pptt) cc_final: 0.8906 (tmmt) REVERT: H 51 PHE cc_start: 0.8231 (t80) cc_final: 0.7760 (t80) REVERT: H 80 MET cc_start: 0.8791 (ttp) cc_final: 0.8362 (tpp) REVERT: H 101 ASP cc_start: 0.8533 (t0) cc_final: 0.7460 (t70) REVERT: I 33 MET cc_start: 0.8956 (tpp) cc_final: 0.8604 (tpp) REVERT: I 46 LEU cc_start: 0.9286 (tt) cc_final: 0.9029 (mp) REVERT: I 73 LEU cc_start: 0.9227 (tt) cc_final: 0.8748 (tt) REVERT: I 75 ILE cc_start: 0.9194 (mp) cc_final: 0.8894 (tp) REVERT: E 563 MET cc_start: 0.1638 (mtp) cc_final: 0.1243 (tpt) REVERT: E 638 LEU cc_start: 0.9007 (tp) cc_final: 0.8602 (tp) REVERT: E 662 ILE cc_start: 0.9653 (mp) cc_final: 0.9400 (pt) REVERT: E 677 VAL cc_start: 0.9301 (p) cc_final: 0.9082 (p) REVERT: F 49 ASP cc_start: 0.6984 (t0) cc_final: 0.6547 (t0) REVERT: F 256 ILE cc_start: 0.8619 (mm) cc_final: 0.8229 (mm) REVERT: F 324 LEU cc_start: 0.9187 (mt) cc_final: 0.8983 (mt) REVERT: F 343 ASP cc_start: 0.8479 (m-30) cc_final: 0.8267 (p0) REVERT: F 406 ASN cc_start: 0.8145 (m110) cc_final: 0.7850 (m110) REVERT: F 441 LEU cc_start: 0.8721 (tp) cc_final: 0.8173 (mp) REVERT: F 479 LEU cc_start: 0.7903 (mt) cc_final: 0.7640 (tp) REVERT: F 589 GLU cc_start: 0.7143 (mt-10) cc_final: 0.6665 (pm20) REVERT: F 686 MET cc_start: 0.6434 (mmm) cc_final: 0.5663 (mmm) REVERT: J 148 MET cc_start: 0.9202 (ttm) cc_final: 0.8829 (tpp) REVERT: J 168 THR cc_start: 0.8530 (p) cc_final: 0.7508 (p) REVERT: J 278 MET cc_start: 0.8685 (mmm) cc_final: 0.7231 (mmm) REVERT: J 333 ILE cc_start: 0.9156 (mt) cc_final: 0.8927 (mm) REVERT: J 563 MET cc_start: 0.7657 (mmm) cc_final: 0.5962 (tpt) REVERT: J 686 MET cc_start: 0.7067 (mmt) cc_final: 0.6614 (mmm) REVERT: J 696 MET cc_start: 0.6178 (mmm) cc_final: 0.5898 (mmm) outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 0.1853 time to fit residues: 102.8914 Evaluate side-chains 227 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 227 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 351 optimal weight: 6.9990 chunk 265 optimal weight: 20.0000 chunk 66 optimal weight: 7.9990 chunk 99 optimal weight: 5.9990 chunk 237 optimal weight: 30.0000 chunk 8 optimal weight: 9.9990 chunk 244 optimal weight: 20.0000 chunk 310 optimal weight: 0.0270 chunk 30 optimal weight: 8.9990 chunk 393 optimal weight: 10.0000 chunk 143 optimal weight: 10.0000 overall best weight: 6.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 839 ASN ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 GLN D 815 GLN ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1084 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN F 60 GLN F 193 ASN F 406 ASN J 280 GLN J 406 ASN J 421 ASN J 522 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.066696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.049607 restraints weight = 221892.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.050902 restraints weight = 137284.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.051760 restraints weight = 97221.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.052347 restraints weight = 76637.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.052737 restraints weight = 64748.767| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.4103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 31917 Z= 0.225 Angle : 0.679 9.234 43446 Z= 0.367 Chirality : 0.044 0.195 4816 Planarity : 0.005 0.068 5634 Dihedral : 5.122 30.898 4371 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.25 % Allowed : 4.58 % Favored : 95.17 % Rotamer: Outliers : 0.03 % Allowed : 1.71 % Favored : 98.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.13), residues: 3993 helix: 1.19 (0.20), residues: 676 sheet: 0.07 (0.16), residues: 935 loop : 0.23 (0.13), residues: 2382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG J 626 TYR 0.027 0.002 TYR E 287 PHE 0.021 0.002 PHE E 204 TRP 0.026 0.002 TRP E 553 HIS 0.008 0.002 HIS E 670 Details of bonding type rmsd covalent geometry : bond 0.00478 (31861) covalent geometry : angle 0.67554 (43336) SS BOND : bond 0.00486 ( 55) SS BOND : angle 1.54404 ( 110) hydrogen bonds : bond 0.04938 ( 1176) hydrogen bonds : angle 5.99808 ( 3027) Misc. bond : bond 0.01547 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 272 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1036 LEU cc_start: 0.9737 (tp) cc_final: 0.9502 (tp) REVERT: A 1063 GLN cc_start: 0.8773 (tt0) cc_final: 0.8559 (tt0) REVERT: B 28 THR cc_start: 0.8293 (m) cc_final: 0.7566 (p) REVERT: B 35 HIS cc_start: 0.9141 (m-70) cc_final: 0.8757 (m-70) REVERT: B 56 ASN cc_start: 0.8867 (t0) cc_final: 0.8666 (t0) REVERT: B 80 MET cc_start: 0.8988 (ttm) cc_final: 0.8411 (ttp) REVERT: C 33 MET cc_start: 0.8488 (tpp) cc_final: 0.7955 (mmm) REVERT: C 36 PHE cc_start: 0.9258 (m-80) cc_final: 0.8878 (m-80) REVERT: C 85 MET cc_start: 0.9007 (mmm) cc_final: 0.8587 (mmm) REVERT: D 977 PHE cc_start: 0.8467 (m-80) cc_final: 0.7358 (m-80) REVERT: D 990 LEU cc_start: 0.9463 (mt) cc_final: 0.8554 (mt) REVERT: D 1001 PHE cc_start: 0.9227 (t80) cc_final: 0.8860 (t80) REVERT: D 1027 ASN cc_start: 0.9290 (m-40) cc_final: 0.9074 (m110) REVERT: D 1067 ILE cc_start: 0.9580 (mt) cc_final: 0.9181 (tt) REVERT: D 1136 PHE cc_start: 0.8605 (m-80) cc_final: 0.8326 (m-10) REVERT: G 757 MET cc_start: 0.8771 (mmt) cc_final: 0.8144 (tpp) REVERT: G 939 MET cc_start: 0.7879 (tpt) cc_final: 0.7478 (tpt) REVERT: G 943 MET cc_start: 0.9364 (mtp) cc_final: 0.8831 (mmm) REVERT: G 1039 GLU cc_start: 0.9332 (mm-30) cc_final: 0.9046 (tp30) REVERT: G 1042 ASN cc_start: 0.8997 (t0) cc_final: 0.8605 (t0) REVERT: H 31 ASP cc_start: 0.8684 (m-30) cc_final: 0.8292 (m-30) REVERT: H 38 LYS cc_start: 0.9592 (pptt) cc_final: 0.9373 (tmmt) REVERT: H 51 PHE cc_start: 0.8317 (t80) cc_final: 0.7746 (t80) REVERT: H 56 ASN cc_start: 0.8730 (m-40) cc_final: 0.8472 (m-40) REVERT: H 80 MET cc_start: 0.8788 (ttp) cc_final: 0.8329 (tpp) REVERT: I 33 MET cc_start: 0.9059 (tpp) cc_final: 0.8649 (tpp) REVERT: I 38 GLN cc_start: 0.8525 (tt0) cc_final: 0.8200 (tt0) REVERT: I 85 MET cc_start: 0.9014 (mpp) cc_final: 0.8690 (mpp) REVERT: E 563 MET cc_start: 0.1893 (mtp) cc_final: 0.1341 (tpt) REVERT: E 638 LEU cc_start: 0.9254 (tp) cc_final: 0.8913 (tp) REVERT: E 662 ILE cc_start: 0.9639 (mp) cc_final: 0.9415 (pt) REVERT: F 49 ASP cc_start: 0.6902 (t0) cc_final: 0.6405 (t0) REVERT: F 84 MET cc_start: 0.8351 (mtm) cc_final: 0.7701 (pmm) REVERT: F 406 ASN cc_start: 0.8116 (m-40) cc_final: 0.7816 (m110) REVERT: F 479 LEU cc_start: 0.7896 (mt) cc_final: 0.7577 (tp) REVERT: F 589 GLU cc_start: 0.7069 (mt-10) cc_final: 0.6654 (pm20) REVERT: F 686 MET cc_start: 0.6642 (mmm) cc_final: 0.5951 (mmm) REVERT: F 700 ARG cc_start: 0.6819 (mtt90) cc_final: 0.6354 (mmm160) REVERT: F 725 GLU cc_start: 0.8572 (pm20) cc_final: 0.7812 (tp30) REVERT: J 148 MET cc_start: 0.9115 (ttm) cc_final: 0.8821 (tpp) REVERT: J 278 MET cc_start: 0.8680 (mmm) cc_final: 0.7433 (mmm) REVERT: J 333 ILE cc_start: 0.9216 (mt) cc_final: 0.8996 (mm) REVERT: J 563 MET cc_start: 0.7596 (mmm) cc_final: 0.6172 (tpt) REVERT: J 686 MET cc_start: 0.7335 (mmt) cc_final: 0.6739 (mmm) outliers start: 1 outliers final: 0 residues processed: 273 average time/residue: 0.1849 time to fit residues: 85.3780 Evaluate side-chains 195 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 195 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 290 optimal weight: 0.5980 chunk 300 optimal weight: 9.9990 chunk 391 optimal weight: 5.9990 chunk 384 optimal weight: 7.9990 chunk 369 optimal weight: 20.0000 chunk 242 optimal weight: 9.9990 chunk 378 optimal weight: 20.0000 chunk 33 optimal weight: 6.9990 chunk 252 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 247 optimal weight: 9.9990 overall best weight: 3.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 839 ASN ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 398 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.067477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.050384 restraints weight = 219238.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.051691 restraints weight = 134238.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.052570 restraints weight = 94368.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 64)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.053185 restraints weight = 73968.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 61)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.053599 restraints weight = 62443.321| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.4319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 31917 Z= 0.142 Angle : 0.593 8.167 43446 Z= 0.321 Chirality : 0.042 0.188 4816 Planarity : 0.005 0.063 5634 Dihedral : 4.913 29.511 4371 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.28 % Allowed : 4.51 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.13), residues: 3993 helix: 1.25 (0.20), residues: 700 sheet: 0.11 (0.16), residues: 938 loop : 0.16 (0.13), residues: 2355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 626 TYR 0.025 0.002 TYR A 777 PHE 0.050 0.001 PHE D 850 TRP 0.023 0.001 TRP E 553 HIS 0.005 0.001 HIS H 41 Details of bonding type rmsd covalent geometry : bond 0.00303 (31861) covalent geometry : angle 0.58904 (43336) SS BOND : bond 0.00438 ( 55) SS BOND : angle 1.53591 ( 110) hydrogen bonds : bond 0.04633 ( 1176) hydrogen bonds : angle 5.67149 ( 3027) Misc. bond : bond 0.00566 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 943 MET cc_start: 0.9153 (tpp) cc_final: 0.8815 (tpt) REVERT: A 976 ILE cc_start: 0.9651 (mm) cc_final: 0.9441 (mm) REVERT: A 1036 LEU cc_start: 0.9739 (tp) cc_final: 0.9363 (tp) REVERT: A 1039 GLU cc_start: 0.8657 (mp0) cc_final: 0.8296 (mp0) REVERT: A 1042 ASN cc_start: 0.8935 (t0) cc_final: 0.8731 (t0) REVERT: A 1063 GLN cc_start: 0.8678 (tt0) cc_final: 0.8306 (tt0) REVERT: B 28 THR cc_start: 0.8200 (m) cc_final: 0.7468 (p) REVERT: B 35 HIS cc_start: 0.9111 (m-70) cc_final: 0.8731 (m-70) REVERT: B 56 ASN cc_start: 0.8905 (t0) cc_final: 0.8664 (t0) REVERT: C 33 MET cc_start: 0.8405 (tpp) cc_final: 0.7713 (mmm) REVERT: C 36 PHE cc_start: 0.9251 (m-80) cc_final: 0.8796 (m-80) REVERT: C 62 PHE cc_start: 0.8302 (m-80) cc_final: 0.8066 (m-80) REVERT: C 85 MET cc_start: 0.9056 (mmm) cc_final: 0.8619 (mmm) REVERT: D 771 ASP cc_start: 0.8786 (m-30) cc_final: 0.8480 (t0) REVERT: D 835 LEU cc_start: 0.9558 (mm) cc_final: 0.9237 (tp) REVERT: D 836 HIS cc_start: 0.9109 (t70) cc_final: 0.8705 (t-90) REVERT: D 839 ASN cc_start: 0.9177 (m-40) cc_final: 0.8215 (m-40) REVERT: D 944 GLU cc_start: 0.8834 (pm20) cc_final: 0.8444 (pm20) REVERT: D 977 PHE cc_start: 0.8362 (m-80) cc_final: 0.7940 (m-80) REVERT: D 1001 PHE cc_start: 0.9121 (t80) cc_final: 0.8660 (t80) REVERT: D 1067 ILE cc_start: 0.9557 (mt) cc_final: 0.9119 (tt) REVERT: D 1136 PHE cc_start: 0.8614 (m-80) cc_final: 0.8262 (m-10) REVERT: G 757 MET cc_start: 0.8709 (mmt) cc_final: 0.8240 (tpp) REVERT: G 939 MET cc_start: 0.7935 (tpt) cc_final: 0.7608 (tpt) REVERT: G 943 MET cc_start: 0.9299 (mtp) cc_final: 0.8731 (mmm) REVERT: G 1042 ASN cc_start: 0.9132 (t0) cc_final: 0.8465 (t0) REVERT: H 31 ASP cc_start: 0.8549 (m-30) cc_final: 0.8189 (m-30) REVERT: H 51 PHE cc_start: 0.8187 (t80) cc_final: 0.7653 (t80) REVERT: H 101 ASP cc_start: 0.8803 (t0) cc_final: 0.7966 (t0) REVERT: I 32 PHE cc_start: 0.8757 (m-10) cc_final: 0.8442 (m-10) REVERT: I 33 MET cc_start: 0.9058 (tpp) cc_final: 0.8685 (tpp) REVERT: I 38 GLN cc_start: 0.8639 (tt0) cc_final: 0.7776 (tt0) REVERT: I 46 LEU cc_start: 0.9411 (tt) cc_final: 0.8955 (tp) REVERT: I 73 LEU cc_start: 0.9139 (tt) cc_final: 0.8416 (tp) REVERT: I 75 ILE cc_start: 0.9250 (mp) cc_final: 0.8700 (tt) REVERT: I 85 MET cc_start: 0.9031 (mpp) cc_final: 0.8766 (mpp) REVERT: E 240 MET cc_start: 0.8120 (mmm) cc_final: 0.7878 (mmm) REVERT: E 563 MET cc_start: 0.1770 (mtp) cc_final: 0.1227 (tpt) REVERT: E 638 LEU cc_start: 0.9158 (tp) cc_final: 0.8825 (tp) REVERT: E 662 ILE cc_start: 0.9667 (mp) cc_final: 0.9445 (pt) REVERT: F 49 ASP cc_start: 0.7063 (t0) cc_final: 0.6568 (t0) REVERT: F 84 MET cc_start: 0.8372 (mtm) cc_final: 0.7517 (pmm) REVERT: F 343 ASP cc_start: 0.8535 (p0) cc_final: 0.8212 (p0) REVERT: F 406 ASN cc_start: 0.8067 (m-40) cc_final: 0.7775 (m110) REVERT: F 479 LEU cc_start: 0.7954 (mt) cc_final: 0.7620 (tp) REVERT: F 589 GLU cc_start: 0.7049 (mt-10) cc_final: 0.6645 (pm20) REVERT: F 686 MET cc_start: 0.6580 (mmm) cc_final: 0.5906 (mmm) REVERT: F 700 ARG cc_start: 0.6914 (mtt90) cc_final: 0.6689 (mmm160) REVERT: F 725 GLU cc_start: 0.8465 (pm20) cc_final: 0.7673 (tp30) REVERT: J 148 MET cc_start: 0.9054 (ttm) cc_final: 0.8808 (tpp) REVERT: J 278 MET cc_start: 0.8753 (mmm) cc_final: 0.7296 (mmm) REVERT: J 333 ILE cc_start: 0.9223 (mt) cc_final: 0.8999 (mm) REVERT: J 563 MET cc_start: 0.7543 (mmm) cc_final: 0.5860 (tpt) REVERT: J 686 MET cc_start: 0.7317 (mmt) cc_final: 0.6551 (mmm) REVERT: J 696 MET cc_start: 0.6218 (mmm) cc_final: 0.5892 (mmm) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1764 time to fit residues: 85.1344 Evaluate side-chains 205 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 205 time to evaluate : 1.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 298 optimal weight: 30.0000 chunk 115 optimal weight: 10.0000 chunk 345 optimal weight: 6.9990 chunk 118 optimal weight: 0.0570 chunk 178 optimal weight: 7.9990 chunk 357 optimal weight: 10.0000 chunk 119 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 264 optimal weight: 10.0000 chunk 106 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 overall best weight: 4.6106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 927 GLN ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1110 GLN ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 377 GLN J 406 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.066528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.049507 restraints weight = 219803.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.050758 restraints weight = 135589.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.051636 restraints weight = 96200.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.052219 restraints weight = 75547.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.052639 restraints weight = 63928.246| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.4629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 31917 Z= 0.179 Angle : 0.622 8.261 43446 Z= 0.335 Chirality : 0.043 0.193 4816 Planarity : 0.005 0.063 5634 Dihedral : 4.990 29.838 4371 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.28 % Allowed : 5.13 % Favored : 94.59 % Rotamer: Outliers : 0.03 % Allowed : 1.19 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.13), residues: 3993 helix: 1.02 (0.20), residues: 722 sheet: -0.01 (0.16), residues: 945 loop : -0.01 (0.13), residues: 2326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 626 TYR 0.030 0.002 TYR G 777 PHE 0.029 0.002 PHE D 850 TRP 0.021 0.002 TRP E 553 HIS 0.009 0.001 HIS D1122 Details of bonding type rmsd covalent geometry : bond 0.00383 (31861) covalent geometry : angle 0.61724 (43336) SS BOND : bond 0.00370 ( 55) SS BOND : angle 1.67378 ( 110) hydrogen bonds : bond 0.04636 ( 1176) hydrogen bonds : angle 5.77593 ( 3027) Misc. bond : bond 0.00199 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 256 time to evaluate : 1.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1036 LEU cc_start: 0.9742 (tp) cc_final: 0.9525 (tp) REVERT: B 28 THR cc_start: 0.8182 (m) cc_final: 0.7424 (p) REVERT: B 35 HIS cc_start: 0.9126 (m-70) cc_final: 0.8807 (m-70) REVERT: B 36 TRP cc_start: 0.8506 (m100) cc_final: 0.6697 (m100) REVERT: B 80 MET cc_start: 0.8351 (ttm) cc_final: 0.8059 (tmm) REVERT: C 33 MET cc_start: 0.8373 (tpp) cc_final: 0.7976 (mmm) REVERT: C 36 PHE cc_start: 0.9300 (m-80) cc_final: 0.8988 (m-80) REVERT: C 62 PHE cc_start: 0.8407 (m-80) cc_final: 0.8185 (m-80) REVERT: C 85 MET cc_start: 0.9061 (mmm) cc_final: 0.8627 (mmm) REVERT: D 836 HIS cc_start: 0.9116 (t70) cc_final: 0.8807 (t-90) REVERT: D 977 PHE cc_start: 0.8443 (m-80) cc_final: 0.8025 (m-80) REVERT: D 1001 PHE cc_start: 0.9169 (t80) cc_final: 0.8651 (t80) REVERT: D 1067 ILE cc_start: 0.9583 (mt) cc_final: 0.9155 (tt) REVERT: D 1136 PHE cc_start: 0.8613 (m-80) cc_final: 0.8373 (m-10) REVERT: G 757 MET cc_start: 0.8771 (mmt) cc_final: 0.8184 (tpp) REVERT: G 939 MET cc_start: 0.7977 (tpt) cc_final: 0.7686 (tpt) REVERT: G 943 MET cc_start: 0.9362 (mtp) cc_final: 0.8843 (mmm) REVERT: G 1042 ASN cc_start: 0.8878 (t0) cc_final: 0.8674 (t0) REVERT: H 31 ASP cc_start: 0.8639 (m-30) cc_final: 0.8225 (m-30) REVERT: H 56 ASN cc_start: 0.8868 (m-40) cc_final: 0.8520 (m-40) REVERT: I 32 PHE cc_start: 0.8848 (m-10) cc_final: 0.8433 (m-80) REVERT: I 33 MET cc_start: 0.9125 (tpp) cc_final: 0.8733 (tpp) REVERT: I 38 GLN cc_start: 0.8631 (tt0) cc_final: 0.7826 (tt0) REVERT: I 46 LEU cc_start: 0.9212 (tt) cc_final: 0.8907 (tp) REVERT: I 73 LEU cc_start: 0.9193 (tt) cc_final: 0.8973 (tt) REVERT: I 85 MET cc_start: 0.9073 (mpp) cc_final: 0.8780 (mpp) REVERT: E 240 MET cc_start: 0.8124 (mmm) cc_final: 0.7920 (mmm) REVERT: E 563 MET cc_start: 0.2018 (mtp) cc_final: 0.1439 (tpt) REVERT: E 638 LEU cc_start: 0.9166 (tp) cc_final: 0.8847 (tp) REVERT: E 662 ILE cc_start: 0.9667 (mp) cc_final: 0.9458 (pt) REVERT: E 704 TYR cc_start: 0.5528 (t80) cc_final: 0.5323 (t80) REVERT: F 49 ASP cc_start: 0.7124 (t0) cc_final: 0.6584 (t0) REVERT: F 84 MET cc_start: 0.8450 (mtm) cc_final: 0.7609 (pmm) REVERT: F 343 ASP cc_start: 0.8654 (p0) cc_final: 0.8429 (p0) REVERT: F 406 ASN cc_start: 0.8036 (m-40) cc_final: 0.7771 (m110) REVERT: F 479 LEU cc_start: 0.7921 (mt) cc_final: 0.7578 (tp) REVERT: F 589 GLU cc_start: 0.7072 (mt-10) cc_final: 0.6672 (pm20) REVERT: F 686 MET cc_start: 0.6904 (mmm) cc_final: 0.6302 (mmm) REVERT: F 700 ARG cc_start: 0.6911 (mtt90) cc_final: 0.6534 (mmm160) REVERT: F 725 GLU cc_start: 0.8642 (pm20) cc_final: 0.7773 (tp30) REVERT: J 148 MET cc_start: 0.9058 (ttm) cc_final: 0.8812 (tpp) REVERT: J 278 MET cc_start: 0.8697 (mmm) cc_final: 0.7273 (mmm) REVERT: J 333 ILE cc_start: 0.9248 (mt) cc_final: 0.9025 (mm) REVERT: J 563 MET cc_start: 0.7590 (mmm) cc_final: 0.6158 (tpp) REVERT: J 686 MET cc_start: 0.7450 (mmt) cc_final: 0.6685 (mmm) REVERT: J 696 MET cc_start: 0.6209 (mmm) cc_final: 0.5891 (mmm) outliers start: 1 outliers final: 1 residues processed: 257 average time/residue: 0.1789 time to fit residues: 78.0152 Evaluate side-chains 193 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 192 time to evaluate : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 195 optimal weight: 30.0000 chunk 35 optimal weight: 0.1980 chunk 98 optimal weight: 7.9990 chunk 384 optimal weight: 7.9990 chunk 116 optimal weight: 9.9990 chunk 285 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 253 optimal weight: 20.0000 chunk 188 optimal weight: 50.0000 chunk 232 optimal weight: 4.9990 chunk 309 optimal weight: 20.0000 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 800 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.066651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.049644 restraints weight = 219406.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 65)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.050873 restraints weight = 134544.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.051749 restraints weight = 95008.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 52)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.052361 restraints weight = 74554.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.052732 restraints weight = 63012.196| |-----------------------------------------------------------------------------| r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 31917 Z= 0.161 Angle : 0.608 8.535 43446 Z= 0.327 Chirality : 0.043 0.180 4816 Planarity : 0.005 0.063 5634 Dihedral : 4.935 28.947 4371 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.26 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.13), residues: 3993 helix: 1.09 (0.20), residues: 708 sheet: -0.07 (0.16), residues: 945 loop : -0.09 (0.13), residues: 2340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 626 TYR 0.022 0.002 TYR G 777 PHE 0.027 0.002 PHE A 850 TRP 0.019 0.002 TRP E 553 HIS 0.005 0.001 HIS H 41 Details of bonding type rmsd covalent geometry : bond 0.00344 (31861) covalent geometry : angle 0.60308 (43336) SS BOND : bond 0.00345 ( 55) SS BOND : angle 1.60944 ( 110) hydrogen bonds : bond 0.04582 ( 1176) hydrogen bonds : angle 5.71140 ( 3027) Misc. bond : bond 0.00355 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 ASP cc_start: 0.8660 (m-30) cc_final: 0.8346 (p0) REVERT: A 943 MET cc_start: 0.9258 (tpp) cc_final: 0.8913 (tpt) REVERT: A 1036 LEU cc_start: 0.9729 (tp) cc_final: 0.9343 (tp) REVERT: A 1039 GLU cc_start: 0.8650 (mp0) cc_final: 0.8429 (mp0) REVERT: B 28 THR cc_start: 0.8167 (m) cc_final: 0.7395 (p) REVERT: B 35 HIS cc_start: 0.9163 (m-70) cc_final: 0.8832 (m-70) REVERT: B 36 TRP cc_start: 0.8651 (m100) cc_final: 0.6742 (m100) REVERT: B 56 ASN cc_start: 0.8820 (t0) cc_final: 0.8601 (t0) REVERT: B 80 MET cc_start: 0.8567 (ttm) cc_final: 0.8144 (tmm) REVERT: C 33 MET cc_start: 0.8307 (tpp) cc_final: 0.7936 (mmm) REVERT: C 36 PHE cc_start: 0.9342 (m-80) cc_final: 0.9047 (m-80) REVERT: C 62 PHE cc_start: 0.8436 (m-80) cc_final: 0.8154 (m-80) REVERT: C 85 MET cc_start: 0.8927 (mmm) cc_final: 0.8412 (mmm) REVERT: D 771 ASP cc_start: 0.8937 (m-30) cc_final: 0.8528 (t0) REVERT: D 836 HIS cc_start: 0.9108 (t70) cc_final: 0.8795 (t-90) REVERT: D 977 PHE cc_start: 0.8435 (m-80) cc_final: 0.8065 (m-80) REVERT: D 1001 PHE cc_start: 0.9153 (t80) cc_final: 0.8650 (t80) REVERT: D 1067 ILE cc_start: 0.9588 (mt) cc_final: 0.9185 (tt) REVERT: D 1136 PHE cc_start: 0.8634 (m-80) cc_final: 0.8300 (m-10) REVERT: G 757 MET cc_start: 0.8803 (mmt) cc_final: 0.8222 (tpp) REVERT: G 843 ASP cc_start: 0.9273 (p0) cc_final: 0.8952 (p0) REVERT: G 909 TYR cc_start: 0.7437 (t80) cc_final: 0.7230 (t80) REVERT: G 939 MET cc_start: 0.7977 (tpt) cc_final: 0.7513 (tpp) REVERT: G 943 MET cc_start: 0.9369 (mtp) cc_final: 0.8811 (mmm) REVERT: G 1042 ASN cc_start: 0.8847 (t0) cc_final: 0.8626 (t0) REVERT: H 31 ASP cc_start: 0.8562 (m-30) cc_final: 0.8156 (m-30) REVERT: H 38 LYS cc_start: 0.9647 (tmmt) cc_final: 0.9402 (tmtt) REVERT: H 56 ASN cc_start: 0.8843 (m-40) cc_final: 0.8563 (m-40) REVERT: I 32 PHE cc_start: 0.8838 (m-10) cc_final: 0.8364 (m-80) REVERT: I 33 MET cc_start: 0.9121 (tpp) cc_final: 0.8771 (tpp) REVERT: I 38 GLN cc_start: 0.8621 (tt0) cc_final: 0.7776 (tt0) REVERT: I 46 LEU cc_start: 0.9170 (tt) cc_final: 0.8848 (tp) REVERT: I 73 LEU cc_start: 0.9169 (tt) cc_final: 0.8899 (tp) REVERT: I 85 MET cc_start: 0.9054 (mpp) cc_final: 0.8731 (mpp) REVERT: E 563 MET cc_start: 0.1999 (mtp) cc_final: 0.1377 (tpt) REVERT: E 638 LEU cc_start: 0.9286 (tp) cc_final: 0.8956 (tp) REVERT: E 662 ILE cc_start: 0.9662 (mp) cc_final: 0.9460 (pt) REVERT: E 704 TYR cc_start: 0.5527 (t80) cc_final: 0.5266 (t80) REVERT: F 49 ASP cc_start: 0.7182 (t0) cc_final: 0.6605 (t0) REVERT: F 84 MET cc_start: 0.8474 (mtm) cc_final: 0.7724 (pmm) REVERT: F 343 ASP cc_start: 0.8624 (p0) cc_final: 0.8391 (p0) REVERT: F 377 GLN cc_start: 0.9128 (mt0) cc_final: 0.8923 (mt0) REVERT: F 406 ASN cc_start: 0.8039 (m-40) cc_final: 0.7802 (m110) REVERT: F 589 GLU cc_start: 0.7060 (mt-10) cc_final: 0.6647 (pm20) REVERT: F 686 MET cc_start: 0.7048 (mmm) cc_final: 0.6462 (mmm) REVERT: F 700 ARG cc_start: 0.6998 (mtt90) cc_final: 0.6571 (mmm160) REVERT: F 725 GLU cc_start: 0.8675 (pm20) cc_final: 0.7768 (tp30) REVERT: J 148 MET cc_start: 0.9103 (ttm) cc_final: 0.8839 (tpp) REVERT: J 278 MET cc_start: 0.8639 (mmm) cc_final: 0.7216 (mmm) REVERT: J 563 MET cc_start: 0.7535 (mmm) cc_final: 0.6088 (tpp) REVERT: J 686 MET cc_start: 0.7200 (mmt) cc_final: 0.6504 (mmm) REVERT: J 696 MET cc_start: 0.6205 (mmm) cc_final: 0.5872 (mmm) outliers start: 0 outliers final: 0 residues processed: 265 average time/residue: 0.1858 time to fit residues: 83.0006 Evaluate side-chains 194 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 1.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 323 optimal weight: 9.9990 chunk 231 optimal weight: 10.0000 chunk 349 optimal weight: 2.9990 chunk 265 optimal weight: 8.9990 chunk 359 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 217 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 275 optimal weight: 5.9990 chunk 43 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN E 519 ASN E 576 GLN ** E 688 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 258 GLN F 398 ASN J 60 GLN J 98 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.065810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.049112 restraints weight = 224106.695| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.050242 restraints weight = 141121.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.051047 restraints weight = 101101.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.051610 restraints weight = 80129.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.051971 restraints weight = 68581.030| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 31917 Z= 0.203 Angle : 0.650 9.129 43446 Z= 0.350 Chirality : 0.043 0.180 4816 Planarity : 0.005 0.062 5634 Dihedral : 5.103 30.354 4371 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 12.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 5.66 % Favored : 94.11 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.47 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.13), residues: 3993 helix: 0.88 (0.19), residues: 712 sheet: -0.16 (0.16), residues: 933 loop : -0.27 (0.13), residues: 2348 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG J 626 TYR 0.026 0.002 TYR G 777 PHE 0.028 0.002 PHE A1001 TRP 0.028 0.002 TRP F 253 HIS 0.008 0.001 HIS I 76 Details of bonding type rmsd covalent geometry : bond 0.00435 (31861) covalent geometry : angle 0.64488 (43336) SS BOND : bond 0.00401 ( 55) SS BOND : angle 1.68566 ( 110) hydrogen bonds : bond 0.04744 ( 1176) hydrogen bonds : angle 5.91861 ( 3027) Misc. bond : bond 0.00280 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 246 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 843 ASP cc_start: 0.8660 (m-30) cc_final: 0.8379 (p0) REVERT: A 1036 LEU cc_start: 0.9746 (tp) cc_final: 0.9257 (tp) REVERT: A 1039 GLU cc_start: 0.8713 (mp0) cc_final: 0.8483 (mp0) REVERT: B 28 THR cc_start: 0.8216 (m) cc_final: 0.7442 (p) REVERT: B 36 TRP cc_start: 0.8658 (m100) cc_final: 0.6712 (m100) REVERT: B 56 ASN cc_start: 0.8779 (t0) cc_final: 0.8548 (t0) REVERT: B 80 MET cc_start: 0.8641 (ttm) cc_final: 0.8111 (tmm) REVERT: C 33 MET cc_start: 0.8312 (tpp) cc_final: 0.7956 (mmm) REVERT: C 62 PHE cc_start: 0.8389 (m-80) cc_final: 0.8133 (m-80) REVERT: C 85 MET cc_start: 0.8916 (mmm) cc_final: 0.8442 (mmm) REVERT: D 977 PHE cc_start: 0.8375 (m-80) cc_final: 0.8012 (m-80) REVERT: D 1001 PHE cc_start: 0.9186 (t80) cc_final: 0.8721 (t80) REVERT: D 1067 ILE cc_start: 0.9610 (mt) cc_final: 0.9158 (tt) REVERT: G 757 MET cc_start: 0.8806 (mmt) cc_final: 0.8265 (tpp) REVERT: G 939 MET cc_start: 0.8000 (tpt) cc_final: 0.7502 (tpp) REVERT: G 943 MET cc_start: 0.9372 (mtp) cc_final: 0.8808 (mmm) REVERT: G 1042 ASN cc_start: 0.8872 (t0) cc_final: 0.8666 (t0) REVERT: H 31 ASP cc_start: 0.8595 (m-30) cc_final: 0.8209 (m-30) REVERT: H 56 ASN cc_start: 0.8814 (m-40) cc_final: 0.8482 (m-40) REVERT: I 32 PHE cc_start: 0.8922 (m-10) cc_final: 0.8431 (m-10) REVERT: I 33 MET cc_start: 0.9143 (tpp) cc_final: 0.8743 (tpp) REVERT: I 38 GLN cc_start: 0.8657 (tt0) cc_final: 0.7833 (tt0) REVERT: I 46 LEU cc_start: 0.9154 (tt) cc_final: 0.8835 (tp) REVERT: I 85 MET cc_start: 0.9040 (mpp) cc_final: 0.8735 (mpp) REVERT: E 148 MET cc_start: 0.8649 (tmm) cc_final: 0.7977 (tmm) REVERT: E 563 MET cc_start: 0.2319 (mtp) cc_final: 0.1581 (tpt) REVERT: E 638 LEU cc_start: 0.9338 (tp) cc_final: 0.9046 (tp) REVERT: E 662 ILE cc_start: 0.9679 (mp) cc_final: 0.9464 (pt) REVERT: E 704 TYR cc_start: 0.5739 (t80) cc_final: 0.5449 (t80) REVERT: F 49 ASP cc_start: 0.7239 (t0) cc_final: 0.6610 (t0) REVERT: F 71 TYR cc_start: 0.8836 (t80) cc_final: 0.8483 (t80) REVERT: F 84 MET cc_start: 0.8504 (mtm) cc_final: 0.7764 (pmm) REVERT: F 278 MET cc_start: 0.8764 (mmp) cc_final: 0.8503 (mmp) REVERT: F 343 ASP cc_start: 0.8507 (p0) cc_final: 0.8250 (p0) REVERT: F 406 ASN cc_start: 0.7999 (m-40) cc_final: 0.7760 (m110) REVERT: F 589 GLU cc_start: 0.7108 (mt-10) cc_final: 0.6709 (pm20) REVERT: F 686 MET cc_start: 0.7357 (mmm) cc_final: 0.6845 (mmm) REVERT: F 700 ARG cc_start: 0.6956 (mtt90) cc_final: 0.6704 (mmm160) REVERT: F 725 GLU cc_start: 0.8660 (pm20) cc_final: 0.7846 (tp30) REVERT: J 148 MET cc_start: 0.9027 (ttm) cc_final: 0.8810 (tpp) REVERT: J 278 MET cc_start: 0.8657 (mmm) cc_final: 0.7406 (mmm) REVERT: J 399 PHE cc_start: 0.6218 (m-10) cc_final: 0.5824 (m-10) REVERT: J 523 TYR cc_start: 0.6490 (m-10) cc_final: 0.6142 (m-80) REVERT: J 563 MET cc_start: 0.7626 (mmm) cc_final: 0.6191 (tpp) REVERT: J 686 MET cc_start: 0.7297 (mmt) cc_final: 0.6550 (mmm) REVERT: J 696 MET cc_start: 0.6220 (mmm) cc_final: 0.5893 (mmm) outliers start: 0 outliers final: 0 residues processed: 246 average time/residue: 0.1907 time to fit residues: 79.1666 Evaluate side-chains 181 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 181 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 129 optimal weight: 10.0000 chunk 356 optimal weight: 0.5980 chunk 322 optimal weight: 0.0370 chunk 139 optimal weight: 6.9990 chunk 33 optimal weight: 10.0000 chunk 282 optimal weight: 5.9990 chunk 328 optimal weight: 0.0970 chunk 211 optimal weight: 8.9990 chunk 370 optimal weight: 20.0000 chunk 298 optimal weight: 20.0000 chunk 39 optimal weight: 0.9990 overall best weight: 1.5460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN E 519 ASN F 398 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.067420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.050314 restraints weight = 217097.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.051615 restraints weight = 132971.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.052516 restraints weight = 93945.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 65)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.053148 restraints weight = 73471.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 71)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.053568 restraints weight = 61771.403| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 31917 Z= 0.114 Angle : 0.588 9.223 43446 Z= 0.312 Chirality : 0.043 0.181 4816 Planarity : 0.005 0.063 5634 Dihedral : 4.822 29.437 4371 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.13), residues: 3993 helix: 1.19 (0.20), residues: 711 sheet: -0.02 (0.16), residues: 931 loop : -0.19 (0.13), residues: 2351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG J 626 TYR 0.031 0.001 TYR J 469 PHE 0.024 0.001 PHE A 850 TRP 0.020 0.001 TRP F 253 HIS 0.007 0.001 HIS H 41 Details of bonding type rmsd covalent geometry : bond 0.00237 (31861) covalent geometry : angle 0.58389 (43336) SS BOND : bond 0.00275 ( 55) SS BOND : angle 1.43862 ( 110) hydrogen bonds : bond 0.04418 ( 1176) hydrogen bonds : angle 5.55432 ( 3027) Misc. bond : bond 0.00193 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7986 Ramachandran restraints generated. 3993 Oldfield, 0 Emsley, 3993 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 1.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 801 LYS cc_start: 0.9078 (mtmm) cc_final: 0.8646 (mtmt) REVERT: A 1036 LEU cc_start: 0.9680 (tp) cc_final: 0.9371 (tp) REVERT: A 1039 GLU cc_start: 0.8778 (mp0) cc_final: 0.8457 (mp0) REVERT: B 28 THR cc_start: 0.8094 (m) cc_final: 0.7322 (p) REVERT: B 36 TRP cc_start: 0.8681 (m100) cc_final: 0.6941 (m100) REVERT: B 56 ASN cc_start: 0.8846 (t0) cc_final: 0.8632 (t0) REVERT: B 80 MET cc_start: 0.8613 (ttm) cc_final: 0.8158 (tmm) REVERT: C 33 MET cc_start: 0.8195 (tpp) cc_final: 0.7900 (mmm) REVERT: C 36 PHE cc_start: 0.9370 (m-80) cc_final: 0.9115 (m-80) REVERT: C 85 MET cc_start: 0.8848 (mmm) cc_final: 0.8440 (mmm) REVERT: D 771 ASP cc_start: 0.8854 (m-30) cc_final: 0.8582 (t0) REVERT: D 809 TYR cc_start: 0.8325 (t80) cc_final: 0.7937 (t80) REVERT: D 977 PHE cc_start: 0.8393 (m-80) cc_final: 0.8025 (m-80) REVERT: D 1001 PHE cc_start: 0.9078 (t80) cc_final: 0.8536 (t80) REVERT: D 1136 PHE cc_start: 0.8589 (m-80) cc_final: 0.8363 (m-10) REVERT: G 757 MET cc_start: 0.8772 (mmt) cc_final: 0.8219 (tpp) REVERT: G 943 MET cc_start: 0.9372 (mtp) cc_final: 0.8815 (mmm) REVERT: H 31 ASP cc_start: 0.8559 (m-30) cc_final: 0.8304 (m-30) REVERT: H 56 ASN cc_start: 0.8807 (m-40) cc_final: 0.8538 (m-40) REVERT: H 69 MET cc_start: 0.7268 (ttp) cc_final: 0.6801 (ttt) REVERT: H 80 MET cc_start: 0.8856 (ttp) cc_final: 0.8576 (tpp) REVERT: I 32 PHE cc_start: 0.8800 (m-10) cc_final: 0.8274 (m-80) REVERT: I 33 MET cc_start: 0.9131 (tpp) cc_final: 0.8759 (tpp) REVERT: I 38 GLN cc_start: 0.8649 (tt0) cc_final: 0.7818 (tt0) REVERT: I 46 LEU cc_start: 0.9184 (tt) cc_final: 0.8800 (tp) REVERT: I 73 LEU cc_start: 0.9108 (tt) cc_final: 0.8754 (tt) REVERT: I 75 ILE cc_start: 0.9287 (mp) cc_final: 0.8970 (tp) REVERT: E 148 MET cc_start: 0.8706 (tmm) cc_final: 0.8315 (tmm) REVERT: E 240 MET cc_start: 0.8277 (mmm) cc_final: 0.8050 (mmm) REVERT: E 288 ASP cc_start: 0.8042 (m-30) cc_final: 0.7171 (t0) REVERT: E 563 MET cc_start: 0.2213 (mtp) cc_final: 0.1597 (tpt) REVERT: E 638 LEU cc_start: 0.9280 (tp) cc_final: 0.8953 (tp) REVERT: E 662 ILE cc_start: 0.9649 (mp) cc_final: 0.9431 (pt) REVERT: E 704 TYR cc_start: 0.5616 (t80) cc_final: 0.5350 (t80) REVERT: F 49 ASP cc_start: 0.7185 (t0) cc_final: 0.6541 (t0) REVERT: F 71 TYR cc_start: 0.8751 (t80) cc_final: 0.8438 (t80) REVERT: F 84 MET cc_start: 0.8552 (mtm) cc_final: 0.7761 (pmm) REVERT: F 278 MET cc_start: 0.8734 (mmp) cc_final: 0.8449 (mmp) REVERT: F 324 LEU cc_start: 0.9311 (mt) cc_final: 0.9106 (mt) REVERT: F 343 ASP cc_start: 0.8620 (p0) cc_final: 0.8298 (p0) REVERT: F 406 ASN cc_start: 0.8045 (m-40) cc_final: 0.7789 (m110) REVERT: F 589 GLU cc_start: 0.7090 (mt-10) cc_final: 0.6677 (pm20) REVERT: F 686 MET cc_start: 0.7099 (mmm) cc_final: 0.6540 (mmm) REVERT: F 700 ARG cc_start: 0.6983 (mtt90) cc_final: 0.6618 (mmm160) REVERT: F 725 GLU cc_start: 0.8697 (pm20) cc_final: 0.7857 (tp30) REVERT: J 148 MET cc_start: 0.9087 (ttm) cc_final: 0.8850 (tpp) REVERT: J 278 MET cc_start: 0.8618 (mmm) cc_final: 0.7210 (mmm) REVERT: J 563 MET cc_start: 0.7593 (mmm) cc_final: 0.6071 (tpp) REVERT: J 686 MET cc_start: 0.7185 (mmt) cc_final: 0.6517 (mmm) REVERT: J 696 MET cc_start: 0.6247 (mmm) cc_final: 0.5916 (mmm) outliers start: 0 outliers final: 0 residues processed: 275 average time/residue: 0.1862 time to fit residues: 86.3443 Evaluate side-chains 191 residues out of total 3453 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 397 random chunks: chunk 188 optimal weight: 50.0000 chunk 79 optimal weight: 0.9990 chunk 291 optimal weight: 20.0000 chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 9.9990 chunk 326 optimal weight: 1.9990 chunk 278 optimal weight: 20.0000 chunk 78 optimal weight: 6.9990 chunk 381 optimal weight: 10.0000 chunk 375 optimal weight: 8.9990 chunk 178 optimal weight: 7.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 427 GLN F 398 ASN F 475 ASN F 576 GLN J 348 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.066495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.049619 restraints weight = 218837.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.050885 restraints weight = 134382.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.051693 restraints weight = 95468.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 69)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.052301 restraints weight = 75123.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.052692 restraints weight = 63275.898| |-----------------------------------------------------------------------------| r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 31917 Z= 0.154 Angle : 0.606 16.391 43446 Z= 0.324 Chirality : 0.042 0.296 4816 Planarity : 0.005 0.064 5634 Dihedral : 4.864 38.552 4371 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.66 % Favored : 94.14 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.59 % Cis-general : 0.50 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.13), residues: 3993 helix: 1.17 (0.20), residues: 713 sheet: -0.05 (0.16), residues: 930 loop : -0.26 (0.13), residues: 2350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 626 TYR 0.021 0.002 TYR J 469 PHE 0.030 0.002 PHE C 62 TRP 0.017 0.002 TRP F 253 HIS 0.005 0.001 HIS E 681 Details of bonding type rmsd covalent geometry : bond 0.00332 (31861) covalent geometry : angle 0.59660 (43336) SS BOND : bond 0.00342 ( 55) SS BOND : angle 2.15013 ( 110) hydrogen bonds : bond 0.04437 ( 1176) hydrogen bonds : angle 5.63952 ( 3027) Misc. bond : bond 0.00178 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5641.26 seconds wall clock time: 98 minutes 30.60 seconds (5910.60 seconds total)