Starting phenix.real_space_refine on Tue Feb 20 13:58:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9p_8791/02_2024/5w9p_8791.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9p_8791/02_2024/5w9p_8791.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9p_8791/02_2024/5w9p_8791.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9p_8791/02_2024/5w9p_8791.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9p_8791/02_2024/5w9p_8791.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5w9p_8791/02_2024/5w9p_8791.pdb" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 147 5.16 5 C 17748 2.51 5 N 4689 2.21 5 O 5430 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 28014 Number of models: 1 Model: "" Number of chains: 12 Chain: "J" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain breaks: 1 Chain: "A" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 22, 'TRANS': 490} Chain breaks: 1 Chain: "F" 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: "G" 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: "B" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain breaks: 1 Chain: "C" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 22, 'TRANS': 490} Chain breaks: 1 Chain: "D" 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: "E" 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: "H" Number of atoms: 3545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 463, 3545 Classifications: {'peptide': 463} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 439} Chain breaks: 1 Chain: "I" Number of atoms: 4010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 513, 4010 Classifications: {'peptide': 513} Link IDs: {'PTRANS': 22, 'TRANS': 490} Chain breaks: 1 Chain: "K" 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: "L" 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} Time building chain proxies: 14.70, per 1000 atoms: 0.52 Number of scatterers: 28014 At special positions: 0 Unit cell: (155.04, 155.04, 179.52, 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 147 16.00 O 5430 8.00 N 4689 7.00 C 17748 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS J 806 " - pdb=" SG CYS J 828 " distance=2.06 Simple disulfide: pdb=" SG CYS J 811 " - pdb=" SG CYS J 817 " distance=2.01 Simple disulfide: pdb=" SG CYS J 912 " - pdb=" SG CYS J 925 " distance=2.03 Simple disulfide: pdb=" SG CYS J1156 " - pdb=" SG CYS J1164 " distance=2.03 Simple disulfide: pdb=" SG CYS A 30 " - pdb=" SG CYS A 195 " distance=2.10 Simple disulfide: pdb=" SG CYS A 176 " - pdb=" SG CYS A 214 " distance=2.14 Simple disulfide: pdb=" SG CYS A 185 " - pdb=" SG CYS A 237 " distance=2.04 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 349 " distance=2.02 Simple disulfide: pdb=" SG CYS A 603 " - pdb=" SG CYS A 654 " distance=2.06 Simple disulfide: pdb=" SG CYS A 620 " - pdb=" SG CYS A 650 " distance=2.04 Simple disulfide: pdb=" SG CYS A 679 " - pdb=" SG CYS A 713 " distance=2.04 Simple disulfide: pdb=" SG CYS A 727 " - pdb=" SG CYS A 736 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.08 Simple disulfide: pdb=" SG CYS G1135 " - pdb=" SG CYS G1204 " distance=2.03 Simple disulfide: pdb=" SG CYS B 806 " - pdb=" SG CYS B 828 " distance=2.06 Simple disulfide: pdb=" SG CYS B 811 " - pdb=" SG CYS B 817 " distance=2.01 Simple disulfide: pdb=" SG CYS B 912 " - pdb=" SG CYS B 925 " distance=2.03 Simple disulfide: pdb=" SG CYS B1156 " - pdb=" SG CYS B1164 " distance=2.03 Simple disulfide: pdb=" SG CYS C 30 " - pdb=" SG CYS C 195 " distance=2.10 Simple disulfide: pdb=" SG CYS C 176 " - pdb=" SG CYS C 214 " distance=2.14 Simple disulfide: pdb=" SG CYS C 185 " - pdb=" SG CYS C 237 " distance=2.04 Simple disulfide: pdb=" SG CYS C 339 " - pdb=" SG CYS C 349 " distance=2.02 Simple disulfide: pdb=" SG CYS C 603 " - pdb=" SG CYS C 654 " distance=2.06 Simple disulfide: pdb=" SG CYS C 620 " - pdb=" SG CYS C 650 " distance=2.04 Simple disulfide: pdb=" SG CYS C 679 " - pdb=" SG CYS C 713 " distance=2.04 Simple disulfide: pdb=" SG CYS C 727 " - pdb=" SG CYS C 736 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.08 Simple disulfide: pdb=" SG CYS E1135 " - pdb=" SG CYS E1204 " distance=2.03 Simple disulfide: pdb=" SG CYS H 806 " - pdb=" SG CYS H 828 " distance=2.06 Simple disulfide: pdb=" SG CYS H 811 " - pdb=" SG CYS H 817 " distance=2.01 Simple disulfide: pdb=" SG CYS H 912 " - pdb=" SG CYS H 925 " distance=2.03 Simple disulfide: pdb=" SG CYS H1156 " - pdb=" SG CYS H1164 " distance=2.03 Simple disulfide: pdb=" SG CYS I 30 " - pdb=" SG CYS I 195 " distance=2.10 Simple disulfide: pdb=" SG CYS I 176 " - pdb=" SG CYS I 214 " distance=2.14 Simple disulfide: pdb=" SG CYS I 185 " - pdb=" SG CYS I 237 " distance=2.04 Simple disulfide: pdb=" SG CYS I 339 " - pdb=" SG CYS I 349 " distance=2.02 Simple disulfide: pdb=" SG CYS I 603 " - pdb=" SG CYS I 654 " distance=2.06 Simple disulfide: pdb=" SG CYS I 620 " - pdb=" SG CYS I 650 " distance=2.04 Simple disulfide: pdb=" SG CYS I 679 " - pdb=" SG CYS I 713 " distance=2.04 Simple disulfide: pdb=" SG CYS I 727 " - pdb=" SG CYS I 736 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 92 " distance=2.08 Simple disulfide: pdb=" SG CYS L1135 " - pdb=" SG CYS L1204 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.92 Conformation dependent library (CDL) restraints added in 5.2 seconds 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6690 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 66 sheets defined 24.6% alpha, 25.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.26 Creating SS restraints... Processing helix chain 'J' and resid 805 through 811 Processing helix chain 'J' and resid 814 through 822 Processing helix chain 'J' and resid 824 through 854 removed outlier: 3.859A pdb=" N CYS J 828 " --> pdb=" O TYR J 824 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER J 852 " --> pdb=" O ASN J 848 " (cutoff:3.500A) Processing helix chain 'J' and resid 888 through 898 Processing helix chain 'J' and resid 907 through 912 Processing helix chain 'J' and resid 922 through 931 removed outlier: 4.301A pdb=" N TYR J 928 " --> pdb=" O ILE J 924 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL J 929 " --> pdb=" O CYS J 925 " (cutoff:3.500A) Processing helix chain 'J' and resid 940 through 955 removed outlier: 3.557A pdb=" N ILE J 955 " --> pdb=" O LEU J 951 " (cutoff:3.500A) Processing helix chain 'J' and resid 971 through 982 Processing helix chain 'J' and resid 986 through 993 Processing helix chain 'J' and resid 993 through 1007 Processing helix chain 'J' and resid 1008 through 1011 Processing helix chain 'J' and resid 1016 through 1039 removed outlier: 3.502A pdb=" N LEU J1033 " --> pdb=" O ASN J1029 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J1036 " --> pdb=" O ALA J1032 " (cutoff:3.500A) Processing helix chain 'J' and resid 1040 through 1042 No H-bonds generated for 'chain 'J' and resid 1040 through 1042' Processing helix chain 'J' and resid 1050 through 1058 Processing helix chain 'J' and resid 1059 through 1104 removed outlier: 4.253A pdb=" N ALA J1065 " --> pdb=" O PRO J1061 " (cutoff:3.500A) Processing helix chain 'J' and resid 1198 through 1200 No H-bonds generated for 'chain 'J' and resid 1198 through 1200' Processing helix chain 'A' and resid 37 through 41 Processing helix chain 'A' and resid 49 through 53 Processing helix chain 'A' and resid 104 through 108 Processing helix chain 'A' and resid 133 through 137 Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 303 through 307 removed outlier: 4.079A pdb=" N ARG A 307 " --> pdb=" O GLN A 304 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 351 Processing helix chain 'A' and resid 675 through 682 removed outlier: 4.405A pdb=" N ALA A 678 " --> pdb=" O GLY A 675 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS A 679 " --> pdb=" O SER A 676 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLU A 680 " --> pdb=" O VAL A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 702 removed outlier: 5.056A pdb=" N ARG A 700 " --> pdb=" O MET A 696 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 32 Processing helix chain 'F' and resid 61 through 64 Processing helix chain 'F' and resid 73 through 75 No H-bonds generated for 'chain 'F' and resid 73 through 75' Processing helix chain 'F' and resid 83 through 87 Processing helix chain 'G' and resid 1195 through 1199 Processing helix chain 'B' and resid 805 through 811 Processing helix chain 'B' and resid 814 through 822 Processing helix chain 'B' and resid 824 through 854 removed outlier: 3.858A pdb=" N CYS B 828 " --> pdb=" O TYR B 824 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 852 " --> pdb=" O ASN B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 888 through 898 Processing helix chain 'B' and resid 907 through 912 Processing helix chain 'B' and resid 922 through 931 removed outlier: 4.301A pdb=" N TYR B 928 " --> pdb=" O ILE B 924 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL B 929 " --> pdb=" O CYS B 925 " (cutoff:3.500A) Processing helix chain 'B' and resid 940 through 955 removed outlier: 3.557A pdb=" N ILE B 955 " --> pdb=" O LEU B 951 " (cutoff:3.500A) Processing helix chain 'B' and resid 971 through 982 Processing helix chain 'B' and resid 986 through 993 Processing helix chain 'B' and resid 993 through 1007 Processing helix chain 'B' and resid 1008 through 1011 Processing helix chain 'B' and resid 1016 through 1039 removed outlier: 3.502A pdb=" N LEU B1033 " --> pdb=" O ASN B1029 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B1036 " --> pdb=" O ALA B1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 1040 through 1042 No H-bonds generated for 'chain 'B' and resid 1040 through 1042' Processing helix chain 'B' and resid 1050 through 1058 Processing helix chain 'B' and resid 1059 through 1104 removed outlier: 4.253A pdb=" N ALA B1065 " --> pdb=" O PRO B1061 " (cutoff:3.500A) Processing helix chain 'B' and resid 1198 through 1200 No H-bonds generated for 'chain 'B' and resid 1198 through 1200' Processing helix chain 'C' and resid 37 through 41 Processing helix chain 'C' and resid 49 through 53 Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 133 through 137 Processing helix chain 'C' and resid 222 through 230 Processing helix chain 'C' and resid 303 through 307 removed outlier: 4.080A pdb=" N ARG C 307 " --> pdb=" O GLN C 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 351 Processing helix chain 'C' and resid 675 through 682 removed outlier: 4.405A pdb=" N ALA C 678 " --> pdb=" O GLY C 675 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N CYS C 679 " --> pdb=" O SER C 676 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLU C 680 " --> pdb=" O VAL C 677 " (cutoff:3.500A) Processing helix chain 'C' and resid 694 through 702 removed outlier: 5.055A pdb=" N ARG C 700 " --> pdb=" O MET C 696 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 32 Processing helix chain 'D' and resid 61 through 64 Processing helix chain 'D' and resid 73 through 75 No H-bonds generated for 'chain 'D' and resid 73 through 75' Processing helix chain 'D' and resid 83 through 87 Processing helix chain 'E' and resid 1195 through 1199 Processing helix chain 'H' and resid 805 through 811 Processing helix chain 'H' and resid 814 through 822 Processing helix chain 'H' and resid 824 through 854 removed outlier: 3.859A pdb=" N CYS H 828 " --> pdb=" O TYR H 824 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N SER H 852 " --> pdb=" O ASN H 848 " (cutoff:3.500A) Processing helix chain 'H' and resid 888 through 898 Processing helix chain 'H' and resid 907 through 912 Processing helix chain 'H' and resid 922 through 931 removed outlier: 4.301A pdb=" N TYR H 928 " --> pdb=" O ILE H 924 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N VAL H 929 " --> pdb=" O CYS H 925 " (cutoff:3.500A) Processing helix chain 'H' and resid 940 through 955 removed outlier: 3.557A pdb=" N ILE H 955 " --> pdb=" O LEU H 951 " (cutoff:3.500A) Processing helix chain 'H' and resid 971 through 982 Processing helix chain 'H' and resid 986 through 993 Processing helix chain 'H' and resid 993 through 1007 Processing helix chain 'H' and resid 1008 through 1011 Processing helix chain 'H' and resid 1016 through 1039 removed outlier: 3.502A pdb=" N LEU H1033 " --> pdb=" O ASN H1029 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU H1036 " --> pdb=" O ALA H1032 " (cutoff:3.500A) Processing helix chain 'H' and resid 1040 through 1042 No H-bonds generated for 'chain 'H' and resid 1040 through 1042' Processing helix chain 'H' and resid 1050 through 1058 Processing helix chain 'H' and resid 1059 through 1104 removed outlier: 4.254A pdb=" N ALA H1065 " --> pdb=" O PRO H1061 " (cutoff:3.500A) Processing helix chain 'H' and resid 1198 through 1200 No H-bonds generated for 'chain 'H' and resid 1198 through 1200' Processing helix chain 'I' and resid 37 through 41 Processing helix chain 'I' and resid 49 through 53 Processing helix chain 'I' and resid 104 through 108 Processing helix chain 'I' and resid 133 through 137 Processing helix chain 'I' and resid 222 through 230 Processing helix chain 'I' and resid 303 through 307 removed outlier: 4.078A pdb=" N ARG I 307 " --> pdb=" O GLN I 304 " (cutoff:3.500A) Processing helix chain 'I' and resid 342 through 351 Processing helix chain 'I' and resid 675 through 682 removed outlier: 4.405A pdb=" N ALA I 678 " --> pdb=" O GLY I 675 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N CYS I 679 " --> pdb=" O SER I 676 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N GLU I 680 " --> pdb=" O VAL I 677 " (cutoff:3.500A) Processing helix chain 'I' and resid 694 through 702 removed outlier: 5.056A pdb=" N ARG I 700 " --> pdb=" O MET I 696 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 32 Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 73 through 75 No H-bonds generated for 'chain 'K' and resid 73 through 75' Processing helix chain 'K' and resid 83 through 87 Processing helix chain 'L' and resid 1195 through 1199 Processing sheet with id=AA1, first strand: chain 'A' and resid 719 through 724 removed outlier: 7.313A pdb=" N LEU J 759 " --> pdb=" O SER A 720 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU A 722 " --> pdb=" O LEU J 759 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU A 735 " --> pdb=" O LEU A 731 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'J' and resid 768 through 769 removed outlier: 5.923A pdb=" N ILE J 768 " --> pdb=" O SER H 858 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'J' and resid 777 through 782 removed outlier: 6.027A pdb=" N VAL J1150 " --> pdb=" O LYS J1174 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE J1172 " --> pdb=" O ALA J1152 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 785 through 796 Processing sheet with id=AA5, first strand: chain 'J' and resid 802 through 804 Processing sheet with id=AA6, first strand: chain 'J' and resid 857 through 858 Processing sheet with id=AA7, first strand: chain 'J' and resid 1202 through 1205 removed outlier: 4.333A pdb=" N CYS J1164 " --> pdb=" O VAL J1205 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N CYS J1156 " --> pdb=" O ILE J1214 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 33 through 35 Processing sheet with id=AA9, first strand: chain 'A' and resid 63 through 64 removed outlier: 6.332A pdb=" N THR A 63 " --> pdb=" O TYR C 632 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N VAL C 639 " --> pdb=" O LEU C 651 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 68 through 75 removed outlier: 3.650A pdb=" N ARG A 335 " --> pdb=" O ASP A 326 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.500A pdb=" N SER A 267 " --> pdb=" O GLN A 280 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLN A 280 " --> pdb=" O SER A 267 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 88 through 89 removed outlier: 7.394A pdb=" N SER A 88 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR A 206 " --> pdb=" O SER A 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 92 through 93 Processing sheet with id=AB5, first strand: chain 'A' and resid 110 through 111 removed outlier: 4.492A pdb=" N ALA A 146 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE A 186 " --> pdb=" O CYS A 237 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N CYS A 237 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU A 188 " --> pdb=" O ARG A 235 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG A 235 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 126 through 127 removed outlier: 4.559A pdb=" N SER A 126 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA A 309 " --> pdb=" O THR A 139 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'A' and resid 359 through 366 removed outlier: 4.553A pdb=" N VAL A 659 " --> pdb=" O VAL A 363 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER A 365 " --> pdb=" O VAL A 657 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL A 657 " --> pdb=" O SER A 365 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 371 through 376 removed outlier: 4.603A pdb=" N GLU A 605 " --> pdb=" O GLY A 372 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 617 through 619 removed outlier: 5.061A pdb=" N VAL A 639 " --> pdb=" O LEU A 651 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 3 through 6 Processing sheet with id=AC3, first strand: chain 'F' and resid 57 through 59 removed outlier: 6.419A pdb=" N SER F 44 " --> pdb=" O SER F 40 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP F 36 " --> pdb=" O ILE F 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL F 50 " --> pdb=" O ILE F 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE F 34 " --> pdb=" O VAL F 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 96 through 99 removed outlier: 4.635A pdb=" N TYR F 98 " --> pdb=" O VAL F 100B" (cutoff:3.500A) removed outlier: 7.474A pdb=" N VAL F 100B" --> pdb=" O TYR F 98 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 1116 through 1119 Processing sheet with id=AC6, first strand: chain 'G' and resid 1122 through 1125 removed outlier: 6.383A pdb=" N LEU G1123 " --> pdb=" O GLU G1221 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP G1151 " --> pdb=" O LEU G1163 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 719 through 724 removed outlier: 7.312A pdb=" N LEU B 759 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU C 722 " --> pdb=" O LEU B 759 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU C 735 " --> pdb=" O LEU C 731 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 777 through 782 removed outlier: 6.027A pdb=" N VAL B1150 " --> pdb=" O LYS B1174 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N PHE B1172 " --> pdb=" O ALA B1152 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 785 through 796 Processing sheet with id=AD1, first strand: chain 'B' and resid 802 through 804 Processing sheet with id=AD2, first strand: chain 'B' and resid 857 through 858 Processing sheet with id=AD3, first strand: chain 'B' and resid 1202 through 1205 removed outlier: 4.334A pdb=" N CYS B1164 " --> pdb=" O VAL B1205 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N CYS B1156 " --> pdb=" O ILE B1214 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 33 through 35 Processing sheet with id=AD5, first strand: chain 'C' and resid 63 through 64 removed outlier: 6.331A pdb=" N THR C 63 " --> pdb=" O TYR I 632 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL I 639 " --> pdb=" O LEU I 651 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 68 through 75 removed outlier: 3.651A pdb=" N ARG C 335 " --> pdb=" O ASP C 326 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.500A pdb=" N SER C 267 " --> pdb=" O GLN C 280 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLN C 280 " --> pdb=" O SER C 267 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 88 through 89 removed outlier: 7.392A pdb=" N SER C 88 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 92 through 93 Processing sheet with id=AE1, first strand: chain 'C' and resid 110 through 111 removed outlier: 4.493A pdb=" N ALA C 146 " --> pdb=" O ILE C 296 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N ILE C 186 " --> pdb=" O CYS C 237 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N CYS C 237 " --> pdb=" O ILE C 186 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLU C 188 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG C 235 " --> pdb=" O GLU C 188 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 126 through 127 removed outlier: 4.558A pdb=" N SER C 126 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA C 309 " --> pdb=" O THR C 139 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AE4, first strand: chain 'C' and resid 359 through 366 removed outlier: 4.553A pdb=" N VAL C 659 " --> pdb=" O VAL C 363 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER C 365 " --> pdb=" O VAL C 657 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL C 657 " --> pdb=" O SER C 365 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 371 through 376 removed outlier: 4.604A pdb=" N GLU C 605 " --> pdb=" O GLY C 372 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AE7, first strand: chain 'D' and resid 57 through 59 removed outlier: 6.419A pdb=" N SER D 44 " --> pdb=" O SER D 40 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 4.472A pdb=" N VAL D 50 " --> pdb=" O ILE D 34 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ILE D 34 " --> pdb=" O VAL D 50 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 96 through 99 removed outlier: 4.635A pdb=" N TYR D 98 " --> pdb=" O VAL D 100B" (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL D 100B" --> pdb=" O TYR D 98 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 1116 through 1119 Processing sheet with id=AF1, first strand: chain 'E' and resid 1122 through 1125 removed outlier: 6.383A pdb=" N LEU E1123 " --> pdb=" O GLU E1221 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP E1151 " --> pdb=" O LEU E1163 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'I' and resid 719 through 724 removed outlier: 7.313A pdb=" N LEU H 759 " --> pdb=" O SER I 720 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N LEU I 722 " --> pdb=" O LEU H 759 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N LEU I 735 " --> pdb=" O LEU I 731 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'H' and resid 777 through 782 removed outlier: 6.027A pdb=" N VAL H1150 " --> pdb=" O LYS H1174 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N PHE H1172 " --> pdb=" O ALA H1152 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'H' and resid 785 through 796 Processing sheet with id=AF5, first strand: chain 'H' and resid 802 through 804 Processing sheet with id=AF6, first strand: chain 'H' and resid 1202 through 1205 removed outlier: 4.334A pdb=" N CYS H1164 " --> pdb=" O VAL H1205 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N CYS H1156 " --> pdb=" O ILE H1214 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'I' and resid 33 through 35 Processing sheet with id=AF8, first strand: chain 'I' and resid 68 through 75 removed outlier: 3.650A pdb=" N ARG I 335 " --> pdb=" O ASP I 326 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 83 through 85 removed outlier: 6.501A pdb=" N SER I 267 " --> pdb=" O GLN I 280 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLN I 280 " --> pdb=" O SER I 267 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'I' and resid 88 through 89 removed outlier: 7.393A pdb=" N SER I 88 " --> pdb=" O ILE I 300 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N THR I 206 " --> pdb=" O SER I 299 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG1 Processing sheet with id=AG2, first strand: chain 'I' and resid 92 through 93 Processing sheet with id=AG3, first strand: chain 'I' and resid 110 through 111 removed outlier: 4.493A pdb=" N ALA I 146 " --> pdb=" O ILE I 296 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE I 186 " --> pdb=" O CYS I 237 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N CYS I 237 " --> pdb=" O ILE I 186 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N GLU I 188 " --> pdb=" O ARG I 235 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ARG I 235 " --> pdb=" O GLU I 188 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'I' and resid 126 through 127 removed outlier: 4.559A pdb=" N SER I 126 " --> pdb=" O ILE I 140 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA I 309 " --> pdb=" O THR I 139 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'I' and resid 153 through 154 Processing sheet with id=AG6, first strand: chain 'I' and resid 359 through 366 removed outlier: 4.553A pdb=" N VAL I 659 " --> pdb=" O VAL I 363 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER I 365 " --> pdb=" O VAL I 657 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N VAL I 657 " --> pdb=" O SER I 365 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'I' and resid 371 through 376 removed outlier: 4.603A pdb=" N GLU I 605 " --> pdb=" O GLY I 372 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'K' and resid 3 through 6 Processing sheet with id=AG9, first strand: chain 'K' and resid 57 through 59 removed outlier: 6.419A pdb=" N SER K 44 " --> pdb=" O SER K 40 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N TRP K 36 " --> pdb=" O ILE K 48 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N VAL K 50 " --> pdb=" O ILE K 34 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE K 34 " --> pdb=" O VAL K 50 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'K' and resid 96 through 99 removed outlier: 4.635A pdb=" N TYR K 98 " --> pdb=" O VAL K 100B" (cutoff:3.500A) removed outlier: 7.475A pdb=" N VAL K 100B" --> pdb=" O TYR K 98 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'L' and resid 1116 through 1119 Processing sheet with id=AH3, first strand: chain 'L' and resid 1122 through 1125 removed outlier: 6.383A pdb=" N LEU L1123 " --> pdb=" O GLU L1221 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N TRP L1151 " --> pdb=" O LEU L1163 " (cutoff:3.500A) 1143 hydrogen bonds defined for protein. 2940 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: 11.69 Time building geometry restraints manager: 10.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 5990 1.33 - 1.45: 7976 1.45 - 1.58: 14492 1.58 - 1.70: 0 1.70 - 1.83: 204 Bond restraints: 28662 Sorted by residual: bond pdb=" CA PRO H1060 " pdb=" C PRO H1060 " ideal model delta sigma weight residual 1.517 1.560 -0.043 9.30e-03 1.16e+04 2.16e+01 bond pdb=" CA PRO B1060 " pdb=" C PRO B1060 " ideal model delta sigma weight residual 1.517 1.560 -0.043 9.30e-03 1.16e+04 2.11e+01 bond pdb=" CA PRO J1060 " pdb=" C PRO J1060 " ideal model delta sigma weight residual 1.517 1.559 -0.042 9.30e-03 1.16e+04 2.07e+01 bond pdb=" N TYR J 905 " pdb=" CA TYR J 905 " ideal model delta sigma weight residual 1.457 1.513 -0.056 1.29e-02 6.01e+03 1.86e+01 bond pdb=" N TYR H 905 " pdb=" CA TYR H 905 " ideal model delta sigma weight residual 1.457 1.513 -0.055 1.29e-02 6.01e+03 1.85e+01 ... (remaining 28657 not shown) Histogram of bond angle deviations from ideal: 97.40 - 104.71: 480 104.71 - 112.03: 12667 112.03 - 119.34: 10373 119.34 - 126.66: 15192 126.66 - 133.98: 231 Bond angle restraints: 38943 Sorted by residual: angle pdb=" C LEU A 284 " pdb=" N PRO A 285 " pdb=" CA PRO A 285 " ideal model delta sigma weight residual 119.87 129.23 -9.36 1.04e+00 9.25e-01 8.10e+01 angle pdb=" C LEU C 284 " pdb=" N PRO C 285 " pdb=" CA PRO C 285 " ideal model delta sigma weight residual 119.87 129.15 -9.28 1.04e+00 9.25e-01 7.96e+01 angle pdb=" C LEU I 284 " pdb=" N PRO I 285 " pdb=" CA PRO I 285 " ideal model delta sigma weight residual 119.87 129.15 -9.28 1.04e+00 9.25e-01 7.96e+01 angle pdb=" C VAL L1174 " pdb=" N PRO L1175 " pdb=" CA PRO L1175 " ideal model delta sigma weight residual 120.03 128.20 -8.17 9.90e-01 1.02e+00 6.82e+01 angle pdb=" C VAL G1174 " pdb=" N PRO G1175 " pdb=" CA PRO G1175 " ideal model delta sigma weight residual 120.03 128.16 -8.13 9.90e-01 1.02e+00 6.75e+01 ... (remaining 38938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 16141 17.82 - 35.64: 683 35.64 - 53.46: 132 53.46 - 71.28: 66 71.28 - 89.10: 36 Dihedral angle restraints: 17058 sinusoidal: 6558 harmonic: 10500 Sorted by residual: dihedral pdb=" CB CYS E1135 " pdb=" SG CYS E1135 " pdb=" SG CYS E1204 " pdb=" CB CYS E1204 " ideal model delta sinusoidal sigma weight residual 93.00 170.18 -77.18 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS L1135 " pdb=" SG CYS L1135 " pdb=" SG CYS L1204 " pdb=" CB CYS L1204 " ideal model delta sinusoidal sigma weight residual 93.00 170.16 -77.16 1 1.00e+01 1.00e-02 7.47e+01 dihedral pdb=" CB CYS G1135 " pdb=" SG CYS G1135 " pdb=" SG CYS G1204 " pdb=" CB CYS G1204 " ideal model delta sinusoidal sigma weight residual 93.00 170.16 -77.16 1 1.00e+01 1.00e-02 7.47e+01 ... (remaining 17055 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 2283 0.054 - 0.109: 1381 0.109 - 0.163: 498 0.163 - 0.217: 113 0.217 - 0.272: 24 Chirality restraints: 4299 Sorted by residual: chirality pdb=" CA MET J 939 " pdb=" N MET J 939 " pdb=" C MET J 939 " pdb=" CB MET J 939 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA MET H 939 " pdb=" N MET H 939 " pdb=" C MET H 939 " pdb=" CB MET H 939 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CA MET B 939 " pdb=" N MET B 939 " pdb=" C MET B 939 " pdb=" CB MET B 939 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.82e+00 ... (remaining 4296 not shown) Planarity restraints: 5070 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS L1192 " 0.108 5.00e-02 4.00e+02 1.62e-01 4.22e+01 pdb=" N PRO L1193 " -0.281 5.00e-02 4.00e+02 pdb=" CA PRO L1193 " 0.090 5.00e-02 4.00e+02 pdb=" CD PRO L1193 " 0.083 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS G1192 " -0.108 5.00e-02 4.00e+02 1.62e-01 4.21e+01 pdb=" N PRO G1193 " 0.280 5.00e-02 4.00e+02 pdb=" CA PRO G1193 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO G1193 " -0.082 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E1192 " -0.108 5.00e-02 4.00e+02 1.62e-01 4.21e+01 pdb=" N PRO E1193 " 0.280 5.00e-02 4.00e+02 pdb=" CA PRO E1193 " -0.090 5.00e-02 4.00e+02 pdb=" CD PRO E1193 " -0.083 5.00e-02 4.00e+02 ... (remaining 5067 not shown) Histogram of nonbonded interaction distances: 1.35 - 2.06: 15 2.06 - 2.77: 5141 2.77 - 3.48: 36321 3.48 - 4.19: 68623 4.19 - 4.90: 114164 Nonbonded interactions: 224264 Sorted by model distance: nonbonded pdb=" OH TYR J 905 " pdb=" C LEU J 935 " model vdw 1.350 3.270 nonbonded pdb=" OH TYR H 905 " pdb=" O LEU H 935 " model vdw 1.351 2.440 nonbonded pdb=" OH TYR B 905 " pdb=" O LEU B 935 " model vdw 1.351 2.440 nonbonded pdb=" OH TYR J 905 " pdb=" O LEU J 935 " model vdw 1.351 2.440 nonbonded pdb=" OH TYR B 905 " pdb=" C LEU B 935 " model vdw 1.352 3.270 ... (remaining 224259 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'I' } ncs_group { reference = chain 'B' selection = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'D' selection = chain 'F' selection = chain 'K' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'L' } 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: 1.480 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: 7.450 Check model and map are aligned: 0.440 Set scattering table: 0.290 Process input model: 71.650 Find NCS groups from input model: 1.820 Set up NCS constraints: 0.200 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 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 : 0.013 0.056 28662 Z= 0.862 Angle : 1.586 11.379 38943 Z= 1.066 Chirality : 0.076 0.272 4299 Planarity : 0.018 0.162 5070 Dihedral : 12.109 89.099 10242 Min Nonbonded Distance : 1.350 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 1.17 % Allowed : 4.36 % Favored : 94.47 % Rotamer: Outliers : 0.68 % Allowed : 1.30 % Favored : 98.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.14), residues: 3582 helix: 1.03 (0.18), residues: 648 sheet: 0.76 (0.17), residues: 759 loop : 0.80 (0.14), residues: 2175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.073 0.009 TRP D 47 HIS 0.004 0.001 HIS B1122 PHE 0.032 0.005 PHE G1214 TYR 0.046 0.005 TYR C 85 ARG 0.003 0.000 ARG I 190 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 690 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 669 time to evaluate : 3.488 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: J 1137 MET cc_start: 0.8833 (mtm) cc_final: 0.8558 (mtp) REVERT: A 41 ASP cc_start: 0.7981 (t0) cc_final: 0.7289 (m-30) REVERT: A 148 MET cc_start: 0.9181 (ttm) cc_final: 0.8861 (ttp) REVERT: F 45 LEU cc_start: 0.7955 (mp) cc_final: 0.7596 (mp) REVERT: F 100 MET cc_start: 0.8151 (mmt) cc_final: 0.7788 (mpp) REVERT: G 1149 MET cc_start: 0.8750 (tpp) cc_final: 0.8535 (tpp) REVERT: B 996 LEU cc_start: 0.9286 (mt) cc_final: 0.8995 (tt) REVERT: B 1039 GLU cc_start: 0.8243 (tp30) cc_final: 0.7729 (tp30) REVERT: B 1067 ILE cc_start: 0.9224 (mt) cc_final: 0.9005 (mm) REVERT: B 1137 MET cc_start: 0.8846 (mtm) cc_final: 0.8622 (mtp) REVERT: C 41 ASP cc_start: 0.8103 (t0) cc_final: 0.7282 (m-30) REVERT: C 148 MET cc_start: 0.9230 (ttm) cc_final: 0.8928 (ttp) REVERT: C 259 THR cc_start: 0.8572 (p) cc_final: 0.8370 (t) REVERT: D 2 VAL cc_start: 0.8635 (t) cc_final: 0.8265 (m) REVERT: D 86 ASP cc_start: 0.7924 (m-30) cc_final: 0.7647 (m-30) REVERT: D 94 ARG cc_start: 0.7717 (ttp-170) cc_final: 0.6819 (ttt180) REVERT: D 100 MET cc_start: 0.8286 (mmt) cc_final: 0.7861 (mpp) REVERT: E 1162 LEU cc_start: 0.8470 (tp) cc_final: 0.8200 (tt) REVERT: H 809 TYR cc_start: 0.9269 (t80) cc_final: 0.9061 (t80) REVERT: I 41 ASP cc_start: 0.8198 (t0) cc_final: 0.7544 (m-30) REVERT: I 56 ILE cc_start: 0.9304 (mm) cc_final: 0.9025 (tt) REVERT: I 148 MET cc_start: 0.9030 (ttm) cc_final: 0.8765 (ttp) REVERT: I 350 SER cc_start: 0.9189 (p) cc_final: 0.8984 (t) REVERT: I 602 ASN cc_start: 0.8815 (t0) cc_final: 0.8478 (m-40) REVERT: I 686 MET cc_start: 0.6151 (mmm) cc_final: 0.5644 (mmp) REVERT: K 2 VAL cc_start: 0.8798 (t) cc_final: 0.8409 (m) REVERT: K 73 LYS cc_start: 0.8453 (mttt) cc_final: 0.8129 (tmtt) REVERT: K 94 ARG cc_start: 0.7804 (ttp-170) cc_final: 0.6991 (ttt-90) REVERT: K 100 MET cc_start: 0.8265 (mmt) cc_final: 0.8010 (mpp) REVERT: L 1162 LEU cc_start: 0.8430 (tp) cc_final: 0.8188 (tt) REVERT: L 1214 PHE cc_start: 0.8220 (p90) cc_final: 0.7706 (p90) outliers start: 21 outliers final: 15 residues processed: 690 average time/residue: 0.4482 time to fit residues: 476.0251 Evaluate side-chains 310 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 295 time to evaluate : 3.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 971 PRO Chi-restraints excluded: chain J residue 1060 PRO Chi-restraints excluded: chain A residue 189 PRO Chi-restraints excluded: chain A residue 196 PRO Chi-restraints excluded: chain A residue 730 PRO Chi-restraints excluded: chain B residue 971 PRO Chi-restraints excluded: chain C residue 189 PRO Chi-restraints excluded: chain C residue 196 PRO Chi-restraints excluded: chain C residue 730 PRO Chi-restraints excluded: chain H residue 971 PRO Chi-restraints excluded: chain H residue 1060 PRO Chi-restraints excluded: chain H residue 1143 PRO Chi-restraints excluded: chain I residue 189 PRO Chi-restraints excluded: chain I residue 196 PRO Chi-restraints excluded: chain I residue 730 PRO Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 301 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 182 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 279 optimal weight: 0.9980 chunk 108 optimal weight: 3.9990 chunk 170 optimal weight: 1.9990 chunk 208 optimal weight: 0.9990 chunk 324 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 842 GLN J1129 ASN J1201 ASN A 98 GLN A 236 ASN A 261 GLN A 681 HIS F 41 HIS ** G1192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G1206 GLN B 772 GLN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN C 98 GLN C 236 ASN C 280 GLN C 681 HIS D 41 HIS D 105 GLN E1154 GLN H 974 GLN H1201 ASN I 98 GLN I 236 ASN I 280 GLN I 627 GLN I 670 HIS I 681 HIS K 41 HIS Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 28662 Z= 0.228 Angle : 0.698 12.782 38943 Z= 0.380 Chirality : 0.044 0.232 4299 Planarity : 0.008 0.091 5070 Dihedral : 5.744 27.955 3984 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.52 % Favored : 95.06 % Rotamer: Outliers : 2.18 % Allowed : 8.98 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.06 (0.14), residues: 3582 helix: 2.26 (0.20), residues: 630 sheet: 0.71 (0.17), residues: 816 loop : 0.31 (0.14), residues: 2136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP F 47 HIS 0.012 0.001 HIS D 41 PHE 0.020 0.002 PHE A 254 TYR 0.025 0.002 TYR J 905 ARG 0.006 0.001 ARG J1113 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 350 time to evaluate : 3.326 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: J 842 GLN cc_start: 0.8215 (mm110) cc_final: 0.7982 (mm-40) REVERT: A 41 ASP cc_start: 0.8061 (t0) cc_final: 0.7318 (m-30) REVERT: A 357 GLU cc_start: 0.8418 (mp0) cc_final: 0.8172 (mt-10) REVERT: A 696 MET cc_start: 0.5348 (ttm) cc_final: 0.5042 (ttp) REVERT: F 43 LYS cc_start: 0.9059 (mttt) cc_final: 0.8836 (mmtp) REVERT: F 73 LYS cc_start: 0.8134 (mtmt) cc_final: 0.7774 (tmtt) REVERT: F 101 ASP cc_start: 0.8426 (t0) cc_final: 0.8225 (t0) REVERT: G 1206 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6967 (pp30) REVERT: G 1209 GLU cc_start: 0.8712 (pt0) cc_final: 0.7611 (pm20) REVERT: B 842 GLN cc_start: 0.8487 (mm-40) cc_final: 0.8025 (mm-40) REVERT: C 41 ASP cc_start: 0.8016 (t0) cc_final: 0.7238 (m-30) REVERT: D 100 ASP cc_start: 0.8310 (t0) cc_final: 0.8099 (t0) REVERT: D 100 MET cc_start: 0.8139 (mmt) cc_final: 0.7784 (mmm) REVERT: D 105 GLN cc_start: 0.8104 (OUTLIER) cc_final: 0.7543 (pm20) REVERT: E 1209 GLU cc_start: 0.8485 (pt0) cc_final: 0.8001 (pm20) REVERT: I 41 ASP cc_start: 0.8220 (t0) cc_final: 0.7524 (m-30) REVERT: K 2 VAL cc_start: 0.8241 (t) cc_final: 0.7961 (t) REVERT: K 3 GLN cc_start: 0.8631 (mm-40) cc_final: 0.8333 (mm-40) REVERT: K 73 LYS cc_start: 0.8525 (mttt) cc_final: 0.8061 (tmtt) REVERT: K 100 MET cc_start: 0.8336 (mmt) cc_final: 0.8006 (mmm) REVERT: K 102 TYR cc_start: 0.8702 (m-10) cc_final: 0.8443 (m-10) REVERT: L 1201 MET cc_start: 0.8384 (tpt) cc_final: 0.7953 (tpp) outliers start: 67 outliers final: 41 residues processed: 400 average time/residue: 0.3849 time to fit residues: 245.4169 Evaluate side-chains 310 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 267 time to evaluate : 3.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 845 SER Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1062 GLU Chi-restraints excluded: chain J residue 1127 VAL Chi-restraints excluded: chain J residue 1145 ASN Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1201 ASN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain F residue 2 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 1206 GLN Chi-restraints excluded: chain G residue 1208 LYS Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1127 VAL Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1185 SER Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain D residue 82 ARG Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 1154 GLN Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain H residue 845 SER Chi-restraints excluded: chain H residue 1031 GLN Chi-restraints excluded: chain H residue 1039 GLU Chi-restraints excluded: chain H residue 1062 GLU Chi-restraints excluded: chain H residue 1127 VAL Chi-restraints excluded: chain H residue 1185 SER Chi-restraints excluded: chain H residue 1201 ASN Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 293 TYR Chi-restraints excluded: chain K residue 100 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 180 optimal weight: 0.0770 chunk 100 optimal weight: 8.9990 chunk 269 optimal weight: 10.0000 chunk 220 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 0.7980 chunk 350 optimal weight: 10.0000 chunk 289 optimal weight: 9.9990 chunk 322 optimal weight: 5.9990 chunk 110 optimal weight: 20.0000 chunk 260 optimal weight: 0.2980 overall best weight: 3.0342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1104 ASN ** J1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1217 ASN A 208 HIS ** G1158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1129 ASN ** B1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1217 ASN E1154 GLN E1158 GLN H1129 ASN ** H1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 28662 Z= 0.261 Angle : 0.646 9.645 38943 Z= 0.347 Chirality : 0.044 0.271 4299 Planarity : 0.006 0.072 5070 Dihedral : 5.272 24.052 3939 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.34 % Allowed : 5.22 % Favored : 94.44 % Rotamer: Outliers : 2.67 % Allowed : 9.66 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.14), residues: 3582 helix: 2.41 (0.20), residues: 633 sheet: 0.74 (0.16), residues: 867 loop : 0.04 (0.14), residues: 2082 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 253 HIS 0.005 0.001 HIS I 208 PHE 0.022 0.002 PHE A 254 TYR 0.029 0.002 TYR A 689 ARG 0.004 0.000 ARG B1074 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 297 time to evaluate : 2.995 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: A 41 ASP cc_start: 0.8099 (t0) cc_final: 0.7348 (m-30) REVERT: A 270 TYR cc_start: 0.7897 (OUTLIER) cc_final: 0.7645 (m-80) REVERT: F 43 LYS cc_start: 0.9178 (mttt) cc_final: 0.8877 (mmtp) REVERT: F 73 LYS cc_start: 0.8106 (mtmt) cc_final: 0.7694 (tmtt) REVERT: F 85 GLU cc_start: 0.8682 (mt-10) cc_final: 0.8304 (mp0) REVERT: F 100 MET cc_start: 0.7657 (mpp) cc_final: 0.7291 (mmm) REVERT: B 927 GLN cc_start: 0.8300 (mt0) cc_final: 0.7843 (mp10) REVERT: B 990 LEU cc_start: 0.9364 (mt) cc_final: 0.9161 (mt) REVERT: C 41 ASP cc_start: 0.8031 (t0) cc_final: 0.7270 (m-30) REVERT: D 100 MET cc_start: 0.8242 (mmt) cc_final: 0.8019 (mmm) REVERT: E 1201 MET cc_start: 0.8096 (mmm) cc_final: 0.7879 (mmm) REVERT: E 1209 GLU cc_start: 0.8631 (pt0) cc_final: 0.8244 (pm20) REVERT: I 41 ASP cc_start: 0.8045 (t0) cc_final: 0.7396 (m-30) REVERT: K 73 LYS cc_start: 0.8392 (mttt) cc_final: 0.8064 (tmtt) REVERT: K 82 LEU cc_start: 0.8436 (pt) cc_final: 0.8019 (tp) REVERT: L 1201 MET cc_start: 0.8364 (tpt) cc_final: 0.7822 (tpp) outliers start: 82 outliers final: 63 residues processed: 357 average time/residue: 0.3826 time to fit residues: 224.4517 Evaluate side-chains 314 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 250 time to evaluate : 3.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 817 CYS Chi-restraints excluded: chain J residue 843 ASP Chi-restraints excluded: chain J residue 845 SER Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1058 LEU Chi-restraints excluded: chain J residue 1062 GLU Chi-restraints excluded: chain J residue 1127 VAL Chi-restraints excluded: chain J residue 1132 ASN Chi-restraints excluded: chain J residue 1145 ASN Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1201 ASN Chi-restraints excluded: chain J residue 1218 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain G residue 1142 ASP Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1095 SER Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1185 SER Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain E residue 1133 ILE Chi-restraints excluded: chain E residue 1154 GLN Chi-restraints excluded: chain E residue 1162 LEU Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain H residue 817 CYS Chi-restraints excluded: chain H residue 845 SER Chi-restraints excluded: chain H residue 1031 GLN Chi-restraints excluded: chain H residue 1127 VAL Chi-restraints excluded: chain H residue 1150 VAL Chi-restraints excluded: chain H residue 1185 SER Chi-restraints excluded: chain H residue 1201 ASN Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 293 TYR Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 666 GLU Chi-restraints excluded: chain I residue 711 VAL Chi-restraints excluded: chain I residue 727 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 1133 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 320 optimal weight: 9.9990 chunk 244 optimal weight: 10.0000 chunk 168 optimal weight: 9.9990 chunk 35 optimal weight: 9.9990 chunk 154 optimal weight: 9.9990 chunk 218 optimal weight: 20.0000 chunk 325 optimal weight: 10.0000 chunk 345 optimal weight: 8.9990 chunk 170 optimal weight: 0.8980 chunk 308 optimal weight: 9.9990 chunk 92 optimal weight: 0.0010 overall best weight: 5.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1097 GLN J1104 ASN J1201 ASN J1212 GLN ** A 167 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G1158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G1206 GLN B 842 GLN B 988 GLN B1097 GLN B1201 ASN ** B1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1212 GLN C 167 HIS D 39 GLN D 105 GLN E1154 GLN H 842 GLN ** H 915 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1104 ASN H1201 ASN ** H1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H1212 GLN I 167 HIS ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 28662 Z= 0.440 Angle : 0.742 14.449 38943 Z= 0.397 Chirality : 0.046 0.286 4299 Planarity : 0.006 0.068 5070 Dihedral : 5.555 23.370 3939 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.34 % Allowed : 6.39 % Favored : 93.27 % Rotamer: Outliers : 3.87 % Allowed : 10.83 % Favored : 85.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.14), residues: 3582 helix: 2.10 (0.19), residues: 618 sheet: 0.17 (0.16), residues: 876 loop : -0.37 (0.14), residues: 2088 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP F 47 HIS 0.007 0.002 HIS I 670 PHE 0.024 0.002 PHE I 254 TYR 0.026 0.002 TYR J 978 ARG 0.006 0.001 ARG C 163 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 270 time to evaluate : 3.245 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: A 41 ASP cc_start: 0.8132 (t0) cc_final: 0.7862 (p0) REVERT: A 270 TYR cc_start: 0.8049 (OUTLIER) cc_final: 0.7762 (m-80) REVERT: A 602 ASN cc_start: 0.8530 (t0) cc_final: 0.7899 (m-40) REVERT: F 43 LYS cc_start: 0.9284 (mttt) cc_final: 0.8998 (mmtp) REVERT: G 1206 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.7665 (pp30) REVERT: G 1209 GLU cc_start: 0.8889 (pt0) cc_final: 0.8086 (pm20) REVERT: G 1222 ILE cc_start: 0.4476 (OUTLIER) cc_final: 0.4243 (tp) REVERT: B 944 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7597 (pt0) REVERT: C 41 ASP cc_start: 0.7915 (t0) cc_final: 0.7639 (p0) REVERT: C 148 MET cc_start: 0.8966 (ttt) cc_final: 0.8660 (tmm) REVERT: C 602 ASN cc_start: 0.8574 (t0) cc_final: 0.7931 (m-40) REVERT: E 1155 LYS cc_start: 0.8511 (mttt) cc_final: 0.8145 (mtpp) REVERT: E 1197 ASP cc_start: 0.7954 (t0) cc_final: 0.7466 (t0) REVERT: E 1201 MET cc_start: 0.8212 (mmm) cc_final: 0.7972 (mmm) REVERT: E 1209 GLU cc_start: 0.8872 (pt0) cc_final: 0.8520 (pm20) REVERT: H 1104 ASN cc_start: 0.9121 (OUTLIER) cc_final: 0.8921 (t0) REVERT: I 41 ASP cc_start: 0.8128 (t0) cc_final: 0.7423 (m-30) REVERT: I 602 ASN cc_start: 0.8483 (t0) cc_final: 0.7809 (m-40) REVERT: K 73 LYS cc_start: 0.8439 (mttt) cc_final: 0.7848 (tmtt) REVERT: K 82 LEU cc_start: 0.8378 (pt) cc_final: 0.8085 (tp) REVERT: L 1209 GLU cc_start: 0.8761 (pt0) cc_final: 0.8245 (pm20) outliers start: 119 outliers final: 86 residues processed: 360 average time/residue: 0.3625 time to fit residues: 213.7418 Evaluate side-chains 327 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 237 time to evaluate : 3.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 817 CYS Chi-restraints excluded: chain J residue 843 ASP Chi-restraints excluded: chain J residue 845 SER Chi-restraints excluded: chain J residue 857 GLN Chi-restraints excluded: chain J residue 986 THR Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1097 GLN Chi-restraints excluded: chain J residue 1124 VAL Chi-restraints excluded: chain J residue 1127 VAL Chi-restraints excluded: chain J residue 1132 ASN Chi-restraints excluded: chain J residue 1145 ASN Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1201 ASN Chi-restraints excluded: chain J residue 1218 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain F residue 16 VAL Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain G residue 1162 LEU Chi-restraints excluded: chain G residue 1204 CYS Chi-restraints excluded: chain G residue 1206 GLN Chi-restraints excluded: chain G residue 1222 ILE Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 857 GLN Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1051 ILE Chi-restraints excluded: chain B residue 1097 GLN Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1185 SER Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain C residue 306 ASP Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 676 SER Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain D residue 2 VAL Chi-restraints excluded: chain D residue 4 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain E residue 1162 LEU Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain H residue 817 CYS Chi-restraints excluded: chain H residue 845 SER Chi-restraints excluded: chain H residue 857 GLN Chi-restraints excluded: chain H residue 932 TYR Chi-restraints excluded: chain H residue 935 LEU Chi-restraints excluded: chain H residue 1005 LEU Chi-restraints excluded: chain H residue 1031 GLN Chi-restraints excluded: chain H residue 1104 ASN Chi-restraints excluded: chain H residue 1127 VAL Chi-restraints excluded: chain H residue 1145 ASN Chi-restraints excluded: chain H residue 1150 VAL Chi-restraints excluded: chain H residue 1185 SER Chi-restraints excluded: chain H residue 1201 ASN Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 293 TYR Chi-restraints excluded: chain I residue 306 ASP Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 666 GLU Chi-restraints excluded: chain I residue 711 VAL Chi-restraints excluded: chain I residue 727 CYS Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 16 VAL Chi-restraints excluded: chain K residue 89 ILE Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 1142 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 287 optimal weight: 9.9990 chunk 195 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 256 optimal weight: 7.9990 chunk 142 optimal weight: 1.9990 chunk 294 optimal weight: 6.9990 chunk 238 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 309 optimal weight: 9.9990 chunk 87 optimal weight: 0.0870 overall best weight: 3.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J1132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J1201 ASN J1208 GLN A 167 HIS G1158 GLN B 842 GLN B1201 ASN ** B1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN E1154 GLN H 842 GLN H1104 ASN H1201 ASN H1208 GLN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1158 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 28662 Z= 0.251 Angle : 0.641 13.950 38943 Z= 0.338 Chirality : 0.043 0.239 4299 Planarity : 0.005 0.058 5070 Dihedral : 5.203 24.171 3939 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.03 % Favored : 93.69 % Rotamer: Outliers : 3.09 % Allowed : 12.16 % Favored : 84.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.14), residues: 3582 helix: 2.32 (0.20), residues: 636 sheet: 0.42 (0.16), residues: 900 loop : -0.57 (0.14), residues: 2046 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP K 47 HIS 0.005 0.001 HIS I 670 PHE 0.019 0.001 PHE C 313 TYR 0.019 0.001 TYR C 314 ARG 0.004 0.000 ARG A 181 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 273 time to evaluate : 3.263 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: A 41 ASP cc_start: 0.8122 (t0) cc_final: 0.7342 (m-30) REVERT: A 270 TYR cc_start: 0.8072 (OUTLIER) cc_final: 0.7754 (m-80) REVERT: F 43 LYS cc_start: 0.9248 (mttt) cc_final: 0.9005 (mmtp) REVERT: G 1206 GLN cc_start: 0.8831 (OUTLIER) cc_final: 0.8080 (pp30) REVERT: G 1209 GLU cc_start: 0.8895 (pt0) cc_final: 0.8110 (pm20) REVERT: B 1005 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9071 (mt) REVERT: C 41 ASP cc_start: 0.7925 (t0) cc_final: 0.7109 (m-30) REVERT: C 148 MET cc_start: 0.9011 (ttt) cc_final: 0.8618 (tmm) REVERT: E 1201 MET cc_start: 0.8350 (mmm) cc_final: 0.7400 (mmm) REVERT: E 1209 GLU cc_start: 0.8798 (pt0) cc_final: 0.8570 (pm20) REVERT: H 1104 ASN cc_start: 0.9047 (OUTLIER) cc_final: 0.8776 (t0) REVERT: I 41 ASP cc_start: 0.8081 (t0) cc_final: 0.7377 (m-30) REVERT: I 221 ARG cc_start: 0.8392 (mtt180) cc_final: 0.7917 (ppt170) REVERT: I 696 MET cc_start: 0.5073 (ttm) cc_final: 0.4812 (ptp) REVERT: K 73 LYS cc_start: 0.8456 (mttt) cc_final: 0.7886 (tmtt) REVERT: K 82 LEU cc_start: 0.8339 (pt) cc_final: 0.8034 (tp) REVERT: L 1142 ASP cc_start: 0.7909 (OUTLIER) cc_final: 0.7692 (t0) REVERT: L 1209 GLU cc_start: 0.8755 (pt0) cc_final: 0.8232 (pm20) outliers start: 95 outliers final: 76 residues processed: 348 average time/residue: 0.3731 time to fit residues: 211.1816 Evaluate side-chains 316 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 235 time to evaluate : 2.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 817 CYS Chi-restraints excluded: chain J residue 843 ASP Chi-restraints excluded: chain J residue 845 SER Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 986 THR Chi-restraints excluded: chain J residue 1005 LEU Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1062 GLU Chi-restraints excluded: chain J residue 1127 VAL Chi-restraints excluded: chain J residue 1145 ASN Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1218 LEU Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 1163 LEU Chi-restraints excluded: chain G residue 1204 CYS Chi-restraints excluded: chain G residue 1206 GLN Chi-restraints excluded: chain G residue 1213 THR Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 857 GLN Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1185 SER Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 199 ASN Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 1154 GLN Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain H residue 817 CYS Chi-restraints excluded: chain H residue 843 ASP Chi-restraints excluded: chain H residue 845 SER Chi-restraints excluded: chain H residue 857 GLN Chi-restraints excluded: chain H residue 932 TYR Chi-restraints excluded: chain H residue 935 LEU Chi-restraints excluded: chain H residue 986 THR Chi-restraints excluded: chain H residue 1031 GLN Chi-restraints excluded: chain H residue 1104 ASN Chi-restraints excluded: chain H residue 1127 VAL Chi-restraints excluded: chain H residue 1132 ASN Chi-restraints excluded: chain H residue 1150 VAL Chi-restraints excluded: chain H residue 1185 SER Chi-restraints excluded: chain H residue 1201 ASN Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 293 TYR Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 711 VAL Chi-restraints excluded: chain I residue 727 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain L residue 1142 ASP Chi-restraints excluded: chain L residue 1194 VAL Chi-restraints excluded: chain L residue 1213 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 116 optimal weight: 6.9990 chunk 310 optimal weight: 3.9990 chunk 68 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 chunk 345 optimal weight: 7.9990 chunk 286 optimal weight: 6.9990 chunk 159 optimal weight: 9.9990 chunk 28 optimal weight: 0.0070 chunk 114 optimal weight: 1.9990 chunk 181 optimal weight: 3.9990 overall best weight: 3.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1201 ASN B 842 GLN B1056 GLN ** B1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E1154 GLN H 772 GLN H 842 GLN ** L1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.4673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 28662 Z= 0.270 Angle : 0.641 12.827 38943 Z= 0.337 Chirality : 0.043 0.305 4299 Planarity : 0.005 0.055 5070 Dihedral : 5.085 21.295 3939 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 11.57 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.62 % Favored : 93.13 % Rotamer: Outliers : 3.19 % Allowed : 12.91 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.14), residues: 3582 helix: 2.36 (0.20), residues: 642 sheet: 0.21 (0.16), residues: 933 loop : -0.57 (0.14), residues: 2007 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 47 HIS 0.004 0.001 HIS I 670 PHE 0.019 0.001 PHE I 254 TYR 0.030 0.001 TYR A 689 ARG 0.005 0.000 ARG G1130 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 244 time to evaluate : 3.370 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 41 ASP cc_start: 0.8130 (t0) cc_final: 0.7357 (m-30) REVERT: A 270 TYR cc_start: 0.8082 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: A 602 ASN cc_start: 0.8521 (t0) cc_final: 0.7872 (m-40) REVERT: F 43 LYS cc_start: 0.9286 (mttt) cc_final: 0.9079 (mmtp) REVERT: G 1209 GLU cc_start: 0.8977 (pt0) cc_final: 0.8500 (pm20) REVERT: B 939 MET cc_start: 0.8421 (mmm) cc_final: 0.8194 (tmm) REVERT: B 944 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7540 (pt0) REVERT: B 1005 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9088 (mt) REVERT: C 41 ASP cc_start: 0.7975 (t0) cc_final: 0.7123 (m-30) REVERT: C 148 MET cc_start: 0.9037 (ttt) cc_final: 0.8638 (tmm) REVERT: C 602 ASN cc_start: 0.8588 (t0) cc_final: 0.8115 (t0) REVERT: C 696 MET cc_start: 0.5105 (ptp) cc_final: 0.4877 (ptm) REVERT: D 43 LYS cc_start: 0.8929 (mmmt) cc_final: 0.8670 (mmmt) REVERT: E 1201 MET cc_start: 0.8223 (mmm) cc_final: 0.7684 (tpp) REVERT: E 1209 GLU cc_start: 0.8861 (pt0) cc_final: 0.8629 (pm20) REVERT: H 939 MET cc_start: 0.8620 (tpt) cc_final: 0.8276 (tpt) REVERT: I 41 ASP cc_start: 0.8048 (t0) cc_final: 0.7380 (m-30) REVERT: I 602 ASN cc_start: 0.8480 (t0) cc_final: 0.8075 (t0) REVERT: I 696 MET cc_start: 0.5248 (ttm) cc_final: 0.4856 (ptp) REVERT: K 73 LYS cc_start: 0.8509 (mttt) cc_final: 0.7926 (tmtt) REVERT: K 82 LEU cc_start: 0.8306 (pt) cc_final: 0.8014 (tp) REVERT: L 1142 ASP cc_start: 0.7816 (OUTLIER) cc_final: 0.7615 (t0) REVERT: L 1209 GLU cc_start: 0.8870 (pt0) cc_final: 0.8413 (pm20) outliers start: 98 outliers final: 78 residues processed: 323 average time/residue: 0.3755 time to fit residues: 198.0069 Evaluate side-chains 308 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 227 time to evaluate : 3.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 817 CYS Chi-restraints excluded: chain J residue 843 ASP Chi-restraints excluded: chain J residue 845 SER Chi-restraints excluded: chain J residue 857 GLN Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 986 THR Chi-restraints excluded: chain J residue 1005 LEU Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1062 GLU Chi-restraints excluded: chain J residue 1127 VAL Chi-restraints excluded: chain J residue 1132 ASN Chi-restraints excluded: chain J residue 1145 ASN Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1201 ASN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 1204 CYS Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1185 SER Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain B residue 1218 LEU Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain E residue 1133 ILE Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain H residue 817 CYS Chi-restraints excluded: chain H residue 843 ASP Chi-restraints excluded: chain H residue 845 SER Chi-restraints excluded: chain H residue 857 GLN Chi-restraints excluded: chain H residue 932 TYR Chi-restraints excluded: chain H residue 935 LEU Chi-restraints excluded: chain H residue 986 THR Chi-restraints excluded: chain H residue 1005 LEU Chi-restraints excluded: chain H residue 1031 GLN Chi-restraints excluded: chain H residue 1127 VAL Chi-restraints excluded: chain H residue 1132 ASN Chi-restraints excluded: chain H residue 1150 VAL Chi-restraints excluded: chain H residue 1185 SER Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 293 TYR Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 711 VAL Chi-restraints excluded: chain I residue 727 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 1142 ASP Chi-restraints excluded: chain L residue 1194 VAL Chi-restraints excluded: chain L residue 1213 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 333 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 196 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 195 optimal weight: 0.7980 chunk 290 optimal weight: 9.9990 chunk 192 optimal weight: 6.9990 chunk 344 optimal weight: 9.9990 chunk 215 optimal weight: 9.9990 chunk 209 optimal weight: 0.0040 chunk 158 optimal weight: 5.9990 overall best weight: 3.3598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 772 GLN ** J 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN ** B1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 670 HIS D 105 GLN H1104 ASN H1201 ASN ** L1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 28662 Z= 0.267 Angle : 0.641 14.499 38943 Z= 0.334 Chirality : 0.043 0.280 4299 Planarity : 0.005 0.053 5070 Dihedral : 5.000 22.821 3939 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.59 % Favored : 93.16 % Rotamer: Outliers : 3.25 % Allowed : 13.37 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.14), residues: 3582 helix: 2.46 (0.20), residues: 639 sheet: 0.09 (0.16), residues: 996 loop : -0.73 (0.14), residues: 1947 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 47 HIS 0.004 0.001 HIS K 41 PHE 0.018 0.001 PHE I 254 TYR 0.017 0.001 TYR C 314 ARG 0.004 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 237 time to evaluate : 3.374 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 41 ASP cc_start: 0.8097 (t0) cc_final: 0.7353 (m-30) REVERT: A 270 TYR cc_start: 0.8083 (OUTLIER) cc_final: 0.7786 (m-80) REVERT: A 602 ASN cc_start: 0.8567 (t0) cc_final: 0.7927 (m-40) REVERT: B 944 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7545 (pt0) REVERT: B 1005 LEU cc_start: 0.9338 (OUTLIER) cc_final: 0.9113 (mt) REVERT: B 1031 GLN cc_start: 0.8955 (OUTLIER) cc_final: 0.8638 (tt0) REVERT: C 41 ASP cc_start: 0.7974 (t0) cc_final: 0.7128 (m-30) REVERT: C 148 MET cc_start: 0.9042 (ttt) cc_final: 0.8583 (tmm) REVERT: C 602 ASN cc_start: 0.8636 (t0) cc_final: 0.7986 (m-40) REVERT: C 696 MET cc_start: 0.4942 (ptp) cc_final: 0.4740 (ptm) REVERT: D 43 LYS cc_start: 0.8924 (mmmt) cc_final: 0.8634 (mmtm) REVERT: E 1197 ASP cc_start: 0.7598 (t0) cc_final: 0.7242 (t0) REVERT: E 1201 MET cc_start: 0.8199 (mmm) cc_final: 0.6648 (mmm) REVERT: E 1209 GLU cc_start: 0.8907 (pt0) cc_final: 0.8622 (pm20) REVERT: H 939 MET cc_start: 0.8677 (tpt) cc_final: 0.8339 (tpt) REVERT: H 1104 ASN cc_start: 0.9115 (OUTLIER) cc_final: 0.8818 (t0) REVERT: I 41 ASP cc_start: 0.8035 (t0) cc_final: 0.7374 (m-30) REVERT: I 602 ASN cc_start: 0.8499 (t0) cc_final: 0.8052 (t0) REVERT: I 696 MET cc_start: 0.5163 (ttm) cc_final: 0.4620 (ptp) REVERT: K 73 LYS cc_start: 0.8621 (mttt) cc_final: 0.8015 (tmtt) REVERT: K 82 LEU cc_start: 0.8273 (pt) cc_final: 0.7955 (tp) REVERT: L 1209 GLU cc_start: 0.8936 (pt0) cc_final: 0.8480 (pm20) outliers start: 100 outliers final: 80 residues processed: 316 average time/residue: 0.3599 time to fit residues: 189.7967 Evaluate side-chains 303 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 219 time to evaluate : 3.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 817 CYS Chi-restraints excluded: chain J residue 843 ASP Chi-restraints excluded: chain J residue 845 SER Chi-restraints excluded: chain J residue 857 GLN Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 1005 LEU Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1127 VAL Chi-restraints excluded: chain J residue 1132 ASN Chi-restraints excluded: chain J residue 1145 ASN Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1201 ASN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 1204 CYS Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 857 GLN Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1031 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1185 SER Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain H residue 817 CYS Chi-restraints excluded: chain H residue 843 ASP Chi-restraints excluded: chain H residue 845 SER Chi-restraints excluded: chain H residue 857 GLN Chi-restraints excluded: chain H residue 862 ILE Chi-restraints excluded: chain H residue 935 LEU Chi-restraints excluded: chain H residue 986 THR Chi-restraints excluded: chain H residue 1005 LEU Chi-restraints excluded: chain H residue 1031 GLN Chi-restraints excluded: chain H residue 1054 ILE Chi-restraints excluded: chain H residue 1104 ASN Chi-restraints excluded: chain H residue 1127 VAL Chi-restraints excluded: chain H residue 1132 ASN Chi-restraints excluded: chain H residue 1150 VAL Chi-restraints excluded: chain H residue 1185 SER Chi-restraints excluded: chain H residue 1201 ASN Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 293 TYR Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 711 VAL Chi-restraints excluded: chain I residue 727 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 1190 ASN Chi-restraints excluded: chain L residue 1213 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 212 optimal weight: 6.9990 chunk 137 optimal weight: 9.9990 chunk 205 optimal weight: 8.9990 chunk 103 optimal weight: 7.9990 chunk 67 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 218 optimal weight: 20.0000 chunk 234 optimal weight: 20.0000 chunk 170 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 overall best weight: 4.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1201 ASN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN ** B1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN D 105 GLN I 261 GLN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.5104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 28662 Z= 0.358 Angle : 0.689 14.020 38943 Z= 0.359 Chirality : 0.044 0.264 4299 Planarity : 0.005 0.052 5070 Dihedral : 5.148 22.011 3939 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.01 % Favored : 92.71 % Rotamer: Outliers : 3.64 % Allowed : 13.43 % Favored : 82.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3582 helix: 2.11 (0.20), residues: 654 sheet: -0.01 (0.16), residues: 972 loop : -0.79 (0.14), residues: 1956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP F 47 HIS 0.006 0.001 HIS K 41 PHE 0.019 0.002 PHE A 313 TYR 0.031 0.002 TYR A 689 ARG 0.004 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 221 time to evaluate : 3.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 757 MET cc_start: 0.7421 (mmm) cc_final: 0.7008 (mmp) REVERT: A 41 ASP cc_start: 0.8024 (t0) cc_final: 0.7276 (m-30) REVERT: A 270 TYR cc_start: 0.8111 (OUTLIER) cc_final: 0.7807 (m-80) REVERT: A 602 ASN cc_start: 0.8585 (t0) cc_final: 0.7961 (m-40) REVERT: F 13 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.6278 (tpt170) REVERT: F 43 LYS cc_start: 0.9175 (mmtp) cc_final: 0.8723 (mmmt) REVERT: G 1201 MET cc_start: 0.8666 (mmm) cc_final: 0.8326 (tpp) REVERT: G 1209 GLU cc_start: 0.9056 (pt0) cc_final: 0.8631 (pm20) REVERT: B 1005 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9132 (mt) REVERT: B 1031 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8641 (tt0) REVERT: C 41 ASP cc_start: 0.8008 (t0) cc_final: 0.7142 (m-30) REVERT: C 148 MET cc_start: 0.9052 (ttt) cc_final: 0.8598 (tmm) REVERT: C 602 ASN cc_start: 0.8699 (t0) cc_final: 0.8080 (m-40) REVERT: D 43 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8701 (mmtm) REVERT: E 1201 MET cc_start: 0.8242 (mmm) cc_final: 0.6734 (mmm) REVERT: E 1209 GLU cc_start: 0.8967 (pt0) cc_final: 0.8631 (pm20) REVERT: I 41 ASP cc_start: 0.8053 (t0) cc_final: 0.7364 (m-30) REVERT: I 148 MET cc_start: 0.8583 (ttp) cc_final: 0.8353 (ttt) REVERT: I 306 ASP cc_start: 0.6768 (OUTLIER) cc_final: 0.6542 (t0) REVERT: I 602 ASN cc_start: 0.8523 (t0) cc_final: 0.8126 (t0) REVERT: I 696 MET cc_start: 0.5335 (ttm) cc_final: 0.4771 (ptp) REVERT: K 73 LYS cc_start: 0.8650 (mttt) cc_final: 0.8065 (tmtt) REVERT: L 1209 GLU cc_start: 0.9006 (pt0) cc_final: 0.8419 (pm20) outliers start: 112 outliers final: 91 residues processed: 314 average time/residue: 0.3762 time to fit residues: 196.9587 Evaluate side-chains 309 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 213 time to evaluate : 3.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 817 CYS Chi-restraints excluded: chain J residue 843 ASP Chi-restraints excluded: chain J residue 845 SER Chi-restraints excluded: chain J residue 857 GLN Chi-restraints excluded: chain J residue 862 ILE Chi-restraints excluded: chain J residue 900 ILE Chi-restraints excluded: chain J residue 986 THR Chi-restraints excluded: chain J residue 1005 LEU Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1127 VAL Chi-restraints excluded: chain J residue 1132 ASN Chi-restraints excluded: chain J residue 1145 ASN Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1201 ASN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 711 VAL Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 1165 SER Chi-restraints excluded: chain G residue 1204 CYS Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 857 GLN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1005 LEU Chi-restraints excluded: chain B residue 1031 GLN Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1185 SER Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain C residue 313 PHE Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain H residue 817 CYS Chi-restraints excluded: chain H residue 843 ASP Chi-restraints excluded: chain H residue 845 SER Chi-restraints excluded: chain H residue 857 GLN Chi-restraints excluded: chain H residue 862 ILE Chi-restraints excluded: chain H residue 932 TYR Chi-restraints excluded: chain H residue 935 LEU Chi-restraints excluded: chain H residue 986 THR Chi-restraints excluded: chain H residue 1005 LEU Chi-restraints excluded: chain H residue 1031 GLN Chi-restraints excluded: chain H residue 1054 ILE Chi-restraints excluded: chain H residue 1127 VAL Chi-restraints excluded: chain H residue 1145 ASN Chi-restraints excluded: chain H residue 1150 VAL Chi-restraints excluded: chain H residue 1185 SER Chi-restraints excluded: chain H residue 1201 ASN Chi-restraints excluded: chain I residue 44 TRP Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 170 VAL Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 293 TYR Chi-restraints excluded: chain I residue 306 ASP Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 711 VAL Chi-restraints excluded: chain I residue 727 CYS Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 MET Chi-restraints excluded: chain L residue 1213 THR Chi-restraints excluded: chain L residue 1220 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 313 optimal weight: 7.9990 chunk 329 optimal weight: 9.9990 chunk 300 optimal weight: 9.9990 chunk 320 optimal weight: 0.0020 chunk 192 optimal weight: 9.9990 chunk 139 optimal weight: 3.9990 chunk 251 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 289 optimal weight: 4.9990 chunk 303 optimal weight: 6.9990 chunk 319 optimal weight: 10.0000 overall best weight: 3.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN ** B1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN H1201 ASN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L1153 GLN ** L1158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.5213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 28662 Z= 0.267 Angle : 0.655 13.282 38943 Z= 0.339 Chirality : 0.043 0.255 4299 Planarity : 0.005 0.053 5070 Dihedral : 5.053 22.986 3939 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.28 % Allowed : 6.62 % Favored : 93.10 % Rotamer: Outliers : 3.28 % Allowed : 13.85 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.14), residues: 3582 helix: 2.11 (0.20), residues: 669 sheet: -0.05 (0.16), residues: 939 loop : -0.79 (0.14), residues: 1974 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP F 47 HIS 0.004 0.001 HIS K 41 PHE 0.018 0.001 PHE A 313 TYR 0.022 0.001 TYR I 314 ARG 0.005 0.000 ARG A 694 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 228 time to evaluate : 3.196 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: J 757 MET cc_start: 0.7440 (mmm) cc_final: 0.7161 (mmp) REVERT: A 41 ASP cc_start: 0.8001 (t0) cc_final: 0.7263 (m-30) REVERT: A 270 TYR cc_start: 0.8107 (OUTLIER) cc_final: 0.7800 (m-80) REVERT: A 602 ASN cc_start: 0.8564 (t0) cc_final: 0.7942 (m-40) REVERT: A 648 TYR cc_start: 0.7796 (t80) cc_final: 0.7431 (t80) REVERT: F 13 ARG cc_start: 0.7924 (OUTLIER) cc_final: 0.6270 (tpt170) REVERT: F 43 LYS cc_start: 0.9172 (mmtp) cc_final: 0.8808 (mmtm) REVERT: G 1201 MET cc_start: 0.8597 (mmm) cc_final: 0.7116 (tmm) REVERT: G 1206 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8292 (pp30) REVERT: G 1209 GLU cc_start: 0.9082 (pt0) cc_final: 0.8492 (pm20) REVERT: B 1031 GLN cc_start: 0.8968 (OUTLIER) cc_final: 0.8641 (tt0) REVERT: C 41 ASP cc_start: 0.7989 (t0) cc_final: 0.7131 (m-30) REVERT: C 148 MET cc_start: 0.9032 (ttt) cc_final: 0.8584 (tmm) REVERT: C 278 MET cc_start: 0.8648 (mmp) cc_final: 0.8321 (mmm) REVERT: C 602 ASN cc_start: 0.8684 (t0) cc_final: 0.8089 (m-40) REVERT: D 43 LYS cc_start: 0.8977 (mmmt) cc_final: 0.8736 (mmtm) REVERT: E 1201 MET cc_start: 0.8231 (mmm) cc_final: 0.7849 (tpp) REVERT: E 1209 GLU cc_start: 0.8968 (pt0) cc_final: 0.8656 (pm20) REVERT: I 41 ASP cc_start: 0.8024 (t0) cc_final: 0.7357 (m-30) REVERT: I 148 MET cc_start: 0.8550 (ttp) cc_final: 0.8332 (ttt) REVERT: I 602 ASN cc_start: 0.8543 (t0) cc_final: 0.8158 (t0) REVERT: I 696 MET cc_start: 0.5191 (ttm) cc_final: 0.4680 (ptp) REVERT: K 13 ARG cc_start: 0.7969 (OUTLIER) cc_final: 0.6399 (tpt170) REVERT: K 73 LYS cc_start: 0.8656 (mttt) cc_final: 0.8087 (tmtt) REVERT: L 1209 GLU cc_start: 0.8944 (pt0) cc_final: 0.8472 (pm20) outliers start: 101 outliers final: 88 residues processed: 311 average time/residue: 0.3470 time to fit residues: 180.7997 Evaluate side-chains 307 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 214 time to evaluate : 3.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 817 CYS Chi-restraints excluded: chain J residue 843 ASP Chi-restraints excluded: chain J residue 845 SER Chi-restraints excluded: chain J residue 857 GLN Chi-restraints excluded: chain J residue 862 ILE Chi-restraints excluded: chain J residue 986 THR Chi-restraints excluded: chain J residue 1005 LEU Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1127 VAL Chi-restraints excluded: chain J residue 1145 ASN Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1201 ASN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 1165 SER Chi-restraints excluded: chain G residue 1204 CYS Chi-restraints excluded: chain G residue 1206 GLN Chi-restraints excluded: chain G residue 1213 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 857 GLN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1031 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1185 SER Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain D residue 105 GLN Chi-restraints excluded: chain E residue 1133 ILE Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain H residue 817 CYS Chi-restraints excluded: chain H residue 843 ASP Chi-restraints excluded: chain H residue 845 SER Chi-restraints excluded: chain H residue 857 GLN Chi-restraints excluded: chain H residue 862 ILE Chi-restraints excluded: chain H residue 935 LEU Chi-restraints excluded: chain H residue 986 THR Chi-restraints excluded: chain H residue 1005 LEU Chi-restraints excluded: chain H residue 1031 GLN Chi-restraints excluded: chain H residue 1054 ILE Chi-restraints excluded: chain H residue 1127 VAL Chi-restraints excluded: chain H residue 1145 ASN Chi-restraints excluded: chain H residue 1150 VAL Chi-restraints excluded: chain H residue 1185 SER Chi-restraints excluded: chain H residue 1201 ASN Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 293 TYR Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 711 VAL Chi-restraints excluded: chain I residue 727 CYS Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 210 optimal weight: 9.9990 chunk 339 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 160 optimal weight: 2.9990 chunk 235 optimal weight: 3.9990 chunk 355 optimal weight: 0.3980 chunk 327 optimal weight: 10.0000 chunk 283 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 218 optimal weight: 20.0000 chunk 173 optimal weight: 20.0000 overall best weight: 2.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1201 ASN F 58 ASN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN ** B1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 39 GLN L1154 GLN ** L1158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.5301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 28662 Z= 0.229 Angle : 0.642 12.513 38943 Z= 0.331 Chirality : 0.043 0.252 4299 Planarity : 0.005 0.050 5070 Dihedral : 4.942 22.842 3939 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.76 % Favored : 92.94 % Rotamer: Outliers : 2.80 % Allowed : 14.44 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.14), residues: 3582 helix: 2.22 (0.20), residues: 669 sheet: 0.10 (0.16), residues: 984 loop : -0.90 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP D 47 HIS 0.004 0.001 HIS K 41 PHE 0.018 0.001 PHE I 313 TYR 0.032 0.001 TYR A 689 ARG 0.004 0.000 ARG A 694 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7164 Ramachandran restraints generated. 3582 Oldfield, 0 Emsley, 3582 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 229 time to evaluate : 3.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 757 MET cc_start: 0.7446 (mmm) cc_final: 0.7191 (mmp) REVERT: J 1035 LYS cc_start: 0.9152 (tptp) cc_final: 0.8790 (tppt) REVERT: A 41 ASP cc_start: 0.7976 (t0) cc_final: 0.7223 (m-30) REVERT: A 148 MET cc_start: 0.8496 (ttp) cc_final: 0.8148 (ttt) REVERT: A 270 TYR cc_start: 0.8094 (OUTLIER) cc_final: 0.7794 (m-80) REVERT: A 602 ASN cc_start: 0.8535 (t0) cc_final: 0.7902 (m-40) REVERT: A 648 TYR cc_start: 0.7757 (t80) cc_final: 0.7390 (t80) REVERT: F 13 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.6317 (tpt170) REVERT: F 43 LYS cc_start: 0.9232 (mmtp) cc_final: 0.8831 (mmtm) REVERT: G 1209 GLU cc_start: 0.9083 (pt0) cc_final: 0.8683 (pm20) REVERT: B 1031 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8612 (tt0) REVERT: C 41 ASP cc_start: 0.7967 (t0) cc_final: 0.7128 (m-30) REVERT: C 148 MET cc_start: 0.9028 (ttt) cc_final: 0.8613 (tmm) REVERT: C 278 MET cc_start: 0.8583 (mmp) cc_final: 0.8292 (mmm) REVERT: C 602 ASN cc_start: 0.8670 (t0) cc_final: 0.8075 (m-40) REVERT: D 43 LYS cc_start: 0.8980 (mmmt) cc_final: 0.8628 (mmtm) REVERT: E 1201 MET cc_start: 0.8263 (mmm) cc_final: 0.6844 (mmm) REVERT: E 1209 GLU cc_start: 0.8960 (pt0) cc_final: 0.8712 (pm20) REVERT: I 41 ASP cc_start: 0.7976 (t0) cc_final: 0.7288 (m-30) REVERT: I 148 MET cc_start: 0.8591 (ttp) cc_final: 0.8354 (ttt) REVERT: I 602 ASN cc_start: 0.8528 (t0) cc_final: 0.8155 (t0) REVERT: I 696 MET cc_start: 0.5083 (ttm) cc_final: 0.4559 (ptp) REVERT: K 13 ARG cc_start: 0.7987 (OUTLIER) cc_final: 0.6375 (tpt170) REVERT: K 73 LYS cc_start: 0.8665 (mttt) cc_final: 0.8121 (tmtt) REVERT: L 1201 MET cc_start: 0.8102 (tpt) cc_final: 0.7769 (tpt) REVERT: L 1209 GLU cc_start: 0.8991 (pt0) cc_final: 0.8542 (pm20) outliers start: 86 outliers final: 79 residues processed: 298 average time/residue: 0.3492 time to fit residues: 174.2840 Evaluate side-chains 300 residues out of total 3075 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 217 time to evaluate : 3.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 817 CYS Chi-restraints excluded: chain J residue 843 ASP Chi-restraints excluded: chain J residue 845 SER Chi-restraints excluded: chain J residue 862 ILE Chi-restraints excluded: chain J residue 986 THR Chi-restraints excluded: chain J residue 1005 LEU Chi-restraints excluded: chain J residue 1031 GLN Chi-restraints excluded: chain J residue 1127 VAL Chi-restraints excluded: chain J residue 1145 ASN Chi-restraints excluded: chain J residue 1185 SER Chi-restraints excluded: chain J residue 1201 ASN Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 270 TYR Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 288 ASP Chi-restraints excluded: chain A residue 293 TYR Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 343 ASP Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 724 VAL Chi-restraints excluded: chain A residue 727 CYS Chi-restraints excluded: chain F residue 13 ARG Chi-restraints excluded: chain F residue 82 ARG Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain G residue 1165 SER Chi-restraints excluded: chain G residue 1204 CYS Chi-restraints excluded: chain G residue 1213 THR Chi-restraints excluded: chain B residue 780 LEU Chi-restraints excluded: chain B residue 817 CYS Chi-restraints excluded: chain B residue 843 ASP Chi-restraints excluded: chain B residue 845 SER Chi-restraints excluded: chain B residue 857 GLN Chi-restraints excluded: chain B residue 862 ILE Chi-restraints excluded: chain B residue 935 LEU Chi-restraints excluded: chain B residue 986 THR Chi-restraints excluded: chain B residue 1031 GLN Chi-restraints excluded: chain B residue 1062 GLU Chi-restraints excluded: chain B residue 1086 LEU Chi-restraints excluded: chain B residue 1132 ASN Chi-restraints excluded: chain B residue 1145 ASN Chi-restraints excluded: chain B residue 1185 SER Chi-restraints excluded: chain B residue 1189 SER Chi-restraints excluded: chain B residue 1201 ASN Chi-restraints excluded: chain C residue 136 THR Chi-restraints excluded: chain C residue 240 MET Chi-restraints excluded: chain C residue 288 ASP Chi-restraints excluded: chain C residue 293 TYR Chi-restraints excluded: chain C residue 343 ASP Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 639 VAL Chi-restraints excluded: chain C residue 666 GLU Chi-restraints excluded: chain C residue 724 VAL Chi-restraints excluded: chain C residue 727 CYS Chi-restraints excluded: chain D residue 82 LEU Chi-restraints excluded: chain D residue 89 ILE Chi-restraints excluded: chain D residue 100 ASP Chi-restraints excluded: chain E residue 1213 THR Chi-restraints excluded: chain H residue 817 CYS Chi-restraints excluded: chain H residue 843 ASP Chi-restraints excluded: chain H residue 845 SER Chi-restraints excluded: chain H residue 935 LEU Chi-restraints excluded: chain H residue 1005 LEU Chi-restraints excluded: chain H residue 1031 GLN Chi-restraints excluded: chain H residue 1127 VAL Chi-restraints excluded: chain H residue 1145 ASN Chi-restraints excluded: chain H residue 1150 VAL Chi-restraints excluded: chain H residue 1185 SER Chi-restraints excluded: chain H residue 1201 ASN Chi-restraints excluded: chain I residue 56 ILE Chi-restraints excluded: chain I residue 136 THR Chi-restraints excluded: chain I residue 273 LEU Chi-restraints excluded: chain I residue 288 ASP Chi-restraints excluded: chain I residue 293 TYR Chi-restraints excluded: chain I residue 350 SER Chi-restraints excluded: chain I residue 362 SER Chi-restraints excluded: chain I residue 655 VAL Chi-restraints excluded: chain I residue 711 VAL Chi-restraints excluded: chain I residue 727 CYS Chi-restraints excluded: chain K residue 13 ARG Chi-restraints excluded: chain K residue 100 ASP Chi-restraints excluded: chain K residue 100 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 357 random chunks: chunk 224 optimal weight: 6.9990 chunk 301 optimal weight: 8.9990 chunk 86 optimal weight: 0.4980 chunk 261 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 283 optimal weight: 4.9990 chunk 118 optimal weight: 5.9990 chunk 291 optimal weight: 40.0000 chunk 35 optimal weight: 0.0170 chunk 52 optimal weight: 10.0000 overall best weight: 2.3024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J1201 ASN ** B 927 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1201 ASN ** B1208 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 105 GLN H1201 ASN ** K 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L1158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.086539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.062740 restraints weight = 93901.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.064697 restraints weight = 53958.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.065983 restraints weight = 38067.820| |-----------------------------------------------------------------------------| r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8272 moved from start: 0.5394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 28662 Z= 0.210 Angle : 0.637 11.736 38943 Z= 0.326 Chirality : 0.042 0.247 4299 Planarity : 0.005 0.051 5070 Dihedral : 4.833 22.303 3939 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.31 % Allowed : 6.45 % Favored : 93.24 % Rotamer: Outliers : 2.89 % Allowed : 14.50 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.14), residues: 3582 helix: 2.29 (0.20), residues: 669 sheet: 0.15 (0.16), residues: 984 loop : -0.89 (0.14), residues: 1929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP D 47 HIS 0.004 0.001 HIS K 41 PHE 0.017 0.001 PHE A 239 TYR 0.019 0.001 TYR I 314 ARG 0.004 0.000 ARG C 301 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5202.85 seconds wall clock time: 96 minutes 31.63 seconds (5791.63 seconds total)