Starting phenix.real_space_refine on Tue Apr 9 10:41:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd8_17605/04_2024/8pd8_17605_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd8_17605/04_2024/8pd8_17605.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd8_17605/04_2024/8pd8_17605.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd8_17605/04_2024/8pd8_17605.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd8_17605/04_2024/8pd8_17605_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pd8_17605/04_2024/8pd8_17605_updated.pdb" } resolution = 3.3 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= 0.001 sd= 0.024 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 82 5.16 5 C 10520 2.51 5 N 2678 2.21 5 O 2840 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 128": "NH1" <-> "NH2" Residue "A ARG 161": "NH1" <-> "NH2" Residue "A ARG 351": "NH1" <-> "NH2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 420": "NH1" <-> "NH2" Residue "A ARG 431": "NH1" <-> "NH2" Residue "A ARG 479": "NH1" <-> "NH2" Residue "A ARG 491": "NH1" <-> "NH2" Residue "A ARG 499": "NH1" <-> "NH2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A ARG 507": "NH1" <-> "NH2" Residue "A ARG 516": "NH1" <-> "NH2" Residue "A ARG 573": "NH1" <-> "NH2" Residue "A ARG 583": "NH1" <-> "NH2" Residue "A ARG 585": "NH1" <-> "NH2" Residue "A ARG 605": "NH1" <-> "NH2" Residue "A ARG 609": "NH1" <-> "NH2" Residue "A PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 646": "NH1" <-> "NH2" Residue "A ARG 733": "NH1" <-> "NH2" Residue "A ARG 756": "NH1" <-> "NH2" Residue "A ARG 803": "NH1" <-> "NH2" Residue "A ARG 806": "NH1" <-> "NH2" Residue "A ARG 809": "NH1" <-> "NH2" Residue "A ARG 812": "NH1" <-> "NH2" Residue "A ARG 856": "NH1" <-> "NH2" Residue "A ARG 865": "NH1" <-> "NH2" Residue "A ARG 875": "NH1" <-> "NH2" Residue "A ARG 887": "NH1" <-> "NH2" Residue "A ARG 899": "NH1" <-> "NH2" Residue "A ARG 903": "NH1" <-> "NH2" Residue "A ARG 910": "NH1" <-> "NH2" Residue "A ARG 940": "NH1" <-> "NH2" Residue "A ARG 976": "NH1" <-> "NH2" Residue "A ARG 990": "NH1" <-> "NH2" Residue "A ARG 1053": "NH1" <-> "NH2" Residue "A ARG 1089": "NH1" <-> "NH2" Residue "A ARG 1092": "NH1" <-> "NH2" Residue "A ARG 1097": "NH1" <-> "NH2" Residue "A ARG 1123": "NH1" <-> "NH2" Residue "A ARG 1158": "NH1" <-> "NH2" Residue "A ARG 1162": "NH1" <-> "NH2" Residue "A ARG 1169": "NH1" <-> "NH2" Residue "A ARG 1185": "NH1" <-> "NH2" Residue "A ARG 1190": "NH1" <-> "NH2" Residue "B ARG 92": "NH1" <-> "NH2" Residue "B ARG 128": "NH1" <-> "NH2" Residue "B ARG 161": "NH1" <-> "NH2" Residue "B ARG 351": "NH1" <-> "NH2" Residue "B ARG 399": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 420": "NH1" <-> "NH2" Residue "B ARG 431": "NH1" <-> "NH2" Residue "B ARG 479": "NH1" <-> "NH2" Residue "B ARG 491": "NH1" <-> "NH2" Residue "B ARG 499": "NH1" <-> "NH2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B ARG 507": "NH1" <-> "NH2" Residue "B ARG 516": "NH1" <-> "NH2" Residue "B ARG 573": "NH1" <-> "NH2" Residue "B ARG 583": "NH1" <-> "NH2" Residue "B ARG 585": "NH1" <-> "NH2" Residue "B ARG 605": "NH1" <-> "NH2" Residue "B ARG 609": "NH1" <-> "NH2" Residue "B PHE 625": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 646": "NH1" <-> "NH2" Residue "B ARG 733": "NH1" <-> "NH2" Residue "B ARG 756": "NH1" <-> "NH2" Residue "B ARG 803": "NH1" <-> "NH2" Residue "B ARG 806": "NH1" <-> "NH2" Residue "B ARG 809": "NH1" <-> "NH2" Residue "B ARG 812": "NH1" <-> "NH2" Residue "B ARG 856": "NH1" <-> "NH2" Residue "B ARG 865": "NH1" <-> "NH2" Residue "B ARG 875": "NH1" <-> "NH2" Residue "B ARG 887": "NH1" <-> "NH2" Residue "B ARG 899": "NH1" <-> "NH2" Residue "B ARG 903": "NH1" <-> "NH2" Residue "B ARG 910": "NH1" <-> "NH2" Residue "B ARG 940": "NH1" <-> "NH2" Residue "B ARG 976": "NH1" <-> "NH2" Residue "B ARG 990": "NH1" <-> "NH2" Residue "B ARG 1053": "NH1" <-> "NH2" Residue "B ARG 1089": "NH1" <-> "NH2" Residue "B ARG 1092": "NH1" <-> "NH2" Residue "B ARG 1097": "NH1" <-> "NH2" Residue "B ARG 1123": "NH1" <-> "NH2" Residue "B ARG 1158": "NH1" <-> "NH2" Residue "B ARG 1162": "NH1" <-> "NH2" Residue "B ARG 1169": "NH1" <-> "NH2" Residue "B ARG 1185": "NH1" <-> "NH2" Residue "B ARG 1190": "NH1" <-> "NH2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16122 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 8039 Classifications: {'peptide': 1018} Link IDs: {'PTRANS': 29, 'TRANS': 988} Chain breaks: 5 Chain: "B" Number of atoms: 8039 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1018, 8039 Classifications: {'peptide': 1018} Link IDs: {'PTRANS': 29, 'TRANS': 988} Chain breaks: 5 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 8.71, per 1000 atoms: 0.54 Number of scatterers: 16122 At special positions: 0 Unit cell: (115.486, 158.41, 126.728, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 2 15.00 O 2840 8.00 N 2678 7.00 C 10520 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.85 Conformation dependent library (CDL) restraints added in 2.6 seconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3840 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 80 helices and 8 sheets defined 71.1% alpha, 3.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.82 Creating SS restraints... Processing helix chain 'A' and resid 73 through 96 removed outlier: 3.999A pdb=" N LYS A 96 " --> pdb=" O ARG A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 119 Processing helix chain 'A' and resid 121 through 131 removed outlier: 4.077A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 142 through 152 Processing helix chain 'A' and resid 156 through 161 Processing helix chain 'A' and resid 163 through 187 removed outlier: 3.925A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 205 Processing helix chain 'A' and resid 210 through 220 removed outlier: 3.923A pdb=" N VAL A 214 " --> pdb=" O VAL A 211 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 215 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU A 220 " --> pdb=" O LEU A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 253 Processing helix chain 'A' and resid 261 through 272 Processing helix chain 'A' and resid 274 through 292 removed outlier: 3.769A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 316 removed outlier: 3.689A pdb=" N TYR A 312 " --> pdb=" O THR A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 336 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 343 through 374 Processing helix chain 'A' and resid 377 through 379 No H-bonds generated for 'chain 'A' and resid 377 through 379' Processing helix chain 'A' and resid 382 through 412 removed outlier: 3.918A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) Proline residue: A 408 - end of helix removed outlier: 4.496A pdb=" N ARG A 412 " --> pdb=" O PRO A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 433 through 446 Processing helix chain 'A' and resid 450 through 480 removed outlier: 3.991A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 514 Processing helix chain 'A' and resid 523 through 530 removed outlier: 3.706A pdb=" N ALA A 528 " --> pdb=" O ASP A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 572 through 600 removed outlier: 3.571A pdb=" N HIS A 600 " --> pdb=" O LYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 620 Processing helix chain 'A' and resid 628 through 635 removed outlier: 3.646A pdb=" N LYS A 633 " --> pdb=" O ASP A 629 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N SER A 634 " --> pdb=" O ASP A 630 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP A 635 " --> pdb=" O LEU A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 652 Processing helix chain 'A' and resid 678 through 704 removed outlier: 4.050A pdb=" N VAL A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 689 " --> pdb=" O ASN A 685 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL A 693 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Proline residue: A 694 - end of helix Processing helix chain 'A' and resid 726 through 760 removed outlier: 3.720A pdb=" N ASP A 730 " --> pdb=" O GLN A 726 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA A 744 " --> pdb=" O PHE A 740 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N ILE A 745 " --> pdb=" O VAL A 741 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU A 746 " --> pdb=" O ILE A 742 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N VAL A 749 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N ARG A 756 " --> pdb=" O LEU A 752 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N HIS A 757 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ILE A 759 " --> pdb=" O GLY A 755 " (cutoff:3.500A) removed outlier: 5.481A pdb=" N VAL A 760 " --> pdb=" O ARG A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 782 removed outlier: 3.730A pdb=" N PHE A 766 " --> pdb=" O HIS A 762 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU A 771 " --> pdb=" O ASP A 767 " (cutoff:3.500A) removed outlier: 4.737A pdb=" N ALA A 781 " --> pdb=" O ASP A 777 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N GLU A 782 " --> pdb=" O ILE A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 795 through 856 removed outlier: 3.741A pdb=" N LYS A 800 " --> pdb=" O ILE A 796 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG A 803 " --> pdb=" O VAL A 799 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ARG A 806 " --> pdb=" O PHE A 802 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG A 809 " --> pdb=" O LEU A 805 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG A 812 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LEU A 813 " --> pdb=" O ARG A 809 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR A 814 " --> pdb=" O MET A 810 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS A 815 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ALA A 816 " --> pdb=" O ARG A 812 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 3.950A pdb=" N LYS A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP A 855 " --> pdb=" O GLY A 851 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG A 856 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 888 removed outlier: 4.258A pdb=" N GLN A 877 " --> pdb=" O THR A 873 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL A 878 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY A 883 " --> pdb=" O VAL A 879 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN A 886 " --> pdb=" O LEU A 882 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG A 887 " --> pdb=" O GLY A 883 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 918 removed outlier: 3.503A pdb=" N GLN A 900 " --> pdb=" O VAL A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 943 removed outlier: 3.642A pdb=" N THR A 933 " --> pdb=" O LYS A 929 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET A 942 " --> pdb=" O MET A 938 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN A 943 " --> pdb=" O LYS A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 953 through 959 Processing helix chain 'A' and resid 967 through 975 Processing helix chain 'A' and resid 1070 through 1079 removed outlier: 3.881A pdb=" N ILE A1075 " --> pdb=" O GLU A1071 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA A1076 " --> pdb=" O ASP A1072 " (cutoff:3.500A) Processing helix chain 'A' and resid 1086 through 1107 removed outlier: 3.698A pdb=" N ARG A1097 " --> pdb=" O VAL A1093 " (cutoff:3.500A) Proline residue: A1101 - end of helix removed outlier: 3.605A pdb=" N GLN A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1114 through 1123 removed outlier: 3.802A pdb=" N ARG A1123 " --> pdb=" O LEU A1119 " (cutoff:3.500A) Processing helix chain 'A' and resid 1180 through 1182 No H-bonds generated for 'chain 'A' and resid 1180 through 1182' Processing helix chain 'B' and resid 73 through 96 removed outlier: 3.998A pdb=" N LYS B 96 " --> pdb=" O ARG B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 102 through 119 Processing helix chain 'B' and resid 121 through 131 removed outlier: 4.077A pdb=" N HIS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 163 through 187 removed outlier: 3.925A pdb=" N VAL B 175 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 205 Processing helix chain 'B' and resid 210 through 220 removed outlier: 3.923A pdb=" N VAL B 214 " --> pdb=" O VAL B 211 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA B 215 " --> pdb=" O ALA B 212 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU B 220 " --> pdb=" O LEU B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 253 Processing helix chain 'B' and resid 261 through 272 Processing helix chain 'B' and resid 274 through 292 removed outlier: 3.769A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 316 removed outlier: 3.688A pdb=" N TYR B 312 " --> pdb=" O THR B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 323 through 336 Processing helix chain 'B' and resid 338 through 340 No H-bonds generated for 'chain 'B' and resid 338 through 340' Processing helix chain 'B' and resid 343 through 374 Processing helix chain 'B' and resid 377 through 379 No H-bonds generated for 'chain 'B' and resid 377 through 379' Processing helix chain 'B' and resid 382 through 412 removed outlier: 3.917A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) Proline residue: B 408 - end of helix removed outlier: 4.496A pdb=" N ARG B 412 " --> pdb=" O PRO B 408 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 433 through 446 Processing helix chain 'B' and resid 450 through 480 removed outlier: 3.991A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 514 Processing helix chain 'B' and resid 523 through 530 removed outlier: 3.706A pdb=" N ALA B 528 " --> pdb=" O ASP B 524 " (cutoff:3.500A) Processing helix chain 'B' and resid 572 through 600 removed outlier: 3.571A pdb=" N HIS B 600 " --> pdb=" O LYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 620 Processing helix chain 'B' and resid 628 through 635 removed outlier: 3.646A pdb=" N LYS B 633 " --> pdb=" O ASP B 629 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N SER B 634 " --> pdb=" O ASP B 630 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP B 635 " --> pdb=" O LEU B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 652 Processing helix chain 'B' and resid 678 through 704 removed outlier: 4.050A pdb=" N VAL B 682 " --> pdb=" O MET B 678 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL B 689 " --> pdb=" O ASN B 685 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL B 693 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Proline residue: B 694 - end of helix Processing helix chain 'B' and resid 726 through 760 removed outlier: 3.720A pdb=" N ASP B 730 " --> pdb=" O GLN B 726 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA B 744 " --> pdb=" O PHE B 740 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ILE B 745 " --> pdb=" O VAL B 741 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLU B 746 " --> pdb=" O ILE B 742 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N VAL B 749 " --> pdb=" O ILE B 745 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N ARG B 756 " --> pdb=" O LEU B 752 " (cutoff:3.500A) removed outlier: 8.047A pdb=" N HIS B 757 " --> pdb=" O GLY B 753 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N TYR B 758 " --> pdb=" O LEU B 754 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N ILE B 759 " --> pdb=" O GLY B 755 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N VAL B 760 " --> pdb=" O ARG B 756 " (cutoff:3.500A) Processing helix chain 'B' and resid 762 through 782 removed outlier: 3.730A pdb=" N PHE B 766 " --> pdb=" O HIS B 762 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 771 " --> pdb=" O ASP B 767 " (cutoff:3.500A) removed outlier: 4.738A pdb=" N ALA B 781 " --> pdb=" O ASP B 777 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLU B 782 " --> pdb=" O ILE B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 856 removed outlier: 3.741A pdb=" N LYS B 800 " --> pdb=" O ILE B 796 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ARG B 803 " --> pdb=" O VAL B 799 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG B 806 " --> pdb=" O PHE B 802 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ARG B 809 " --> pdb=" O LEU B 805 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ARG B 812 " --> pdb=" O LEU B 808 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N LEU B 813 " --> pdb=" O ARG B 809 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N THR B 814 " --> pdb=" O MET B 810 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N LYS B 815 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N ALA B 816 " --> pdb=" O ARG B 812 " (cutoff:3.500A) Proline residue: B 819 - end of helix removed outlier: 3.951A pdb=" N LYS B 852 " --> pdb=" O GLU B 848 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ASP B 855 " --> pdb=" O GLY B 851 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ARG B 856 " --> pdb=" O LYS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 863 through 888 removed outlier: 4.258A pdb=" N GLN B 877 " --> pdb=" O THR B 873 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N VAL B 878 " --> pdb=" O GLY B 874 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLY B 883 " --> pdb=" O VAL B 879 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN B 886 " --> pdb=" O LEU B 882 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ARG B 887 " --> pdb=" O GLY B 883 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 918 removed outlier: 3.503A pdb=" N GLN B 900 " --> pdb=" O VAL B 896 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 943 removed outlier: 3.642A pdb=" N THR B 933 " --> pdb=" O LYS B 929 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N MET B 942 " --> pdb=" O MET B 938 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN B 943 " --> pdb=" O LYS B 939 " (cutoff:3.500A) Processing helix chain 'B' and resid 953 through 959 Processing helix chain 'B' and resid 967 through 975 Processing helix chain 'B' and resid 1070 through 1079 removed outlier: 3.881A pdb=" N ILE B1075 " --> pdb=" O GLU B1071 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA B1076 " --> pdb=" O ASP B1072 " (cutoff:3.500A) Processing helix chain 'B' and resid 1086 through 1107 removed outlier: 3.698A pdb=" N ARG B1097 " --> pdb=" O VAL B1093 " (cutoff:3.500A) Proline residue: B1101 - end of helix removed outlier: 3.605A pdb=" N GLN B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1114 through 1123 removed outlier: 3.802A pdb=" N ARG B1123 " --> pdb=" O LEU B1119 " (cutoff:3.500A) Processing helix chain 'B' and resid 1180 through 1182 No H-bonds generated for 'chain 'B' and resid 1180 through 1182' Processing sheet with id= A, first strand: chain 'A' and resid 978 through 982 removed outlier: 6.155A pdb=" N TYR A1066 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE A1001 " --> pdb=" O TYR A1066 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE A1068 " --> pdb=" O PHE A 999 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N PHE A 999 " --> pdb=" O ILE A1068 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1034 through 1036 Processing sheet with id= C, first strand: chain 'A' and resid 1134 through 1136 Processing sheet with id= D, first strand: chain 'A' and resid 1144 through 1149 removed outlier: 3.625A pdb=" N ASP A1144 " --> pdb=" O VAL A1189 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG A1185 " --> pdb=" O ILE A1148 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 978 through 982 removed outlier: 6.154A pdb=" N TYR B1066 " --> pdb=" O ILE B1001 " (cutoff:3.500A) removed outlier: 5.326A pdb=" N ILE B1001 " --> pdb=" O TYR B1066 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE B1068 " --> pdb=" O PHE B 999 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N PHE B 999 " --> pdb=" O ILE B1068 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 1034 through 1036 Processing sheet with id= G, first strand: chain 'B' and resid 1134 through 1136 Processing sheet with id= H, first strand: chain 'B' and resid 1144 through 1149 removed outlier: 3.625A pdb=" N ASP B1144 " --> pdb=" O VAL B1189 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG B1185 " --> pdb=" O ILE B1148 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 3036 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: 5.25 Time building geometry restraints manager: 7.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4272 1.33 - 1.45: 2725 1.45 - 1.58: 9285 1.58 - 1.70: 4 1.70 - 1.82: 152 Bond restraints: 16438 Sorted by residual: bond pdb=" CZ ARG B 583 " pdb=" NH2 ARG B 583 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.56e+00 bond pdb=" CZ ARG A 583 " pdb=" NH2 ARG A 583 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.41e+00 bond pdb=" CZ ARG B 865 " pdb=" NH2 ARG B 865 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.30e-02 5.92e+03 5.66e+00 bond pdb=" CZ ARG A 865 " pdb=" NH2 ARG A 865 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.30e-02 5.92e+03 5.60e+00 bond pdb=" CZ ARG A 856 " pdb=" NH2 ARG A 856 " ideal model delta sigma weight residual 1.330 1.299 0.031 1.30e-02 5.92e+03 5.58e+00 ... (remaining 16433 not shown) Histogram of bond angle deviations from ideal: 97.48 - 105.14: 264 105.14 - 112.81: 9153 112.81 - 120.48: 7046 120.48 - 128.14: 5703 128.14 - 135.81: 138 Bond angle restraints: 22304 Sorted by residual: angle pdb=" CA LYS B 224 " pdb=" CB LYS B 224 " pdb=" CG LYS B 224 " ideal model delta sigma weight residual 114.10 123.66 -9.56 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA LYS A 224 " pdb=" CB LYS A 224 " pdb=" CG LYS A 224 " ideal model delta sigma weight residual 114.10 123.65 -9.55 2.00e+00 2.50e-01 2.28e+01 angle pdb=" CA ARG B 128 " pdb=" CB ARG B 128 " pdb=" CG ARG B 128 " ideal model delta sigma weight residual 114.10 123.06 -8.96 2.00e+00 2.50e-01 2.01e+01 angle pdb=" CA ARG A 128 " pdb=" CB ARG A 128 " pdb=" CG ARG A 128 " ideal model delta sigma weight residual 114.10 123.05 -8.95 2.00e+00 2.50e-01 2.00e+01 angle pdb=" CA ARG A 756 " pdb=" CB ARG A 756 " pdb=" CG ARG A 756 " ideal model delta sigma weight residual 114.10 122.94 -8.84 2.00e+00 2.50e-01 1.95e+01 ... (remaining 22299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.58: 9582 29.58 - 59.17: 194 59.17 - 88.75: 24 88.75 - 118.34: 0 118.34 - 147.92: 6 Dihedral angle restraints: 9806 sinusoidal: 3886 harmonic: 5920 Sorted by residual: dihedral pdb=" C5' CMP A1401 " pdb=" O5' CMP A1401 " pdb=" P CMP A1401 " pdb=" O1P CMP A1401 " ideal model delta sinusoidal sigma weight residual 60.00 -152.08 -147.92 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C5' CMP B1401 " pdb=" O5' CMP B1401 " pdb=" P CMP B1401 " pdb=" O1P CMP B1401 " ideal model delta sinusoidal sigma weight residual 60.00 -152.10 -147.90 1 2.00e+01 2.50e-03 4.43e+01 dihedral pdb=" C3' CMP B1401 " pdb=" O3' CMP B1401 " pdb=" P CMP B1401 " pdb=" O1P CMP B1401 " ideal model delta sinusoidal sigma weight residual 300.00 159.68 140.32 1 2.00e+01 2.50e-03 4.25e+01 ... (remaining 9803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1715 0.039 - 0.077: 710 0.077 - 0.116: 214 0.116 - 0.155: 34 0.155 - 0.193: 11 Chirality restraints: 2684 Sorted by residual: chirality pdb=" CA LYS B 861 " pdb=" N LYS B 861 " pdb=" C LYS B 861 " pdb=" CB LYS B 861 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.36e-01 chirality pdb=" CA LYS A 861 " pdb=" N LYS A 861 " pdb=" C LYS A 861 " pdb=" CB LYS A 861 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.17e-01 chirality pdb=" CA GLU B 616 " pdb=" N GLU B 616 " pdb=" C GLU B 616 " pdb=" CB GLU B 616 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 2681 not shown) Planarity restraints: 2738 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 843 " 0.023 2.00e-02 2.50e+03 1.91e-02 7.31e+00 pdb=" CG TYR A 843 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR A 843 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR A 843 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR A 843 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 843 " -0.020 2.00e-02 2.50e+03 pdb=" CZ TYR A 843 " -0.022 2.00e-02 2.50e+03 pdb=" OH TYR A 843 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 843 " 0.023 2.00e-02 2.50e+03 1.91e-02 7.27e+00 pdb=" CG TYR B 843 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 843 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 843 " 0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 843 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 843 " -0.019 2.00e-02 2.50e+03 pdb=" CZ TYR B 843 " -0.023 2.00e-02 2.50e+03 pdb=" OH TYR B 843 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS B 614 " 0.029 2.00e-02 2.50e+03 2.17e-02 7.07e+00 pdb=" CG HIS B 614 " -0.037 2.00e-02 2.50e+03 pdb=" ND1 HIS B 614 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 HIS B 614 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 HIS B 614 " 0.013 2.00e-02 2.50e+03 pdb=" NE2 HIS B 614 " 0.016 2.00e-02 2.50e+03 ... (remaining 2735 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2987 2.77 - 3.30: 16810 3.30 - 3.84: 26151 3.84 - 4.37: 30445 4.37 - 4.90: 52126 Nonbonded interactions: 128519 Sorted by model distance: nonbonded pdb=" O ASP A 534 " pdb=" OD1 ASP A 534 " model vdw 2.240 3.040 nonbonded pdb=" O ASP B 534 " pdb=" OD1 ASP B 534 " model vdw 2.240 3.040 nonbonded pdb=" OE2 GLU A 233 " pdb=" NH2 ARG A 399 " model vdw 2.339 2.520 nonbonded pdb=" OE2 GLU B 233 " pdb=" NH2 ARG B 399 " model vdw 2.340 2.520 nonbonded pdb=" O ILE B 81 " pdb=" OG SER B 84 " model vdw 2.344 2.440 ... (remaining 128514 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 1.420 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: 0.020 Extract box with map and model: 6.380 Check model and map are aligned: 0.210 Set scattering table: 0.150 Process input model: 44.320 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.090 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 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 : 0.005 0.044 16438 Z= 0.359 Angle : 0.845 10.292 22304 Z= 0.479 Chirality : 0.046 0.193 2684 Planarity : 0.005 0.050 2738 Dihedral : 13.011 147.921 5966 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.19), residues: 2012 helix: 0.82 (0.13), residues: 1416 sheet: -0.02 (0.52), residues: 82 loop : 0.04 (0.29), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP B 643 HIS 0.007 0.001 HIS A 928 PHE 0.021 0.002 PHE B 625 TYR 0.034 0.003 TYR B 984 ARG 0.011 0.001 ARG B1169 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 530 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 530 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6696 (mmm) cc_final: 0.6060 (mmm) REVERT: A 149 GLU cc_start: 0.7701 (tm-30) cc_final: 0.7391 (tm-30) REVERT: A 155 ASP cc_start: 0.7110 (t70) cc_final: 0.6670 (t70) REVERT: A 164 SER cc_start: 0.8254 (m) cc_final: 0.7699 (t) REVERT: A 209 ASP cc_start: 0.7641 (t0) cc_final: 0.7123 (t0) REVERT: A 300 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7810 (mt-10) REVERT: A 338 LYS cc_start: 0.7787 (mtmt) cc_final: 0.7558 (mtpt) REVERT: A 344 GLU cc_start: 0.7318 (mt-10) cc_final: 0.7028 (mt-10) REVERT: A 375 LYS cc_start: 0.8078 (mttt) cc_final: 0.7652 (mtpp) REVERT: A 380 VAL cc_start: 0.8634 (t) cc_final: 0.8309 (m) REVERT: A 383 MET cc_start: 0.6925 (mmp) cc_final: 0.6433 (mmm) REVERT: A 448 ASN cc_start: 0.8635 (m-40) cc_final: 0.8397 (m110) REVERT: A 485 ASP cc_start: 0.7960 (m-30) cc_final: 0.7646 (p0) REVERT: A 515 ASP cc_start: 0.7650 (t70) cc_final: 0.7340 (t70) REVERT: A 522 ASP cc_start: 0.7097 (t0) cc_final: 0.6579 (t0) REVERT: A 525 ILE cc_start: 0.7205 (mm) cc_final: 0.6839 (mt) REVERT: A 531 GLU cc_start: 0.7957 (tt0) cc_final: 0.7131 (tm-30) REVERT: A 534 ASP cc_start: 0.6889 (p0) cc_final: 0.6507 (p0) REVERT: A 578 MET cc_start: 0.6531 (mmm) cc_final: 0.6033 (mmm) REVERT: A 580 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7519 (tp30) REVERT: A 584 LEU cc_start: 0.8064 (mt) cc_final: 0.7686 (mt) REVERT: A 591 LYS cc_start: 0.8066 (mttp) cc_final: 0.7708 (mtpp) REVERT: A 613 GLN cc_start: 0.7978 (tt0) cc_final: 0.7640 (tm-30) REVERT: A 634 SER cc_start: 0.8462 (m) cc_final: 0.8104 (p) REVERT: A 635 TRP cc_start: 0.7405 (p90) cc_final: 0.7154 (p90) REVERT: A 645 LYS cc_start: 0.7595 (tttt) cc_final: 0.7265 (tttt) REVERT: A 828 LYS cc_start: 0.7315 (mmtt) cc_final: 0.7076 (mmtt) REVERT: A 857 MET cc_start: 0.7329 (ttm) cc_final: 0.6803 (ttm) REVERT: A 869 HIS cc_start: 0.6619 (t70) cc_final: 0.6414 (t-90) REVERT: A 887 ARG cc_start: 0.7249 (mmm-85) cc_final: 0.7019 (mmm-85) REVERT: A 958 LYS cc_start: 0.7961 (tttt) cc_final: 0.7655 (mttm) REVERT: A 991 GLU cc_start: 0.5641 (mt-10) cc_final: 0.5347 (mm-30) REVERT: A 998 LEU cc_start: 0.5553 (mp) cc_final: 0.5106 (mp) REVERT: A 1066 TYR cc_start: 0.6402 (m-80) cc_final: 0.6179 (m-10) REVERT: A 1068 ILE cc_start: 0.6230 (mp) cc_final: 0.5880 (pt) REVERT: B 133 MET cc_start: 0.6528 (mmm) cc_final: 0.5882 (mmm) REVERT: B 155 ASP cc_start: 0.7129 (t70) cc_final: 0.6690 (t70) REVERT: B 160 MET cc_start: 0.7427 (mmt) cc_final: 0.7127 (mmm) REVERT: B 164 SER cc_start: 0.8202 (m) cc_final: 0.7726 (t) REVERT: B 218 LYS cc_start: 0.7676 (mttt) cc_final: 0.7325 (mtpp) REVERT: B 268 PHE cc_start: 0.7618 (t80) cc_final: 0.7378 (t80) REVERT: B 300 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7672 (mt-10) REVERT: B 375 LYS cc_start: 0.8092 (mttt) cc_final: 0.7626 (mtpp) REVERT: B 380 VAL cc_start: 0.8592 (t) cc_final: 0.8276 (m) REVERT: B 383 MET cc_start: 0.7061 (mmp) cc_final: 0.6837 (mmm) REVERT: B 443 GLU cc_start: 0.7983 (tm-30) cc_final: 0.7756 (tm-30) REVERT: B 448 ASN cc_start: 0.8664 (m-40) cc_final: 0.8408 (m-40) REVERT: B 475 GLN cc_start: 0.7997 (tp40) cc_final: 0.7795 (mm-40) REVERT: B 479 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7355 (ttm-80) REVERT: B 485 ASP cc_start: 0.7982 (m-30) cc_final: 0.7661 (p0) REVERT: B 494 MET cc_start: 0.7417 (tpp) cc_final: 0.6959 (tpp) REVERT: B 500 ARG cc_start: 0.7453 (tpp80) cc_final: 0.7112 (tpp80) REVERT: B 515 ASP cc_start: 0.7519 (t70) cc_final: 0.7168 (t70) REVERT: B 522 ASP cc_start: 0.7252 (t0) cc_final: 0.6758 (t0) REVERT: B 525 ILE cc_start: 0.7189 (mm) cc_final: 0.6835 (mt) REVERT: B 534 ASP cc_start: 0.6730 (p0) cc_final: 0.6354 (p0) REVERT: B 578 MET cc_start: 0.6833 (mmm) cc_final: 0.6468 (mmm) REVERT: B 588 LYS cc_start: 0.7631 (ttmt) cc_final: 0.7385 (ttmt) REVERT: B 591 LYS cc_start: 0.8249 (mttp) cc_final: 0.8009 (mtpp) REVERT: B 606 GLU cc_start: 0.7423 (mp0) cc_final: 0.7221 (pm20) REVERT: B 610 LEU cc_start: 0.8041 (mp) cc_final: 0.7784 (mt) REVERT: B 613 GLN cc_start: 0.7807 (tt0) cc_final: 0.7519 (tm-30) REVERT: B 634 SER cc_start: 0.8672 (m) cc_final: 0.8005 (p) REVERT: B 635 TRP cc_start: 0.7447 (p90) cc_final: 0.6263 (p90) REVERT: B 644 LEU cc_start: 0.7971 (mt) cc_final: 0.7650 (mt) REVERT: B 645 LYS cc_start: 0.7959 (tttt) cc_final: 0.7479 (tttt) REVERT: B 828 LYS cc_start: 0.7241 (mmtt) cc_final: 0.6685 (mmmm) REVERT: B 832 GLN cc_start: 0.6965 (tp40) cc_final: 0.6660 (tp-100) REVERT: B 839 VAL cc_start: 0.7759 (m) cc_final: 0.7460 (p) REVERT: B 852 LYS cc_start: 0.8016 (mmtm) cc_final: 0.7450 (mmmm) REVERT: B 857 MET cc_start: 0.7473 (ttm) cc_final: 0.6993 (ttp) REVERT: B 860 ASN cc_start: 0.6801 (t0) cc_final: 0.6584 (t0) REVERT: B 863 ILE cc_start: 0.5962 (mm) cc_final: 0.4759 (tp) REVERT: B 867 LEU cc_start: 0.7526 (mp) cc_final: 0.7276 (mp) REVERT: B 925 MET cc_start: 0.7265 (tmm) cc_final: 0.6879 (tmm) REVERT: B 929 LYS cc_start: 0.7316 (tttt) cc_final: 0.7047 (ttmt) REVERT: B 958 LYS cc_start: 0.7930 (tttt) cc_final: 0.7621 (mttm) REVERT: B 962 TRP cc_start: 0.6463 (p-90) cc_final: 0.5994 (p90) REVERT: B 991 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5664 (mm-30) REVERT: B 998 LEU cc_start: 0.5557 (mp) cc_final: 0.5089 (mp) REVERT: B 1007 LYS cc_start: 0.5593 (tttt) cc_final: 0.5205 (ttpp) REVERT: B 1035 TYR cc_start: 0.7058 (m-80) cc_final: 0.6623 (m-80) REVERT: B 1066 TYR cc_start: 0.6482 (m-80) cc_final: 0.6273 (m-10) REVERT: B 1068 ILE cc_start: 0.6372 (mp) cc_final: 0.6155 (pt) REVERT: B 1104 MET cc_start: 0.6908 (tpp) cc_final: 0.6579 (mmm) REVERT: B 1122 GLU cc_start: 0.7588 (tp30) cc_final: 0.7288 (tp30) outliers start: 0 outliers final: 0 residues processed: 530 average time/residue: 0.2982 time to fit residues: 230.5073 Evaluate side-chains 448 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 448 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 170 optimal weight: 0.9980 chunk 153 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 81 optimal weight: 0.6980 chunk 158 optimal weight: 9.9990 chunk 61 optimal weight: 0.0170 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 183 optimal weight: 0.0970 overall best weight: 0.5616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 421 ASN A 691 ASN A 877 GLN B 126 HIS B 192 ASN B 421 ASN B 510 ASN B 691 ASN B 900 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6860 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16438 Z= 0.192 Angle : 0.579 8.252 22304 Z= 0.300 Chirality : 0.041 0.145 2684 Planarity : 0.004 0.047 2738 Dihedral : 8.589 148.333 2194 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.00 % Allowed : 11.07 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.35 (0.18), residues: 2012 helix: 1.24 (0.13), residues: 1450 sheet: 0.11 (0.55), residues: 82 loop : 0.25 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 962 HIS 0.008 0.001 HIS B 928 PHE 0.016 0.001 PHE B 598 TYR 0.026 0.001 TYR A 309 ARG 0.005 0.001 ARG A 812 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 452 time to evaluate : 1.720 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6512 (mmm) cc_final: 0.5759 (mmm) REVERT: A 149 GLU cc_start: 0.7689 (tm-30) cc_final: 0.7339 (tm-30) REVERT: A 155 ASP cc_start: 0.6923 (t70) cc_final: 0.6450 (t70) REVERT: A 164 SER cc_start: 0.8010 (m) cc_final: 0.7651 (t) REVERT: A 188 LEU cc_start: 0.8143 (OUTLIER) cc_final: 0.7846 (tt) REVERT: A 209 ASP cc_start: 0.7577 (t0) cc_final: 0.7000 (t0) REVERT: A 231 GLU cc_start: 0.7324 (tt0) cc_final: 0.7063 (mt-10) REVERT: A 344 GLU cc_start: 0.7113 (mt-10) cc_final: 0.6840 (mt-10) REVERT: A 375 LYS cc_start: 0.8144 (mttt) cc_final: 0.7736 (mtpp) REVERT: A 380 VAL cc_start: 0.8568 (t) cc_final: 0.8278 (m) REVERT: A 449 ASP cc_start: 0.8078 (t0) cc_final: 0.7738 (t0) REVERT: A 483 MET cc_start: 0.8284 (mtp) cc_final: 0.7915 (mtm) REVERT: A 485 ASP cc_start: 0.8055 (m-30) cc_final: 0.7647 (p0) REVERT: A 500 ARG cc_start: 0.7488 (tpp80) cc_final: 0.7157 (tpp80) REVERT: A 515 ASP cc_start: 0.7645 (t70) cc_final: 0.7364 (t70) REVERT: A 522 ASP cc_start: 0.7333 (t0) cc_final: 0.6737 (t0) REVERT: A 525 ILE cc_start: 0.7191 (mm) cc_final: 0.6797 (mt) REVERT: A 527 THR cc_start: 0.7588 (t) cc_final: 0.7359 (p) REVERT: A 531 GLU cc_start: 0.7973 (tt0) cc_final: 0.7176 (tm-30) REVERT: A 534 ASP cc_start: 0.7173 (p0) cc_final: 0.6760 (p0) REVERT: A 580 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7559 (tp30) REVERT: A 584 LEU cc_start: 0.8069 (mt) cc_final: 0.7764 (mt) REVERT: A 591 LYS cc_start: 0.8066 (mttp) cc_final: 0.7861 (mtpp) REVERT: A 602 MET cc_start: 0.6371 (mmp) cc_final: 0.5993 (mmm) REVERT: A 613 GLN cc_start: 0.7823 (tt0) cc_final: 0.7587 (tm-30) REVERT: A 634 SER cc_start: 0.8466 (m) cc_final: 0.8022 (p) REVERT: A 647 LYS cc_start: 0.7471 (mmmt) cc_final: 0.7033 (mmtt) REVERT: A 828 LYS cc_start: 0.7178 (mmtt) cc_final: 0.6925 (mmtt) REVERT: A 848 GLU cc_start: 0.7286 (mt-10) cc_final: 0.7034 (mt-10) REVERT: A 857 MET cc_start: 0.7423 (ttm) cc_final: 0.6942 (ttp) REVERT: A 863 ILE cc_start: 0.5566 (mm) cc_final: 0.5078 (tp) REVERT: A 872 GLU cc_start: 0.7055 (tp30) cc_final: 0.6786 (tp30) REVERT: A 887 ARG cc_start: 0.7273 (mmm-85) cc_final: 0.6966 (mmm-85) REVERT: A 938 MET cc_start: 0.7729 (tpp) cc_final: 0.7360 (ttt) REVERT: A 947 SER cc_start: 0.7765 (t) cc_final: 0.7365 (p) REVERT: A 958 LYS cc_start: 0.7980 (tttt) cc_final: 0.7634 (mtmm) REVERT: A 991 GLU cc_start: 0.5812 (mt-10) cc_final: 0.5302 (mm-30) REVERT: A 998 LEU cc_start: 0.5571 (mp) cc_final: 0.5359 (mt) REVERT: A 1006 VAL cc_start: 0.4449 (OUTLIER) cc_final: 0.4173 (m) REVERT: A 1007 LYS cc_start: 0.5547 (tttt) cc_final: 0.5089 (tttp) REVERT: A 1122 GLU cc_start: 0.7405 (mm-30) cc_final: 0.6857 (mm-30) REVERT: B 133 MET cc_start: 0.6235 (mmm) cc_final: 0.5464 (mmm) REVERT: B 149 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7519 (tm-30) REVERT: B 155 ASP cc_start: 0.6967 (t70) cc_final: 0.6515 (t70) REVERT: B 160 MET cc_start: 0.7370 (mmt) cc_final: 0.6916 (mmm) REVERT: B 164 SER cc_start: 0.8018 (m) cc_final: 0.7716 (t) REVERT: B 188 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7953 (tt) REVERT: B 199 MET cc_start: 0.8212 (mmm) cc_final: 0.7951 (tpp) REVERT: B 268 PHE cc_start: 0.7791 (t80) cc_final: 0.7419 (t80) REVERT: B 375 LYS cc_start: 0.8155 (mttt) cc_final: 0.7892 (mttp) REVERT: B 380 VAL cc_start: 0.8628 (t) cc_final: 0.8311 (m) REVERT: B 383 MET cc_start: 0.6841 (mmp) cc_final: 0.6623 (mmm) REVERT: B 390 ILE cc_start: 0.7635 (mm) cc_final: 0.7434 (mt) REVERT: B 443 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7699 (tm-30) REVERT: B 479 ARG cc_start: 0.7674 (ttp-170) cc_final: 0.7390 (ttm-80) REVERT: B 483 MET cc_start: 0.8547 (mtp) cc_final: 0.8098 (mtm) REVERT: B 485 ASP cc_start: 0.8005 (m-30) cc_final: 0.7673 (p0) REVERT: B 494 MET cc_start: 0.7475 (tpp) cc_final: 0.7211 (tpp) REVERT: B 500 ARG cc_start: 0.7466 (tpp80) cc_final: 0.7065 (ttm-80) REVERT: B 515 ASP cc_start: 0.7490 (t70) cc_final: 0.7153 (t70) REVERT: B 522 ASP cc_start: 0.7417 (t0) cc_final: 0.6835 (t0) REVERT: B 525 ILE cc_start: 0.7191 (mm) cc_final: 0.6812 (mt) REVERT: B 527 THR cc_start: 0.7712 (t) cc_final: 0.7503 (p) REVERT: B 534 ASP cc_start: 0.7059 (p0) cc_final: 0.6660 (p0) REVERT: B 588 LYS cc_start: 0.7653 (ttmt) cc_final: 0.7274 (ttmt) REVERT: B 591 LYS cc_start: 0.8254 (mttp) cc_final: 0.8018 (mtpp) REVERT: B 610 LEU cc_start: 0.8201 (mp) cc_final: 0.7884 (tp) REVERT: B 613 GLN cc_start: 0.7701 (tt0) cc_final: 0.7262 (tm-30) REVERT: B 623 ASP cc_start: 0.7848 (t0) cc_final: 0.7647 (t0) REVERT: B 634 SER cc_start: 0.8648 (m) cc_final: 0.8160 (p) REVERT: B 645 LYS cc_start: 0.7954 (tttt) cc_final: 0.7445 (tptt) REVERT: B 828 LYS cc_start: 0.7154 (mmtt) cc_final: 0.6648 (mmmm) REVERT: B 832 GLN cc_start: 0.7003 (tp40) cc_final: 0.6677 (tp40) REVERT: B 852 LYS cc_start: 0.8011 (mmtm) cc_final: 0.7527 (mmmm) REVERT: B 857 MET cc_start: 0.7231 (ttm) cc_final: 0.6978 (ttp) REVERT: B 863 ILE cc_start: 0.5775 (mm) cc_final: 0.5224 (tp) REVERT: B 867 LEU cc_start: 0.7744 (mp) cc_final: 0.7428 (mp) REVERT: B 929 LYS cc_start: 0.7196 (tttt) cc_final: 0.6935 (ttmt) REVERT: B 947 SER cc_start: 0.7871 (t) cc_final: 0.7425 (p) REVERT: B 958 LYS cc_start: 0.7995 (tttt) cc_final: 0.7646 (mttm) REVERT: B 982 PHE cc_start: 0.5919 (m-80) cc_final: 0.5706 (m-10) REVERT: B 1073 MET cc_start: 0.6452 (mmm) cc_final: 0.6164 (tmm) REVERT: B 1077 ILE cc_start: 0.7672 (mm) cc_final: 0.7333 (mt) REVERT: B 1104 MET cc_start: 0.6837 (tpp) cc_final: 0.6550 (tpt) REVERT: B 1122 GLU cc_start: 0.7534 (tp30) cc_final: 0.7250 (tp30) outliers start: 35 outliers final: 17 residues processed: 467 average time/residue: 0.2978 time to fit residues: 203.4100 Evaluate side-chains 453 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 433 time to evaluate : 2.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 1006 VAL Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 932 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 101 optimal weight: 0.9980 chunk 56 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 124 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 183 optimal weight: 0.3980 chunk 198 optimal weight: 0.6980 chunk 163 optimal weight: 0.7980 chunk 182 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 860 ASN B 900 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6869 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16438 Z= 0.208 Angle : 0.537 8.472 22304 Z= 0.276 Chirality : 0.040 0.150 2684 Planarity : 0.004 0.041 2738 Dihedral : 8.418 147.501 2194 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.51 % Allowed : 12.33 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.55 (0.19), residues: 2012 helix: 1.40 (0.13), residues: 1460 sheet: 0.47 (0.56), residues: 84 loop : 0.20 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP A 962 HIS 0.005 0.001 HIS A 928 PHE 0.023 0.001 PHE A 982 TYR 0.024 0.001 TYR A 309 ARG 0.005 0.000 ARG B 812 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 497 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 453 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6508 (mmm) cc_final: 0.5973 (mmm) REVERT: A 149 GLU cc_start: 0.7752 (tm-30) cc_final: 0.7358 (tm-30) REVERT: A 155 ASP cc_start: 0.6729 (t70) cc_final: 0.6221 (t70) REVERT: A 164 SER cc_start: 0.7987 (m) cc_final: 0.7599 (t) REVERT: A 188 LEU cc_start: 0.8147 (OUTLIER) cc_final: 0.7831 (tt) REVERT: A 209 ASP cc_start: 0.7610 (t0) cc_final: 0.7097 (t70) REVERT: A 231 GLU cc_start: 0.7282 (tt0) cc_final: 0.7048 (mt-10) REVERT: A 256 GLN cc_start: 0.7491 (mp10) cc_final: 0.7267 (mp10) REVERT: A 268 PHE cc_start: 0.7810 (t80) cc_final: 0.7272 (t80) REVERT: A 375 LYS cc_start: 0.8103 (mttt) cc_final: 0.7676 (mtpp) REVERT: A 380 VAL cc_start: 0.8571 (t) cc_final: 0.8270 (m) REVERT: A 485 ASP cc_start: 0.8050 (m-30) cc_final: 0.7648 (p0) REVERT: A 500 ARG cc_start: 0.7442 (tpp80) cc_final: 0.7095 (tpp80) REVERT: A 515 ASP cc_start: 0.7629 (t70) cc_final: 0.7169 (t70) REVERT: A 518 LEU cc_start: 0.7117 (mt) cc_final: 0.6902 (mt) REVERT: A 522 ASP cc_start: 0.7336 (t0) cc_final: 0.6783 (t0) REVERT: A 524 ASP cc_start: 0.7939 (OUTLIER) cc_final: 0.7716 (m-30) REVERT: A 525 ILE cc_start: 0.7179 (mm) cc_final: 0.6797 (mt) REVERT: A 527 THR cc_start: 0.7600 (t) cc_final: 0.7344 (p) REVERT: A 531 GLU cc_start: 0.7982 (tt0) cc_final: 0.7164 (tm-30) REVERT: A 534 ASP cc_start: 0.7264 (p0) cc_final: 0.6873 (p0) REVERT: A 580 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7628 (tp30) REVERT: A 591 LYS cc_start: 0.8074 (mttp) cc_final: 0.7749 (mtpp) REVERT: A 602 MET cc_start: 0.6367 (mmp) cc_final: 0.6000 (mmm) REVERT: A 606 GLU cc_start: 0.7489 (pm20) cc_final: 0.7231 (pm20) REVERT: A 613 GLN cc_start: 0.7752 (tt0) cc_final: 0.7509 (tm-30) REVERT: A 634 SER cc_start: 0.8488 (m) cc_final: 0.8121 (p) REVERT: A 645 LYS cc_start: 0.7507 (tttt) cc_final: 0.7101 (tttp) REVERT: A 647 LYS cc_start: 0.7438 (mmmt) cc_final: 0.6998 (mmtt) REVERT: A 828 LYS cc_start: 0.7141 (mmtt) cc_final: 0.6875 (mmtt) REVERT: A 857 MET cc_start: 0.7462 (ttm) cc_final: 0.7122 (ttp) REVERT: A 863 ILE cc_start: 0.5850 (mm) cc_final: 0.5648 (mm) REVERT: A 887 ARG cc_start: 0.7372 (mmm-85) cc_final: 0.6959 (mmm-85) REVERT: A 947 SER cc_start: 0.7792 (t) cc_final: 0.7401 (p) REVERT: A 958 LYS cc_start: 0.7968 (tttt) cc_final: 0.7660 (mtmm) REVERT: A 1122 GLU cc_start: 0.7368 (mm-30) cc_final: 0.6756 (mm-30) REVERT: B 133 MET cc_start: 0.6339 (mmm) cc_final: 0.5784 (mmm) REVERT: B 149 GLU cc_start: 0.7803 (tm-30) cc_final: 0.7513 (tm-30) REVERT: B 155 ASP cc_start: 0.6833 (t70) cc_final: 0.6375 (t70) REVERT: B 160 MET cc_start: 0.7444 (mmt) cc_final: 0.7110 (mmm) REVERT: B 164 SER cc_start: 0.7966 (m) cc_final: 0.7643 (t) REVERT: B 197 GLU cc_start: 0.7544 (mt-10) cc_final: 0.7021 (mt-10) REVERT: B 367 MET cc_start: 0.7640 (mtm) cc_final: 0.7429 (mtm) REVERT: B 375 LYS cc_start: 0.8209 (mttt) cc_final: 0.7928 (mttp) REVERT: B 380 VAL cc_start: 0.8660 (t) cc_final: 0.8302 (m) REVERT: B 383 MET cc_start: 0.6827 (mmp) cc_final: 0.6620 (mmm) REVERT: B 443 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7654 (tm-30) REVERT: B 479 ARG cc_start: 0.7680 (ttp-170) cc_final: 0.7408 (ttm-80) REVERT: B 485 ASP cc_start: 0.7989 (m-30) cc_final: 0.7619 (p0) REVERT: B 494 MET cc_start: 0.7463 (tpp) cc_final: 0.7226 (tpp) REVERT: B 500 ARG cc_start: 0.7576 (tpp80) cc_final: 0.7179 (ttm-80) REVERT: B 522 ASP cc_start: 0.7437 (t0) cc_final: 0.6734 (t0) REVERT: B 525 ILE cc_start: 0.7083 (mm) cc_final: 0.6686 (mt) REVERT: B 527 THR cc_start: 0.7669 (t) cc_final: 0.7430 (p) REVERT: B 534 ASP cc_start: 0.7255 (p0) cc_final: 0.6795 (p0) REVERT: B 588 LYS cc_start: 0.7660 (ttmt) cc_final: 0.7257 (ttmt) REVERT: B 610 LEU cc_start: 0.8118 (mp) cc_final: 0.7622 (tp) REVERT: B 613 GLN cc_start: 0.7612 (tt0) cc_final: 0.7308 (tm-30) REVERT: B 634 SER cc_start: 0.8583 (m) cc_final: 0.8118 (p) REVERT: B 828 LYS cc_start: 0.7123 (mmtt) cc_final: 0.6627 (mmmm) REVERT: B 832 GLN cc_start: 0.7080 (tp40) cc_final: 0.6717 (tp40) REVERT: B 852 LYS cc_start: 0.8044 (mmtm) cc_final: 0.7557 (mmmm) REVERT: B 853 ILE cc_start: 0.7492 (OUTLIER) cc_final: 0.7276 (tp) REVERT: B 857 MET cc_start: 0.7536 (ttm) cc_final: 0.7162 (ttm) REVERT: B 860 ASN cc_start: 0.6991 (t0) cc_final: 0.6440 (p0) REVERT: B 861 LYS cc_start: 0.7781 (mtpp) cc_final: 0.7547 (mptt) REVERT: B 929 LYS cc_start: 0.7164 (tttt) cc_final: 0.6882 (ttmt) REVERT: B 938 MET cc_start: 0.7726 (tpp) cc_final: 0.7484 (ttt) REVERT: B 946 SER cc_start: 0.7667 (p) cc_final: 0.7393 (p) REVERT: B 947 SER cc_start: 0.7877 (t) cc_final: 0.7366 (p) REVERT: B 958 LYS cc_start: 0.7960 (tttt) cc_final: 0.7610 (mttm) REVERT: B 1003 SER cc_start: 0.6037 (m) cc_final: 0.5811 (t) REVERT: B 1007 LYS cc_start: 0.5832 (tttt) cc_final: 0.5295 (ttmm) REVERT: B 1104 MET cc_start: 0.6802 (tpp) cc_final: 0.6393 (tpt) REVERT: B 1122 GLU cc_start: 0.7594 (tp30) cc_final: 0.7320 (tp30) outliers start: 44 outliers final: 23 residues processed: 468 average time/residue: 0.2904 time to fit residues: 200.1950 Evaluate side-chains 468 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 442 time to evaluate : 1.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 960 VAL Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1066 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 181 optimal weight: 0.8980 chunk 138 optimal weight: 0.2980 chunk 95 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 123 optimal weight: 0.9990 chunk 184 optimal weight: 0.3980 chunk 195 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 174 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1177 GLN B1064 GLN B1177 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6867 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16438 Z= 0.192 Angle : 0.519 8.324 22304 Z= 0.265 Chirality : 0.039 0.193 2684 Planarity : 0.004 0.041 2738 Dihedral : 8.359 148.183 2194 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.97 % Allowed : 13.64 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.73 (0.19), residues: 2012 helix: 1.54 (0.13), residues: 1466 sheet: 0.87 (0.65), residues: 64 loop : 0.16 (0.30), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP A 962 HIS 0.004 0.001 HIS B 928 PHE 0.017 0.001 PHE B 982 TYR 0.020 0.001 TYR A 309 ARG 0.006 0.000 ARG B 812 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 493 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 441 time to evaluate : 1.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6440 (mmm) cc_final: 0.5959 (mmm) REVERT: A 149 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7363 (tm-30) REVERT: A 155 ASP cc_start: 0.6661 (t70) cc_final: 0.6164 (t70) REVERT: A 164 SER cc_start: 0.7977 (m) cc_final: 0.7608 (t) REVERT: A 188 LEU cc_start: 0.8135 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 209 ASP cc_start: 0.7609 (t0) cc_final: 0.7073 (t70) REVERT: A 231 GLU cc_start: 0.7290 (tt0) cc_final: 0.7072 (mt-10) REVERT: A 256 GLN cc_start: 0.7546 (mp10) cc_final: 0.7340 (mp10) REVERT: A 375 LYS cc_start: 0.8116 (mttt) cc_final: 0.7706 (mtpp) REVERT: A 380 VAL cc_start: 0.8594 (t) cc_final: 0.8294 (m) REVERT: A 485 ASP cc_start: 0.8055 (m-30) cc_final: 0.7657 (p0) REVERT: A 500 ARG cc_start: 0.7436 (tpp80) cc_final: 0.7088 (tpp80) REVERT: A 515 ASP cc_start: 0.7722 (t70) cc_final: 0.7270 (t70) REVERT: A 518 LEU cc_start: 0.7155 (mt) cc_final: 0.6917 (mt) REVERT: A 522 ASP cc_start: 0.7452 (t0) cc_final: 0.6898 (t0) REVERT: A 524 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7710 (m-30) REVERT: A 525 ILE cc_start: 0.7036 (mm) cc_final: 0.6666 (mt) REVERT: A 527 THR cc_start: 0.7649 (t) cc_final: 0.7374 (p) REVERT: A 531 GLU cc_start: 0.7958 (tt0) cc_final: 0.7216 (tm-30) REVERT: A 534 ASP cc_start: 0.7295 (p0) cc_final: 0.6923 (p0) REVERT: A 578 MET cc_start: 0.6589 (mmm) cc_final: 0.6359 (mmm) REVERT: A 591 LYS cc_start: 0.8062 (mttp) cc_final: 0.7796 (mtpp) REVERT: A 602 MET cc_start: 0.6382 (mmp) cc_final: 0.6098 (mmm) REVERT: A 610 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.7905 (tp) REVERT: A 613 GLN cc_start: 0.7741 (tt0) cc_final: 0.7491 (tm-30) REVERT: A 634 SER cc_start: 0.8532 (m) cc_final: 0.8296 (p) REVERT: A 644 LEU cc_start: 0.7678 (OUTLIER) cc_final: 0.7457 (mm) REVERT: A 645 LYS cc_start: 0.7551 (tttt) cc_final: 0.7085 (tttp) REVERT: A 647 LYS cc_start: 0.7505 (mmmt) cc_final: 0.7053 (mmtt) REVERT: A 678 MET cc_start: 0.0311 (ppp) cc_final: -0.0562 (ppp) REVERT: A 828 LYS cc_start: 0.7172 (mmtt) cc_final: 0.6937 (mmtt) REVERT: A 857 MET cc_start: 0.7436 (ttm) cc_final: 0.7000 (ttp) REVERT: A 887 ARG cc_start: 0.7447 (mmm-85) cc_final: 0.6959 (mmm-85) REVERT: A 938 MET cc_start: 0.7797 (tpp) cc_final: 0.7550 (ttt) REVERT: A 947 SER cc_start: 0.7849 (t) cc_final: 0.7468 (p) REVERT: A 958 LYS cc_start: 0.7875 (tttt) cc_final: 0.7538 (mttm) REVERT: A 1122 GLU cc_start: 0.7373 (mm-30) cc_final: 0.6762 (mm-30) REVERT: B 133 MET cc_start: 0.6291 (mmm) cc_final: 0.5823 (mmm) REVERT: B 149 GLU cc_start: 0.7822 (tm-30) cc_final: 0.7489 (tm-30) REVERT: B 155 ASP cc_start: 0.6721 (t70) cc_final: 0.6245 (t70) REVERT: B 160 MET cc_start: 0.7442 (mmt) cc_final: 0.7105 (mmm) REVERT: B 164 SER cc_start: 0.7952 (m) cc_final: 0.7631 (t) REVERT: B 171 LEU cc_start: 0.7576 (mm) cc_final: 0.7333 (mm) REVERT: B 367 MET cc_start: 0.7635 (mtm) cc_final: 0.7428 (mtm) REVERT: B 375 LYS cc_start: 0.8216 (mttt) cc_final: 0.7733 (mtpp) REVERT: B 380 VAL cc_start: 0.8626 (t) cc_final: 0.8268 (m) REVERT: B 383 MET cc_start: 0.6718 (mmp) cc_final: 0.6517 (mmm) REVERT: B 479 ARG cc_start: 0.7678 (ttp-170) cc_final: 0.7414 (ttm-80) REVERT: B 485 ASP cc_start: 0.7980 (m-30) cc_final: 0.7613 (p0) REVERT: B 494 MET cc_start: 0.7493 (tpp) cc_final: 0.7127 (tpp) REVERT: B 500 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7197 (ttm-80) REVERT: B 517 PHE cc_start: 0.8273 (m-80) cc_final: 0.8052 (m-80) REVERT: B 522 ASP cc_start: 0.7341 (t0) cc_final: 0.6589 (t0) REVERT: B 525 ILE cc_start: 0.6999 (mm) cc_final: 0.6600 (mt) REVERT: B 527 THR cc_start: 0.7695 (t) cc_final: 0.7451 (p) REVERT: B 534 ASP cc_start: 0.7342 (p0) cc_final: 0.6938 (p0) REVERT: B 580 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7571 (tp30) REVERT: B 588 LYS cc_start: 0.7535 (ttmt) cc_final: 0.7285 (ttmt) REVERT: B 599 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7426 (mm-30) REVERT: B 610 LEU cc_start: 0.8109 (mp) cc_final: 0.7666 (tp) REVERT: B 613 GLN cc_start: 0.7681 (tt0) cc_final: 0.7356 (tm-30) REVERT: B 634 SER cc_start: 0.8572 (m) cc_final: 0.8315 (p) REVERT: B 644 LEU cc_start: 0.7851 (mm) cc_final: 0.7648 (mm) REVERT: B 676 HIS cc_start: 0.4021 (OUTLIER) cc_final: 0.3024 (m90) REVERT: B 828 LYS cc_start: 0.7109 (mmtt) cc_final: 0.6589 (mmmm) REVERT: B 847 GLU cc_start: 0.7206 (mm-30) cc_final: 0.6927 (mm-30) REVERT: B 852 LYS cc_start: 0.8045 (mmtm) cc_final: 0.7579 (mmmm) REVERT: B 853 ILE cc_start: 0.7506 (OUTLIER) cc_final: 0.7281 (tp) REVERT: B 857 MET cc_start: 0.7320 (ttm) cc_final: 0.6984 (ttm) REVERT: B 860 ASN cc_start: 0.6867 (t0) cc_final: 0.6246 (p0) REVERT: B 861 LYS cc_start: 0.7807 (mtpp) cc_final: 0.7597 (mptt) REVERT: B 862 LYS cc_start: 0.7773 (ttmm) cc_final: 0.7500 (ttpp) REVERT: B 863 ILE cc_start: 0.5995 (mm) cc_final: 0.5472 (mm) REVERT: B 929 LYS cc_start: 0.7224 (tttt) cc_final: 0.6965 (ttmt) REVERT: B 946 SER cc_start: 0.7640 (p) cc_final: 0.7378 (p) REVERT: B 947 SER cc_start: 0.7897 (t) cc_final: 0.7400 (p) REVERT: B 958 LYS cc_start: 0.7958 (tttt) cc_final: 0.7570 (mttp) REVERT: B 986 GLU cc_start: 0.4804 (mt-10) cc_final: 0.4378 (mt-10) REVERT: B 991 GLU cc_start: 0.6114 (mt-10) cc_final: 0.5656 (mm-30) REVERT: B 1003 SER cc_start: 0.6025 (m) cc_final: 0.5787 (t) REVERT: B 1007 LYS cc_start: 0.5709 (tttt) cc_final: 0.5246 (ttmm) REVERT: B 1035 TYR cc_start: 0.6878 (m-80) cc_final: 0.6517 (m-10) REVERT: B 1068 ILE cc_start: 0.6175 (mp) cc_final: 0.5860 (tt) REVERT: B 1104 MET cc_start: 0.6761 (tpp) cc_final: 0.6414 (tpt) REVERT: B 1122 GLU cc_start: 0.7614 (tp30) cc_final: 0.7307 (tp30) outliers start: 52 outliers final: 29 residues processed: 455 average time/residue: 0.3049 time to fit residues: 203.7238 Evaluate side-chains 463 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 428 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 524 ASP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 862 LYS Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 780 ILE Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1119 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 162 optimal weight: 0.9990 chunk 110 optimal weight: 0.2980 chunk 2 optimal weight: 0.0970 chunk 145 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 166 optimal weight: 0.4980 chunk 134 optimal weight: 0.4980 chunk 0 optimal weight: 3.9990 chunk 99 optimal weight: 4.9990 chunk 175 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 676 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6859 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16438 Z= 0.164 Angle : 0.513 8.249 22304 Z= 0.258 Chirality : 0.039 0.226 2684 Planarity : 0.003 0.040 2738 Dihedral : 8.318 148.624 2194 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.80 % Allowed : 14.50 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.94 (0.19), residues: 2012 helix: 1.72 (0.13), residues: 1468 sheet: 0.91 (0.65), residues: 64 loop : 0.13 (0.30), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.001 TRP A 962 HIS 0.013 0.001 HIS A 676 PHE 0.015 0.001 PHE B 982 TYR 0.021 0.001 TYR B 309 ARG 0.008 0.000 ARG B 887 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 478 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 429 time to evaluate : 1.631 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6438 (mmm) cc_final: 0.5967 (mmm) REVERT: A 149 GLU cc_start: 0.7764 (tm-30) cc_final: 0.7314 (tm-30) REVERT: A 164 SER cc_start: 0.7955 (m) cc_final: 0.7590 (t) REVERT: A 188 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7815 (tt) REVERT: A 209 ASP cc_start: 0.7580 (t0) cc_final: 0.7029 (t70) REVERT: A 256 GLN cc_start: 0.7492 (mp10) cc_final: 0.7281 (mp10) REVERT: A 319 LEU cc_start: 0.8033 (mt) cc_final: 0.7830 (mp) REVERT: A 337 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 375 LYS cc_start: 0.8066 (mttt) cc_final: 0.7670 (mtpp) REVERT: A 380 VAL cc_start: 0.8583 (t) cc_final: 0.8289 (m) REVERT: A 485 ASP cc_start: 0.8034 (m-30) cc_final: 0.7710 (p0) REVERT: A 500 ARG cc_start: 0.7448 (tpp80) cc_final: 0.7119 (tpp80) REVERT: A 511 MET cc_start: 0.7168 (tmm) cc_final: 0.6947 (tmm) REVERT: A 522 ASP cc_start: 0.7437 (t0) cc_final: 0.6893 (t0) REVERT: A 524 ASP cc_start: 0.7923 (t0) cc_final: 0.7699 (m-30) REVERT: A 525 ILE cc_start: 0.7001 (mm) cc_final: 0.6684 (mt) REVERT: A 527 THR cc_start: 0.7671 (t) cc_final: 0.7406 (p) REVERT: A 531 GLU cc_start: 0.7937 (tt0) cc_final: 0.7227 (tm-30) REVERT: A 534 ASP cc_start: 0.7335 (p0) cc_final: 0.7009 (p0) REVERT: A 578 MET cc_start: 0.6652 (mmm) cc_final: 0.6440 (mmm) REVERT: A 591 LYS cc_start: 0.8066 (mttp) cc_final: 0.7809 (mtpp) REVERT: A 599 GLU cc_start: 0.7820 (mm-30) cc_final: 0.7573 (mm-30) REVERT: A 602 MET cc_start: 0.6352 (mmp) cc_final: 0.6073 (mmm) REVERT: A 610 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7863 (tp) REVERT: A 613 GLN cc_start: 0.7716 (tt0) cc_final: 0.7460 (tm-30) REVERT: A 634 SER cc_start: 0.8512 (m) cc_final: 0.8263 (p) REVERT: A 636 GLN cc_start: 0.7998 (mm-40) cc_final: 0.7555 (mm-40) REVERT: A 644 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7432 (mm) REVERT: A 647 LYS cc_start: 0.7510 (mmmt) cc_final: 0.7027 (mmtt) REVERT: A 678 MET cc_start: 0.0605 (ppp) cc_final: -0.0247 (ppp) REVERT: A 828 LYS cc_start: 0.7172 (mmtt) cc_final: 0.6821 (mmtt) REVERT: A 857 MET cc_start: 0.7434 (ttm) cc_final: 0.6977 (ttp) REVERT: A 861 LYS cc_start: 0.7602 (mtpp) cc_final: 0.7390 (mptt) REVERT: A 881 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7767 (mm-30) REVERT: A 887 ARG cc_start: 0.7461 (mmm-85) cc_final: 0.7094 (mmm-85) REVERT: A 926 GLU cc_start: 0.7610 (mt-10) cc_final: 0.7354 (mm-30) REVERT: A 935 GLU cc_start: 0.7436 (mt-10) cc_final: 0.6948 (tp30) REVERT: A 938 MET cc_start: 0.7818 (tpp) cc_final: 0.7477 (ttt) REVERT: A 947 SER cc_start: 0.7828 (t) cc_final: 0.7449 (p) REVERT: A 958 LYS cc_start: 0.7805 (tttt) cc_final: 0.7492 (mtmm) REVERT: A 1087 GLU cc_start: 0.6713 (tt0) cc_final: 0.6131 (tp30) REVERT: A 1122 GLU cc_start: 0.7352 (mm-30) cc_final: 0.7100 (tp30) REVERT: B 133 MET cc_start: 0.6297 (mmm) cc_final: 0.5843 (mmm) REVERT: B 149 GLU cc_start: 0.7815 (tm-30) cc_final: 0.7473 (tm-30) REVERT: B 155 ASP cc_start: 0.6686 (t70) cc_final: 0.6215 (t70) REVERT: B 160 MET cc_start: 0.7443 (mmt) cc_final: 0.7099 (mmm) REVERT: B 164 SER cc_start: 0.7926 (m) cc_final: 0.7635 (t) REVERT: B 171 LEU cc_start: 0.7579 (mm) cc_final: 0.7352 (mm) REVERT: B 375 LYS cc_start: 0.8111 (mttt) cc_final: 0.7640 (mtpp) REVERT: B 380 VAL cc_start: 0.8595 (t) cc_final: 0.8266 (m) REVERT: B 479 ARG cc_start: 0.7660 (ttp-170) cc_final: 0.7429 (ttm-80) REVERT: B 483 MET cc_start: 0.8582 (mtp) cc_final: 0.8246 (mtm) REVERT: B 485 ASP cc_start: 0.7948 (m-30) cc_final: 0.7624 (p0) REVERT: B 498 VAL cc_start: 0.7197 (t) cc_final: 0.6994 (p) REVERT: B 500 ARG cc_start: 0.7575 (tpp80) cc_final: 0.7202 (ttm-80) REVERT: B 522 ASP cc_start: 0.7472 (t0) cc_final: 0.6811 (t0) REVERT: B 525 ILE cc_start: 0.6975 (mm) cc_final: 0.6570 (mt) REVERT: B 527 THR cc_start: 0.7687 (t) cc_final: 0.7440 (p) REVERT: B 534 ASP cc_start: 0.7253 (p0) cc_final: 0.6751 (p0) REVERT: B 580 GLU cc_start: 0.7793 (mt-10) cc_final: 0.7513 (tp30) REVERT: B 588 LYS cc_start: 0.7564 (ttmt) cc_final: 0.7255 (ttmt) REVERT: B 599 GLU cc_start: 0.7694 (mm-30) cc_final: 0.7477 (mm-30) REVERT: B 610 LEU cc_start: 0.8068 (mp) cc_final: 0.7639 (tp) REVERT: B 613 GLN cc_start: 0.7652 (tt0) cc_final: 0.7339 (tm-30) REVERT: B 623 ASP cc_start: 0.7846 (t0) cc_final: 0.7623 (t0) REVERT: B 634 SER cc_start: 0.8576 (m) cc_final: 0.8319 (p) REVERT: B 644 LEU cc_start: 0.7819 (mm) cc_final: 0.7585 (mm) REVERT: B 676 HIS cc_start: 0.4236 (OUTLIER) cc_final: 0.3252 (m90) REVERT: B 828 LYS cc_start: 0.7107 (mmtt) cc_final: 0.6600 (mmmm) REVERT: B 847 GLU cc_start: 0.7159 (mm-30) cc_final: 0.6865 (mm-30) REVERT: B 852 LYS cc_start: 0.8210 (mmtm) cc_final: 0.7983 (mmtp) REVERT: B 853 ILE cc_start: 0.7474 (OUTLIER) cc_final: 0.7258 (tp) REVERT: B 857 MET cc_start: 0.7338 (ttm) cc_final: 0.7008 (ttm) REVERT: B 862 LYS cc_start: 0.7836 (ttmm) cc_final: 0.7512 (ttpp) REVERT: B 863 ILE cc_start: 0.5773 (mm) cc_final: 0.5313 (tp) REVERT: B 929 LYS cc_start: 0.7194 (tttt) cc_final: 0.6952 (ttmt) REVERT: B 938 MET cc_start: 0.7899 (tpp) cc_final: 0.7645 (ttt) REVERT: B 946 SER cc_start: 0.7563 (p) cc_final: 0.7340 (p) REVERT: B 947 SER cc_start: 0.7910 (t) cc_final: 0.7411 (p) REVERT: B 958 LYS cc_start: 0.7926 (tttt) cc_final: 0.7560 (mttp) REVERT: B 986 GLU cc_start: 0.4847 (mt-10) cc_final: 0.4425 (mt-10) REVERT: B 989 VAL cc_start: 0.5947 (t) cc_final: 0.5292 (p) REVERT: B 991 GLU cc_start: 0.6109 (mt-10) cc_final: 0.5669 (mm-30) REVERT: B 1003 SER cc_start: 0.6116 (m) cc_final: 0.5866 (t) REVERT: B 1007 LYS cc_start: 0.5725 (tttt) cc_final: 0.5308 (ttmm) REVERT: B 1035 TYR cc_start: 0.7009 (m-80) cc_final: 0.6731 (m-10) REVERT: B 1068 ILE cc_start: 0.6342 (mp) cc_final: 0.6031 (tt) REVERT: B 1122 GLU cc_start: 0.7534 (tp30) cc_final: 0.7206 (tp30) outliers start: 49 outliers final: 28 residues processed: 442 average time/residue: 0.2972 time to fit residues: 191.3221 Evaluate side-chains 444 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 411 time to evaluate : 1.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 822 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1098 ILE Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1001 ILE Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1066 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 65 optimal weight: 3.9990 chunk 175 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 195 optimal weight: 0.6980 chunk 162 optimal weight: 0.2980 chunk 90 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 0.9980 chunk 102 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 860 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6870 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16438 Z= 0.194 Angle : 0.520 8.196 22304 Z= 0.261 Chirality : 0.039 0.198 2684 Planarity : 0.003 0.041 2738 Dihedral : 8.308 148.580 2194 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 3.08 % Allowed : 14.90 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.97 (0.19), residues: 2012 helix: 1.76 (0.13), residues: 1472 sheet: 0.60 (0.66), residues: 74 loop : 0.12 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP A 962 HIS 0.003 0.000 HIS B 928 PHE 0.019 0.001 PHE A 982 TYR 0.024 0.001 TYR B 309 ARG 0.006 0.000 ARG B 887 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 422 time to evaluate : 1.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6440 (mmm) cc_final: 0.5981 (mmm) REVERT: A 149 GLU cc_start: 0.7765 (tm-30) cc_final: 0.7335 (tm-30) REVERT: A 164 SER cc_start: 0.7987 (m) cc_final: 0.7636 (t) REVERT: A 188 LEU cc_start: 0.8085 (OUTLIER) cc_final: 0.7822 (tt) REVERT: A 209 ASP cc_start: 0.7617 (t0) cc_final: 0.7061 (t70) REVERT: A 319 LEU cc_start: 0.8024 (mt) cc_final: 0.7824 (mp) REVERT: A 375 LYS cc_start: 0.8050 (mttt) cc_final: 0.7663 (mtpp) REVERT: A 380 VAL cc_start: 0.8588 (t) cc_final: 0.8301 (m) REVERT: A 418 THR cc_start: 0.7405 (m) cc_final: 0.6712 (p) REVERT: A 483 MET cc_start: 0.8548 (mtp) cc_final: 0.8179 (mtm) REVERT: A 485 ASP cc_start: 0.8113 (m-30) cc_final: 0.7677 (p0) REVERT: A 500 ARG cc_start: 0.7470 (tpp80) cc_final: 0.7126 (tpp80) REVERT: A 527 THR cc_start: 0.7695 (t) cc_final: 0.7410 (p) REVERT: A 531 GLU cc_start: 0.7939 (tt0) cc_final: 0.7237 (tm-30) REVERT: A 534 ASP cc_start: 0.7402 (p0) cc_final: 0.7065 (p0) REVERT: A 591 LYS cc_start: 0.8077 (mttp) cc_final: 0.7852 (mtpp) REVERT: A 599 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7529 (mm-30) REVERT: A 602 MET cc_start: 0.6348 (mmp) cc_final: 0.6073 (mmm) REVERT: A 610 LEU cc_start: 0.8426 (OUTLIER) cc_final: 0.7869 (tp) REVERT: A 613 GLN cc_start: 0.7721 (tt0) cc_final: 0.7443 (tm-30) REVERT: A 634 SER cc_start: 0.8515 (m) cc_final: 0.8258 (p) REVERT: A 644 LEU cc_start: 0.7656 (OUTLIER) cc_final: 0.7434 (mm) REVERT: A 647 LYS cc_start: 0.7514 (mmmt) cc_final: 0.7010 (mmtt) REVERT: A 678 MET cc_start: 0.0667 (ppp) cc_final: -0.0204 (ppp) REVERT: A 828 LYS cc_start: 0.7169 (mmtt) cc_final: 0.6822 (mmtt) REVERT: A 857 MET cc_start: 0.7404 (ttm) cc_final: 0.6960 (ttp) REVERT: A 881 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7768 (mm-30) REVERT: A 887 ARG cc_start: 0.7468 (mmm-85) cc_final: 0.7087 (mmm-85) REVERT: A 935 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6913 (tp30) REVERT: A 938 MET cc_start: 0.7818 (tpp) cc_final: 0.7476 (ttt) REVERT: A 947 SER cc_start: 0.7807 (t) cc_final: 0.7395 (p) REVERT: A 958 LYS cc_start: 0.7774 (tttt) cc_final: 0.7454 (mtmm) REVERT: A 962 TRP cc_start: 0.6759 (p-90) cc_final: 0.6552 (p-90) REVERT: A 1087 GLU cc_start: 0.6682 (tt0) cc_final: 0.6088 (tp30) REVERT: A 1122 GLU cc_start: 0.7348 (mm-30) cc_final: 0.7104 (tp30) REVERT: B 133 MET cc_start: 0.6323 (mmm) cc_final: 0.5871 (mmm) REVERT: B 149 GLU cc_start: 0.7852 (tm-30) cc_final: 0.7526 (tm-30) REVERT: B 155 ASP cc_start: 0.6661 (t70) cc_final: 0.6175 (t70) REVERT: B 160 MET cc_start: 0.7449 (mmt) cc_final: 0.7109 (mmm) REVERT: B 164 SER cc_start: 0.7931 (m) cc_final: 0.7630 (t) REVERT: B 171 LEU cc_start: 0.7596 (mm) cc_final: 0.7360 (mm) REVERT: B 218 LYS cc_start: 0.7554 (mttt) cc_final: 0.7190 (mtpp) REVERT: B 375 LYS cc_start: 0.8163 (mttt) cc_final: 0.7921 (mttp) REVERT: B 380 VAL cc_start: 0.8602 (t) cc_final: 0.8278 (m) REVERT: B 479 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7381 (ttm-80) REVERT: B 483 MET cc_start: 0.8569 (mtp) cc_final: 0.8248 (mtm) REVERT: B 485 ASP cc_start: 0.7997 (m-30) cc_final: 0.7589 (p0) REVERT: B 500 ARG cc_start: 0.7579 (tpp80) cc_final: 0.7201 (ttm-80) REVERT: B 522 ASP cc_start: 0.7530 (t0) cc_final: 0.6852 (t0) REVERT: B 525 ILE cc_start: 0.6987 (mm) cc_final: 0.6581 (mt) REVERT: B 527 THR cc_start: 0.7717 (t) cc_final: 0.7438 (p) REVERT: B 534 ASP cc_start: 0.7346 (p0) cc_final: 0.6895 (p0) REVERT: B 580 GLU cc_start: 0.7800 (mt-10) cc_final: 0.7530 (tp30) REVERT: B 588 LYS cc_start: 0.7558 (ttmt) cc_final: 0.7245 (ttmt) REVERT: B 590 GLU cc_start: 0.7743 (mt-10) cc_final: 0.7375 (mt-10) REVERT: B 599 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7492 (mm-30) REVERT: B 610 LEU cc_start: 0.8060 (mp) cc_final: 0.7644 (tp) REVERT: B 613 GLN cc_start: 0.7644 (tt0) cc_final: 0.7332 (tm-30) REVERT: B 623 ASP cc_start: 0.7939 (t0) cc_final: 0.7711 (t0) REVERT: B 634 SER cc_start: 0.8581 (m) cc_final: 0.8326 (p) REVERT: B 644 LEU cc_start: 0.7837 (mm) cc_final: 0.7594 (mm) REVERT: B 645 LYS cc_start: 0.7973 (tttt) cc_final: 0.7581 (tptt) REVERT: B 847 GLU cc_start: 0.7120 (mm-30) cc_final: 0.6850 (mm-30) REVERT: B 852 LYS cc_start: 0.8243 (mmtm) cc_final: 0.7996 (mmtp) REVERT: B 853 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.7260 (tp) REVERT: B 857 MET cc_start: 0.7343 (ttm) cc_final: 0.6990 (ttm) REVERT: B 860 ASN cc_start: 0.6865 (t0) cc_final: 0.6438 (p0) REVERT: B 862 LYS cc_start: 0.7776 (ttmm) cc_final: 0.7479 (ttpp) REVERT: B 872 GLU cc_start: 0.7115 (tp30) cc_final: 0.6790 (tp30) REVERT: B 887 ARG cc_start: 0.7441 (mmm-85) cc_final: 0.7034 (mmm-85) REVERT: B 929 LYS cc_start: 0.7209 (tttt) cc_final: 0.6962 (ttmt) REVERT: B 938 MET cc_start: 0.7924 (tpp) cc_final: 0.7707 (ttt) REVERT: B 947 SER cc_start: 0.7915 (t) cc_final: 0.7439 (p) REVERT: B 958 LYS cc_start: 0.7905 (tttt) cc_final: 0.7534 (mttp) REVERT: B 989 VAL cc_start: 0.6030 (t) cc_final: 0.5412 (p) REVERT: B 991 GLU cc_start: 0.6134 (mt-10) cc_final: 0.5688 (mm-30) REVERT: B 1003 SER cc_start: 0.6076 (m) cc_final: 0.5815 (t) REVERT: B 1007 LYS cc_start: 0.5708 (tttt) cc_final: 0.5345 (ttmm) REVERT: B 1035 TYR cc_start: 0.7037 (m-80) cc_final: 0.6768 (m-10) REVERT: B 1062 THR cc_start: 0.7126 (m) cc_final: 0.6841 (t) REVERT: B 1068 ILE cc_start: 0.6363 (mp) cc_final: 0.6046 (tt) REVERT: B 1122 GLU cc_start: 0.7535 (tp30) cc_final: 0.7204 (tp30) outliers start: 54 outliers final: 35 residues processed: 438 average time/residue: 0.2938 time to fit residues: 188.6172 Evaluate side-chains 452 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 412 time to evaluate : 1.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1001 ILE Chi-restraints excluded: chain B residue 1058 THR Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1119 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 188 optimal weight: 3.9990 chunk 22 optimal weight: 0.5980 chunk 111 optimal weight: 0.8980 chunk 142 optimal weight: 0.0570 chunk 110 optimal weight: 0.8980 chunk 164 optimal weight: 7.9990 chunk 109 optimal weight: 0.3980 chunk 194 optimal weight: 4.9990 chunk 121 optimal weight: 0.5980 chunk 118 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 overall best weight: 0.5098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1064 GLN B1064 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16438 Z= 0.168 Angle : 0.523 10.978 22304 Z= 0.259 Chirality : 0.039 0.222 2684 Planarity : 0.003 0.041 2738 Dihedral : 8.290 148.976 2194 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.74 % Allowed : 15.81 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.05 (0.19), residues: 2012 helix: 1.85 (0.13), residues: 1472 sheet: 0.66 (0.67), residues: 74 loop : 0.02 (0.30), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP A 962 HIS 0.003 0.000 HIS B 928 PHE 0.022 0.001 PHE B 982 TYR 0.022 0.001 TYR B 309 ARG 0.006 0.000 ARG B 887 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 421 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6430 (mmm) cc_final: 0.5982 (mmm) REVERT: A 149 GLU cc_start: 0.7768 (tm-30) cc_final: 0.7317 (tm-30) REVERT: A 164 SER cc_start: 0.7984 (m) cc_final: 0.7642 (t) REVERT: A 188 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7781 (tt) REVERT: A 209 ASP cc_start: 0.7598 (t0) cc_final: 0.7032 (t70) REVERT: A 256 GLN cc_start: 0.7362 (mp10) cc_final: 0.7063 (mp10) REVERT: A 319 LEU cc_start: 0.8015 (mt) cc_final: 0.7813 (mp) REVERT: A 375 LYS cc_start: 0.8026 (mttt) cc_final: 0.7648 (mtpp) REVERT: A 380 VAL cc_start: 0.8569 (t) cc_final: 0.8287 (m) REVERT: A 483 MET cc_start: 0.8538 (mtp) cc_final: 0.8178 (mtm) REVERT: A 485 ASP cc_start: 0.8116 (m-30) cc_final: 0.7674 (p0) REVERT: A 500 ARG cc_start: 0.7473 (tpp80) cc_final: 0.7130 (tpp80) REVERT: A 527 THR cc_start: 0.7685 (t) cc_final: 0.7403 (p) REVERT: A 531 GLU cc_start: 0.7935 (tt0) cc_final: 0.7234 (tm-30) REVERT: A 534 ASP cc_start: 0.7429 (p0) cc_final: 0.7072 (p0) REVERT: A 599 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7496 (mm-30) REVERT: A 602 MET cc_start: 0.6333 (mmp) cc_final: 0.6053 (mmm) REVERT: A 610 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.7863 (tp) REVERT: A 613 GLN cc_start: 0.7716 (tt0) cc_final: 0.7442 (tm-30) REVERT: A 634 SER cc_start: 0.8462 (m) cc_final: 0.8240 (p) REVERT: A 644 LEU cc_start: 0.7588 (OUTLIER) cc_final: 0.7354 (mm) REVERT: A 647 LYS cc_start: 0.7515 (mmmt) cc_final: 0.7045 (mmtt) REVERT: A 678 MET cc_start: 0.0746 (ppp) cc_final: -0.0115 (ppp) REVERT: A 847 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6599 (mm-30) REVERT: A 857 MET cc_start: 0.7401 (ttm) cc_final: 0.6943 (ttp) REVERT: A 881 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7747 (mm-30) REVERT: A 887 ARG cc_start: 0.7439 (mmm-85) cc_final: 0.7035 (mmm-85) REVERT: A 935 GLU cc_start: 0.7407 (mt-10) cc_final: 0.6928 (tp30) REVERT: A 938 MET cc_start: 0.7815 (tpp) cc_final: 0.7456 (ttt) REVERT: A 947 SER cc_start: 0.7703 (t) cc_final: 0.7458 (p) REVERT: A 954 GLU cc_start: 0.7792 (mp0) cc_final: 0.7391 (pm20) REVERT: A 958 LYS cc_start: 0.7796 (tttt) cc_final: 0.7478 (mtmm) REVERT: A 1122 GLU cc_start: 0.7321 (mm-30) cc_final: 0.7091 (tp30) REVERT: B 133 MET cc_start: 0.6294 (mmm) cc_final: 0.5856 (mmm) REVERT: B 149 GLU cc_start: 0.7868 (tm-30) cc_final: 0.7527 (tm-30) REVERT: B 155 ASP cc_start: 0.6697 (t70) cc_final: 0.6209 (t70) REVERT: B 160 MET cc_start: 0.7414 (mmt) cc_final: 0.7084 (mmm) REVERT: B 164 SER cc_start: 0.7975 (m) cc_final: 0.7673 (t) REVERT: B 171 LEU cc_start: 0.7599 (mm) cc_final: 0.7352 (mm) REVERT: B 199 MET cc_start: 0.8040 (mmm) cc_final: 0.7648 (mmm) REVERT: B 375 LYS cc_start: 0.8094 (mttt) cc_final: 0.7854 (mttp) REVERT: B 380 VAL cc_start: 0.8602 (t) cc_final: 0.8299 (m) REVERT: B 479 ARG cc_start: 0.7643 (ttp-170) cc_final: 0.7387 (ttm-80) REVERT: B 483 MET cc_start: 0.8576 (mtp) cc_final: 0.8247 (mtm) REVERT: B 485 ASP cc_start: 0.8000 (m-30) cc_final: 0.7612 (p0) REVERT: B 500 ARG cc_start: 0.7572 (tpp80) cc_final: 0.7195 (ttm-80) REVERT: B 511 MET cc_start: 0.7108 (tmm) cc_final: 0.6787 (tmm) REVERT: B 522 ASP cc_start: 0.7511 (t0) cc_final: 0.6825 (t0) REVERT: B 525 ILE cc_start: 0.6978 (mm) cc_final: 0.6573 (mt) REVERT: B 527 THR cc_start: 0.7723 (t) cc_final: 0.7442 (p) REVERT: B 534 ASP cc_start: 0.7315 (p0) cc_final: 0.6902 (p0) REVERT: B 580 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7523 (tp30) REVERT: B 588 LYS cc_start: 0.7561 (ttmt) cc_final: 0.7262 (ttmt) REVERT: B 590 GLU cc_start: 0.7725 (mt-10) cc_final: 0.7462 (mt-10) REVERT: B 599 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7504 (mm-30) REVERT: B 606 GLU cc_start: 0.7224 (pm20) cc_final: 0.6910 (pm20) REVERT: B 610 LEU cc_start: 0.8074 (mp) cc_final: 0.7673 (tp) REVERT: B 613 GLN cc_start: 0.7641 (tt0) cc_final: 0.7315 (tm-30) REVERT: B 623 ASP cc_start: 0.7994 (t0) cc_final: 0.7759 (t0) REVERT: B 634 SER cc_start: 0.8575 (m) cc_final: 0.8306 (p) REVERT: B 644 LEU cc_start: 0.7811 (mm) cc_final: 0.7576 (mm) REVERT: B 645 LYS cc_start: 0.7954 (tttt) cc_final: 0.7554 (tptt) REVERT: B 852 LYS cc_start: 0.8232 (mmtm) cc_final: 0.7984 (mmtp) REVERT: B 853 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.7252 (tp) REVERT: B 857 MET cc_start: 0.7334 (ttm) cc_final: 0.6979 (ttm) REVERT: B 872 GLU cc_start: 0.7112 (tp30) cc_final: 0.6800 (tp30) REVERT: B 887 ARG cc_start: 0.7463 (mmm-85) cc_final: 0.7081 (mmm-85) REVERT: B 925 MET cc_start: 0.6505 (tmm) cc_final: 0.6216 (tmm) REVERT: B 929 LYS cc_start: 0.7179 (tttt) cc_final: 0.6927 (ttmt) REVERT: B 938 MET cc_start: 0.7914 (tpp) cc_final: 0.7712 (ttt) REVERT: B 947 SER cc_start: 0.7816 (t) cc_final: 0.7393 (p) REVERT: B 958 LYS cc_start: 0.7871 (tttt) cc_final: 0.7525 (mttp) REVERT: B 989 VAL cc_start: 0.5970 (t) cc_final: 0.5352 (p) REVERT: B 991 GLU cc_start: 0.6199 (mt-10) cc_final: 0.5763 (mm-30) REVERT: B 1003 SER cc_start: 0.6091 (m) cc_final: 0.5832 (t) REVERT: B 1007 LYS cc_start: 0.5718 (tttt) cc_final: 0.5353 (ttmm) REVERT: B 1035 TYR cc_start: 0.7042 (m-80) cc_final: 0.6788 (m-10) REVERT: B 1062 THR cc_start: 0.7130 (m) cc_final: 0.6911 (t) REVERT: B 1068 ILE cc_start: 0.6347 (mp) cc_final: 0.6051 (tt) REVERT: B 1122 GLU cc_start: 0.7540 (tp30) cc_final: 0.7204 (tp30) REVERT: B 1144 ASP cc_start: 0.6184 (OUTLIER) cc_final: 0.5965 (t0) outliers start: 48 outliers final: 36 residues processed: 435 average time/residue: 0.2935 time to fit residues: 186.3391 Evaluate side-chains 447 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 406 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 885 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1071 GLU Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 853 ILE Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1001 ILE Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1144 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 120 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 116 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 132 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 18 optimal weight: 1.9990 chunk 153 optimal weight: 0.0040 overall best weight: 0.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 ASN B 860 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6876 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 16438 Z= 0.213 Angle : 0.535 8.960 22304 Z= 0.268 Chirality : 0.040 0.245 2684 Planarity : 0.003 0.041 2738 Dihedral : 8.297 149.121 2194 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.48 % Allowed : 15.87 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.98 (0.19), residues: 2012 helix: 1.79 (0.13), residues: 1470 sheet: 0.67 (0.67), residues: 74 loop : 0.02 (0.30), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP A 962 HIS 0.002 0.000 HIS B 928 PHE 0.023 0.001 PHE B 982 TYR 0.023 0.001 TYR A 309 ARG 0.006 0.000 ARG A1089 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 420 time to evaluate : 1.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6436 (mmm) cc_final: 0.5991 (mmm) REVERT: A 149 GLU cc_start: 0.7780 (tm-30) cc_final: 0.7356 (tm-30) REVERT: A 164 SER cc_start: 0.7987 (m) cc_final: 0.7640 (t) REVERT: A 188 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7815 (tt) REVERT: A 209 ASP cc_start: 0.7601 (t0) cc_final: 0.7046 (t70) REVERT: A 254 PHE cc_start: 0.7994 (m-10) cc_final: 0.7787 (m-10) REVERT: A 256 GLN cc_start: 0.7428 (mp10) cc_final: 0.7130 (mp10) REVERT: A 319 LEU cc_start: 0.8020 (mt) cc_final: 0.7815 (mp) REVERT: A 375 LYS cc_start: 0.7995 (mttt) cc_final: 0.7633 (mtpp) REVERT: A 380 VAL cc_start: 0.8573 (t) cc_final: 0.8287 (m) REVERT: A 418 THR cc_start: 0.7431 (m) cc_final: 0.6753 (p) REVERT: A 483 MET cc_start: 0.8536 (mtp) cc_final: 0.8187 (mtm) REVERT: A 485 ASP cc_start: 0.8110 (m-30) cc_final: 0.7683 (p0) REVERT: A 500 ARG cc_start: 0.7472 (tpp80) cc_final: 0.7131 (ttp80) REVERT: A 515 ASP cc_start: 0.7736 (t70) cc_final: 0.7338 (t70) REVERT: A 527 THR cc_start: 0.7637 (t) cc_final: 0.7347 (p) REVERT: A 531 GLU cc_start: 0.7949 (tt0) cc_final: 0.7316 (tm-30) REVERT: A 534 ASP cc_start: 0.7492 (p0) cc_final: 0.7151 (p0) REVERT: A 599 GLU cc_start: 0.7777 (mm-30) cc_final: 0.7527 (mm-30) REVERT: A 602 MET cc_start: 0.6396 (mmp) cc_final: 0.6095 (mmm) REVERT: A 610 LEU cc_start: 0.8455 (OUTLIER) cc_final: 0.7893 (tp) REVERT: A 613 GLN cc_start: 0.7718 (tt0) cc_final: 0.7444 (tm-30) REVERT: A 634 SER cc_start: 0.8499 (m) cc_final: 0.8251 (p) REVERT: A 644 LEU cc_start: 0.7579 (OUTLIER) cc_final: 0.7351 (mm) REVERT: A 647 LYS cc_start: 0.7521 (mmmt) cc_final: 0.7054 (mmtt) REVERT: A 678 MET cc_start: 0.0755 (ppp) cc_final: -0.0032 (ppp) REVERT: A 828 LYS cc_start: 0.7211 (mmtt) cc_final: 0.6857 (mmtt) REVERT: A 857 MET cc_start: 0.7426 (ttm) cc_final: 0.7068 (ttp) REVERT: A 877 GLN cc_start: 0.7302 (mt0) cc_final: 0.6390 (tt0) REVERT: A 887 ARG cc_start: 0.7444 (mmm-85) cc_final: 0.6990 (mmm-85) REVERT: A 935 GLU cc_start: 0.7395 (OUTLIER) cc_final: 0.6906 (tp30) REVERT: A 938 MET cc_start: 0.7806 (tpp) cc_final: 0.7453 (ttt) REVERT: A 947 SER cc_start: 0.7814 (t) cc_final: 0.7478 (p) REVERT: A 954 GLU cc_start: 0.7795 (mp0) cc_final: 0.7371 (pm20) REVERT: A 958 LYS cc_start: 0.7713 (tttt) cc_final: 0.7390 (mtmm) REVERT: A 1122 GLU cc_start: 0.7341 (mm-30) cc_final: 0.7096 (tp30) REVERT: B 133 MET cc_start: 0.6307 (mmm) cc_final: 0.5882 (mmm) REVERT: B 149 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7545 (tm-30) REVERT: B 160 MET cc_start: 0.7474 (mmt) cc_final: 0.7140 (mmm) REVERT: B 164 SER cc_start: 0.7984 (m) cc_final: 0.7651 (p) REVERT: B 171 LEU cc_start: 0.7700 (mm) cc_final: 0.7460 (mm) REVERT: B 218 LYS cc_start: 0.7572 (mttt) cc_final: 0.7203 (mtpp) REVERT: B 375 LYS cc_start: 0.8019 (mttt) cc_final: 0.7599 (mtpp) REVERT: B 380 VAL cc_start: 0.8611 (t) cc_final: 0.8309 (m) REVERT: B 479 ARG cc_start: 0.7644 (ttp-170) cc_final: 0.7405 (ttm-80) REVERT: B 483 MET cc_start: 0.8561 (mtp) cc_final: 0.8242 (mtm) REVERT: B 485 ASP cc_start: 0.8005 (m-30) cc_final: 0.7641 (p0) REVERT: B 500 ARG cc_start: 0.7583 (tpp80) cc_final: 0.7124 (tpp80) REVERT: B 511 MET cc_start: 0.7126 (tmm) cc_final: 0.6782 (tmm) REVERT: B 516 ARG cc_start: 0.8230 (ptm160) cc_final: 0.8025 (ptm160) REVERT: B 522 ASP cc_start: 0.7484 (t0) cc_final: 0.6780 (t0) REVERT: B 525 ILE cc_start: 0.6999 (mm) cc_final: 0.6589 (mt) REVERT: B 527 THR cc_start: 0.7739 (t) cc_final: 0.7448 (p) REVERT: B 534 ASP cc_start: 0.7476 (p0) cc_final: 0.6998 (p0) REVERT: B 580 GLU cc_start: 0.7799 (mt-10) cc_final: 0.7533 (tp30) REVERT: B 588 LYS cc_start: 0.7562 (ttmt) cc_final: 0.7252 (ttmt) REVERT: B 590 GLU cc_start: 0.7741 (mt-10) cc_final: 0.7298 (mt-10) REVERT: B 599 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7483 (mm-30) REVERT: B 606 GLU cc_start: 0.7209 (pm20) cc_final: 0.6927 (pm20) REVERT: B 610 LEU cc_start: 0.8078 (mp) cc_final: 0.7674 (tp) REVERT: B 613 GLN cc_start: 0.7649 (tt0) cc_final: 0.7290 (tm-30) REVERT: B 623 ASP cc_start: 0.8011 (t0) cc_final: 0.7780 (t0) REVERT: B 634 SER cc_start: 0.8591 (m) cc_final: 0.8301 (p) REVERT: B 644 LEU cc_start: 0.7805 (mm) cc_final: 0.7578 (mm) REVERT: B 645 LYS cc_start: 0.7949 (tttt) cc_final: 0.7529 (tttt) REVERT: B 676 HIS cc_start: 0.4262 (OUTLIER) cc_final: 0.3502 (m90) REVERT: B 847 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6897 (mm-30) REVERT: B 852 LYS cc_start: 0.8228 (mmtm) cc_final: 0.7970 (mmtp) REVERT: B 857 MET cc_start: 0.7372 (ttm) cc_final: 0.6982 (ttm) REVERT: B 872 GLU cc_start: 0.7141 (tp30) cc_final: 0.6824 (tp30) REVERT: B 887 ARG cc_start: 0.7484 (mmm-85) cc_final: 0.7080 (mmm-85) REVERT: B 929 LYS cc_start: 0.7237 (tttt) cc_final: 0.6992 (ttmt) REVERT: B 938 MET cc_start: 0.7928 (tpp) cc_final: 0.7710 (ttt) REVERT: B 947 SER cc_start: 0.7801 (t) cc_final: 0.7385 (p) REVERT: B 958 LYS cc_start: 0.7828 (tttt) cc_final: 0.7481 (mttp) REVERT: B 989 VAL cc_start: 0.5852 (t) cc_final: 0.5235 (p) REVERT: B 991 GLU cc_start: 0.6197 (mt-10) cc_final: 0.5754 (mm-30) REVERT: B 1003 SER cc_start: 0.6108 (m) cc_final: 0.5841 (t) REVERT: B 1007 LYS cc_start: 0.5716 (tttt) cc_final: 0.5334 (ttmm) REVERT: B 1035 TYR cc_start: 0.7060 (m-80) cc_final: 0.6808 (m-10) REVERT: B 1062 THR cc_start: 0.7211 (m) cc_final: 0.6963 (t) REVERT: B 1068 ILE cc_start: 0.6230 (mp) cc_final: 0.5927 (tt) REVERT: B 1122 GLU cc_start: 0.7588 (tp30) cc_final: 0.7249 (tp30) REVERT: B 1144 ASP cc_start: 0.6111 (OUTLIER) cc_final: 0.5891 (t0) outliers start: 61 outliers final: 41 residues processed: 438 average time/residue: 0.2918 time to fit residues: 187.1292 Evaluate side-chains 453 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 406 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 271 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 448 ASN Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 935 GLU Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 113 LEU Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 271 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 381 ASP Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 448 ASN Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 876 LEU Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 988 ILE Chi-restraints excluded: chain B residue 998 LEU Chi-restraints excluded: chain B residue 1001 ILE Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1144 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 177 optimal weight: 0.4980 chunk 186 optimal weight: 0.8980 chunk 170 optimal weight: 1.9990 chunk 181 optimal weight: 0.9980 chunk 109 optimal weight: 0.5980 chunk 79 optimal weight: 0.0000 chunk 142 optimal weight: 0.0030 chunk 55 optimal weight: 1.9990 chunk 163 optimal weight: 0.7980 chunk 171 optimal weight: 4.9990 chunk 180 optimal weight: 0.0000 overall best weight: 0.2198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6847 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16438 Z= 0.139 Angle : 0.525 10.193 22304 Z= 0.257 Chirality : 0.038 0.215 2684 Planarity : 0.003 0.041 2738 Dihedral : 8.272 149.500 2194 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.45 % Allowed : 17.07 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.19 (0.19), residues: 2012 helix: 1.95 (0.13), residues: 1468 sheet: 1.30 (0.69), residues: 64 loop : -0.00 (0.29), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 278 HIS 0.003 0.000 HIS B 928 PHE 0.020 0.001 PHE B 982 TYR 0.020 0.001 TYR A 309 ARG 0.006 0.000 ARG A1089 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 422 time to evaluate : 1.872 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6399 (mmm) cc_final: 0.5965 (mmm) REVERT: A 149 GLU cc_start: 0.7778 (tm-30) cc_final: 0.7313 (tm-30) REVERT: A 164 SER cc_start: 0.8067 (m) cc_final: 0.7733 (t) REVERT: A 188 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7843 (tt) REVERT: A 254 PHE cc_start: 0.7961 (m-10) cc_final: 0.7759 (m-10) REVERT: A 256 GLN cc_start: 0.7404 (mp10) cc_final: 0.7108 (mp10) REVERT: A 319 LEU cc_start: 0.8000 (mt) cc_final: 0.7794 (mp) REVERT: A 375 LYS cc_start: 0.7953 (mttt) cc_final: 0.7582 (mtpp) REVERT: A 380 VAL cc_start: 0.8567 (t) cc_final: 0.8289 (m) REVERT: A 483 MET cc_start: 0.8503 (mtp) cc_final: 0.8180 (mtm) REVERT: A 485 ASP cc_start: 0.8103 (m-30) cc_final: 0.7738 (p0) REVERT: A 500 ARG cc_start: 0.7464 (tpp80) cc_final: 0.7119 (ttp80) REVERT: A 515 ASP cc_start: 0.7648 (t70) cc_final: 0.7430 (t70) REVERT: A 527 THR cc_start: 0.7669 (t) cc_final: 0.7391 (p) REVERT: A 531 GLU cc_start: 0.7926 (tt0) cc_final: 0.7359 (tm-30) REVERT: A 534 ASP cc_start: 0.7448 (p0) cc_final: 0.7106 (p0) REVERT: A 599 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7490 (mm-30) REVERT: A 602 MET cc_start: 0.6437 (mmp) cc_final: 0.6133 (mmm) REVERT: A 610 LEU cc_start: 0.8415 (OUTLIER) cc_final: 0.7936 (tp) REVERT: A 613 GLN cc_start: 0.7703 (tt0) cc_final: 0.7424 (tm-30) REVERT: A 634 SER cc_start: 0.8455 (m) cc_final: 0.8225 (p) REVERT: A 644 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7298 (mm) REVERT: A 645 LYS cc_start: 0.7557 (tttt) cc_final: 0.7041 (tttp) REVERT: A 647 LYS cc_start: 0.7499 (mmmt) cc_final: 0.7062 (mmtt) REVERT: A 678 MET cc_start: 0.0701 (ppp) cc_final: -0.0073 (ppp) REVERT: A 847 GLU cc_start: 0.6965 (mm-30) cc_final: 0.6727 (mm-30) REVERT: A 857 MET cc_start: 0.7200 (ttm) cc_final: 0.6884 (ttm) REVERT: A 860 ASN cc_start: 0.6783 (t0) cc_final: 0.6498 (p0) REVERT: A 877 GLN cc_start: 0.6962 (mt0) cc_final: 0.6446 (tt0) REVERT: A 887 ARG cc_start: 0.7391 (mmm-85) cc_final: 0.6923 (mmm-85) REVERT: A 935 GLU cc_start: 0.7455 (mt-10) cc_final: 0.7222 (mt-10) REVERT: A 938 MET cc_start: 0.7898 (tpp) cc_final: 0.7539 (ttt) REVERT: A 954 GLU cc_start: 0.7844 (mp0) cc_final: 0.7400 (pm20) REVERT: A 958 LYS cc_start: 0.7639 (tttt) cc_final: 0.7321 (ptpp) REVERT: A 1122 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7130 (tp30) REVERT: B 133 MET cc_start: 0.6295 (mmm) cc_final: 0.5885 (mmm) REVERT: B 149 GLU cc_start: 0.7878 (tm-30) cc_final: 0.7521 (tm-30) REVERT: B 160 MET cc_start: 0.7458 (mmt) cc_final: 0.7198 (mmm) REVERT: B 164 SER cc_start: 0.7948 (m) cc_final: 0.7619 (t) REVERT: B 171 LEU cc_start: 0.7580 (mm) cc_final: 0.7347 (mm) REVERT: B 256 GLN cc_start: 0.6924 (mp10) cc_final: 0.6650 (mp10) REVERT: B 375 LYS cc_start: 0.7979 (mttt) cc_final: 0.7578 (mtpp) REVERT: B 380 VAL cc_start: 0.8601 (t) cc_final: 0.8283 (m) REVERT: B 479 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.7419 (ttm-80) REVERT: B 485 ASP cc_start: 0.7994 (m-30) cc_final: 0.7650 (p0) REVERT: B 500 ARG cc_start: 0.7564 (tpp80) cc_final: 0.7187 (ttm-80) REVERT: B 511 MET cc_start: 0.7131 (tmm) cc_final: 0.6769 (tmm) REVERT: B 516 ARG cc_start: 0.8178 (ptm160) cc_final: 0.7796 (ptt90) REVERT: B 527 THR cc_start: 0.7699 (t) cc_final: 0.7438 (p) REVERT: B 534 ASP cc_start: 0.7447 (p0) cc_final: 0.6960 (p0) REVERT: B 580 GLU cc_start: 0.7794 (mt-10) cc_final: 0.7526 (tp30) REVERT: B 588 LYS cc_start: 0.7521 (ttmt) cc_final: 0.7220 (ttmt) REVERT: B 590 GLU cc_start: 0.7745 (mt-10) cc_final: 0.7401 (mt-10) REVERT: B 599 GLU cc_start: 0.7652 (mm-30) cc_final: 0.7440 (mm-30) REVERT: B 606 GLU cc_start: 0.7212 (pm20) cc_final: 0.6936 (pm20) REVERT: B 610 LEU cc_start: 0.8067 (mp) cc_final: 0.7702 (tt) REVERT: B 613 GLN cc_start: 0.7619 (tt0) cc_final: 0.7267 (tm-30) REVERT: B 623 ASP cc_start: 0.8013 (t0) cc_final: 0.7788 (t0) REVERT: B 634 SER cc_start: 0.8560 (m) cc_final: 0.8287 (p) REVERT: B 644 LEU cc_start: 0.7765 (mm) cc_final: 0.7520 (mm) REVERT: B 645 LYS cc_start: 0.7885 (tttt) cc_final: 0.7494 (tptt) REVERT: B 676 HIS cc_start: 0.4127 (OUTLIER) cc_final: 0.3374 (m90) REVERT: B 847 GLU cc_start: 0.7265 (mm-30) cc_final: 0.6898 (mm-30) REVERT: B 852 LYS cc_start: 0.8108 (mmtm) cc_final: 0.7844 (mmtp) REVERT: B 857 MET cc_start: 0.7383 (ttm) cc_final: 0.6984 (ttm) REVERT: B 872 GLU cc_start: 0.7161 (tp30) cc_final: 0.6798 (tp30) REVERT: B 887 ARG cc_start: 0.7440 (mmm-85) cc_final: 0.7025 (mmm-85) REVERT: B 926 GLU cc_start: 0.7169 (mm-30) cc_final: 0.6828 (mm-30) REVERT: B 929 LYS cc_start: 0.7210 (tttt) cc_final: 0.6953 (ttmt) REVERT: B 947 SER cc_start: 0.7851 (t) cc_final: 0.7405 (p) REVERT: B 958 LYS cc_start: 0.7766 (tttt) cc_final: 0.7427 (mttm) REVERT: B 989 VAL cc_start: 0.5764 (t) cc_final: 0.5144 (p) REVERT: B 991 GLU cc_start: 0.6286 (mt-10) cc_final: 0.5833 (mm-30) REVERT: B 1003 SER cc_start: 0.6168 (m) cc_final: 0.5868 (t) REVERT: B 1007 LYS cc_start: 0.5751 (tttt) cc_final: 0.5365 (ttmm) REVERT: B 1035 TYR cc_start: 0.7026 (m-80) cc_final: 0.6775 (m-10) REVERT: B 1062 THR cc_start: 0.7180 (m) cc_final: 0.6948 (t) REVERT: B 1068 ILE cc_start: 0.6304 (mp) cc_final: 0.6009 (tt) REVERT: B 1122 GLU cc_start: 0.7547 (tp30) cc_final: 0.7194 (tp30) REVERT: B 1144 ASP cc_start: 0.6117 (OUTLIER) cc_final: 0.5892 (t0) outliers start: 43 outliers final: 27 residues processed: 436 average time/residue: 0.2971 time to fit residues: 191.5897 Evaluate side-chains 439 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 407 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1001 ILE Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1144 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 119 optimal weight: 0.9980 chunk 191 optimal weight: 0.3980 chunk 117 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 133 optimal weight: 1.9990 chunk 201 optimal weight: 20.0000 chunk 185 optimal weight: 1.9990 chunk 160 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 98 optimal weight: 0.0470 overall best weight: 0.5878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1054 ASN B 510 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6865 moved from start: 0.3414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16438 Z= 0.181 Angle : 0.544 9.729 22304 Z= 0.265 Chirality : 0.039 0.239 2684 Planarity : 0.003 0.050 2738 Dihedral : 8.265 149.372 2194 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.17 % Allowed : 17.98 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.15 (0.19), residues: 2012 helix: 1.93 (0.13), residues: 1468 sheet: 0.70 (0.67), residues: 74 loop : 0.05 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 278 HIS 0.002 0.000 HIS B 928 PHE 0.022 0.001 PHE B 982 TYR 0.021 0.001 TYR B 309 ARG 0.005 0.000 ARG B1089 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 418 time to evaluate : 1.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 133 MET cc_start: 0.6413 (mmm) cc_final: 0.5992 (mmm) REVERT: A 149 GLU cc_start: 0.7769 (tm-30) cc_final: 0.7318 (tm-30) REVERT: A 164 SER cc_start: 0.7962 (m) cc_final: 0.7658 (t) REVERT: A 188 LEU cc_start: 0.8079 (OUTLIER) cc_final: 0.7815 (tt) REVERT: A 205 MET cc_start: 0.7993 (tpp) cc_final: 0.7539 (mmm) REVERT: A 254 PHE cc_start: 0.7974 (m-10) cc_final: 0.7740 (m-10) REVERT: A 256 GLN cc_start: 0.7432 (mp10) cc_final: 0.7134 (mp10) REVERT: A 319 LEU cc_start: 0.8017 (mt) cc_final: 0.7813 (mp) REVERT: A 375 LYS cc_start: 0.7875 (mttt) cc_final: 0.7548 (mtpp) REVERT: A 380 VAL cc_start: 0.8545 (t) cc_final: 0.8265 (m) REVERT: A 483 MET cc_start: 0.8485 (mtp) cc_final: 0.8171 (mtm) REVERT: A 485 ASP cc_start: 0.8117 (m-30) cc_final: 0.7739 (p0) REVERT: A 500 ARG cc_start: 0.7470 (tpp80) cc_final: 0.7126 (ttp80) REVERT: A 515 ASP cc_start: 0.7689 (t70) cc_final: 0.7471 (t70) REVERT: A 527 THR cc_start: 0.7681 (t) cc_final: 0.7384 (p) REVERT: A 531 GLU cc_start: 0.7936 (tt0) cc_final: 0.7309 (tm-30) REVERT: A 534 ASP cc_start: 0.7477 (p0) cc_final: 0.7073 (p0) REVERT: A 599 GLU cc_start: 0.7758 (mm-30) cc_final: 0.7506 (mm-30) REVERT: A 610 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7948 (tp) REVERT: A 613 GLN cc_start: 0.7750 (tt0) cc_final: 0.7468 (tm-30) REVERT: A 634 SER cc_start: 0.8438 (m) cc_final: 0.8221 (p) REVERT: A 644 LEU cc_start: 0.7537 (OUTLIER) cc_final: 0.7302 (mm) REVERT: A 645 LYS cc_start: 0.7533 (tttt) cc_final: 0.7072 (tttp) REVERT: A 647 LYS cc_start: 0.7553 (mmmt) cc_final: 0.7112 (mmtt) REVERT: A 678 MET cc_start: 0.0848 (ppp) cc_final: 0.0084 (ppp) REVERT: A 823 LEU cc_start: 0.7301 (mm) cc_final: 0.7082 (mp) REVERT: A 847 GLU cc_start: 0.6980 (mm-30) cc_final: 0.6719 (mm-30) REVERT: A 857 MET cc_start: 0.7210 (ttm) cc_final: 0.6848 (ttm) REVERT: A 877 GLN cc_start: 0.7004 (mt0) cc_final: 0.6462 (tt0) REVERT: A 887 ARG cc_start: 0.7404 (mmm-85) cc_final: 0.6935 (mmm-85) REVERT: A 935 GLU cc_start: 0.7443 (mt-10) cc_final: 0.7212 (mt-10) REVERT: A 938 MET cc_start: 0.7811 (tpp) cc_final: 0.7459 (ttt) REVERT: A 954 GLU cc_start: 0.7843 (mp0) cc_final: 0.7391 (pm20) REVERT: A 958 LYS cc_start: 0.7655 (tttt) cc_final: 0.7337 (ptpp) REVERT: A 1122 GLU cc_start: 0.7332 (mm-30) cc_final: 0.7089 (tp30) REVERT: B 133 MET cc_start: 0.6316 (mmm) cc_final: 0.5900 (mmm) REVERT: B 149 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7535 (tm-30) REVERT: B 160 MET cc_start: 0.7503 (mmt) cc_final: 0.7166 (mmm) REVERT: B 164 SER cc_start: 0.7949 (m) cc_final: 0.7627 (p) REVERT: B 171 LEU cc_start: 0.7607 (mm) cc_final: 0.7362 (mm) REVERT: B 218 LYS cc_start: 0.7573 (mttt) cc_final: 0.7205 (mtpp) REVERT: B 256 GLN cc_start: 0.6922 (mp10) cc_final: 0.6657 (mp10) REVERT: B 375 LYS cc_start: 0.8000 (mttt) cc_final: 0.7594 (mtpp) REVERT: B 380 VAL cc_start: 0.8601 (t) cc_final: 0.8305 (m) REVERT: B 479 ARG cc_start: 0.7627 (ttp-170) cc_final: 0.7394 (ttm-80) REVERT: B 485 ASP cc_start: 0.7989 (m-30) cc_final: 0.7656 (p0) REVERT: B 500 ARG cc_start: 0.7573 (tpp80) cc_final: 0.7191 (ttm-80) REVERT: B 511 MET cc_start: 0.7146 (tmm) cc_final: 0.6783 (tmm) REVERT: B 527 THR cc_start: 0.7759 (t) cc_final: 0.7464 (p) REVERT: B 531 GLU cc_start: 0.7835 (tt0) cc_final: 0.7404 (tp30) REVERT: B 534 ASP cc_start: 0.7490 (p0) cc_final: 0.7068 (p0) REVERT: B 580 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7516 (tp30) REVERT: B 588 LYS cc_start: 0.7552 (ttmt) cc_final: 0.7239 (ttmt) REVERT: B 590 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7319 (mt-10) REVERT: B 599 GLU cc_start: 0.7713 (mm-30) cc_final: 0.7447 (mm-30) REVERT: B 606 GLU cc_start: 0.7196 (pm20) cc_final: 0.6920 (pm20) REVERT: B 623 ASP cc_start: 0.7972 (t0) cc_final: 0.7758 (t0) REVERT: B 634 SER cc_start: 0.8587 (m) cc_final: 0.8294 (p) REVERT: B 644 LEU cc_start: 0.7764 (mm) cc_final: 0.7523 (mm) REVERT: B 645 LYS cc_start: 0.7941 (tttt) cc_final: 0.7542 (tptt) REVERT: B 676 HIS cc_start: 0.4272 (OUTLIER) cc_final: 0.3518 (m90) REVERT: B 847 GLU cc_start: 0.7315 (mm-30) cc_final: 0.6930 (mm-30) REVERT: B 852 LYS cc_start: 0.8192 (mmtm) cc_final: 0.7929 (mmtp) REVERT: B 857 MET cc_start: 0.7425 (ttm) cc_final: 0.7024 (ttm) REVERT: B 872 GLU cc_start: 0.7090 (tp30) cc_final: 0.6788 (tp30) REVERT: B 887 ARG cc_start: 0.7458 (mmm-85) cc_final: 0.7037 (mmm-85) REVERT: B 929 LYS cc_start: 0.7216 (tttt) cc_final: 0.7002 (ttmt) REVERT: B 947 SER cc_start: 0.7813 (t) cc_final: 0.7388 (p) REVERT: B 958 LYS cc_start: 0.7804 (tttt) cc_final: 0.7469 (mttm) REVERT: B 989 VAL cc_start: 0.5770 (t) cc_final: 0.5126 (p) REVERT: B 991 GLU cc_start: 0.6287 (mt-10) cc_final: 0.5826 (mm-30) REVERT: B 1003 SER cc_start: 0.6178 (m) cc_final: 0.5887 (t) REVERT: B 1007 LYS cc_start: 0.5722 (tttt) cc_final: 0.5338 (ttmm) REVERT: B 1035 TYR cc_start: 0.7071 (m-80) cc_final: 0.6812 (m-10) REVERT: B 1062 THR cc_start: 0.7188 (m) cc_final: 0.6927 (t) REVERT: B 1068 ILE cc_start: 0.6320 (mp) cc_final: 0.6026 (tt) REVERT: B 1122 GLU cc_start: 0.7553 (tp30) cc_final: 0.7212 (tp30) REVERT: B 1144 ASP cc_start: 0.6095 (OUTLIER) cc_final: 0.5874 (t0) outliers start: 38 outliers final: 29 residues processed: 425 average time/residue: 0.2877 time to fit residues: 180.3349 Evaluate side-chains 445 residues out of total 1752 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 411 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 ASP Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 265 VAL Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 401 MET Chi-restraints excluded: chain A residue 419 TRP Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 837 TYR Chi-restraints excluded: chain A residue 876 LEU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 932 LEU Chi-restraints excluded: chain A residue 960 VAL Chi-restraints excluded: chain A residue 967 MET Chi-restraints excluded: chain A residue 998 LEU Chi-restraints excluded: chain A residue 1001 ILE Chi-restraints excluded: chain A residue 1066 TYR Chi-restraints excluded: chain A residue 1102 LEU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 90 ILE Chi-restraints excluded: chain B residue 134 ASP Chi-restraints excluded: chain B residue 265 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 378 VAL Chi-restraints excluded: chain B residue 419 TRP Chi-restraints excluded: chain B residue 449 ASP Chi-restraints excluded: chain B residue 676 HIS Chi-restraints excluded: chain B residue 837 TYR Chi-restraints excluded: chain B residue 932 LEU Chi-restraints excluded: chain B residue 1001 ILE Chi-restraints excluded: chain B residue 1066 TYR Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1144 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 202 random chunks: chunk 127 optimal weight: 0.8980 chunk 170 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 147 optimal weight: 0.1980 chunk 23 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 160 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 164 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 917 GLN A1054 ASN B 510 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.183154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.152317 restraints weight = 23219.631| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 2.37 r_work: 0.3615 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.3482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16438 Z= 0.186 Angle : 0.548 9.857 22304 Z= 0.267 Chirality : 0.040 0.253 2684 Planarity : 0.003 0.041 2738 Dihedral : 8.281 149.768 2194 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.23 % Allowed : 17.98 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.10 (0.19), residues: 2012 helix: 1.88 (0.13), residues: 1472 sheet: 0.48 (0.64), residues: 78 loop : 0.06 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 278 HIS 0.002 0.000 HIS B 928 PHE 0.025 0.001 PHE A 982 TYR 0.021 0.001 TYR B 309 ARG 0.005 0.000 ARG B1089 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4508.46 seconds wall clock time: 82 minutes 20.78 seconds (4940.78 seconds total)