Starting phenix.real_space_refine on Tue Apr 9 15:14:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otq_17182/04_2024/8otq_17182_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otq_17182/04_2024/8otq_17182.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otq_17182/04_2024/8otq_17182.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otq_17182/04_2024/8otq_17182.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otq_17182/04_2024/8otq_17182_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8otq_17182/04_2024/8otq_17182_updated.pdb" } resolution = 3.22 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.014 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 86 5.16 5 C 10942 2.51 5 N 2754 2.21 5 O 2932 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 337": "OE1" <-> "OE2" Residue "A GLU 346": "OE1" <-> "OE2" Residue "A ARG 500": "NH1" <-> "NH2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 616": "OE1" <-> "OE2" Residue "A GLU 782": "OE1" <-> "OE2" Residue "A GLU 849": "OE1" <-> "OE2" Residue "A TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1071": "OE1" <-> "OE2" Residue "B GLU 337": "OE1" <-> "OE2" Residue "B GLU 346": "OE1" <-> "OE2" Residue "B ARG 500": "NH1" <-> "NH2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B GLU 616": "OE1" <-> "OE2" Residue "B GLU 782": "OE1" <-> "OE2" Residue "B GLU 849": "OE1" <-> "OE2" Residue "B TYR 1009": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1071": "OE1" <-> "OE2" Residue "B GLU 1160": "OE1" <-> "OE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 16716 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8297 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 30, 'TRANS': 1020} Chain breaks: 3 Chain: "B" Number of atoms: 8297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1051, 8297 Classifications: {'peptide': 1051} Link IDs: {'PTRANS': 30, 'TRANS': 1020} Chain breaks: 3 Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'CPL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 61 Unusual residues: {'CPL': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Time building chain proxies: 8.84, per 1000 atoms: 0.53 Number of scatterers: 16716 At special positions: 0 Unit cell: (153.107, 105.074, 126.088, 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 86 16.00 P 2 15.00 O 2932 8.00 N 2754 7.00 C 10942 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 7.26 Conformation dependent library (CDL) restraints added in 3.1 seconds 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3964 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 78 helices and 7 sheets defined 65.0% alpha, 3.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.10 Creating SS restraints... Processing helix chain 'A' and resid 78 through 94 Processing helix chain 'A' and resid 102 through 119 Processing helix chain 'A' and resid 121 through 131 removed outlier: 3.832A pdb=" N HIS A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N VAL A 130 " --> pdb=" O HIS A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 removed outlier: 3.526A pdb=" N LEU A 139 " --> pdb=" O PRO A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 152 Processing helix chain 'A' and resid 156 through 188 removed outlier: 5.810A pdb=" N SER A 164 " --> pdb=" O MET A 160 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N GLN A 165 " --> pdb=" O ARG A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 195 through 206 Processing helix chain 'A' and resid 211 through 220 Processing helix chain 'A' and resid 224 through 253 Processing helix chain 'A' and resid 261 through 292 removed outlier: 3.561A pdb=" N LEU A 266 " --> pdb=" O GLY A 262 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ALA A 274 " --> pdb=" O GLN A 270 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY A 275 " --> pdb=" O VAL A 271 " (cutoff:3.500A) Proline residue: A 276 - end of helix removed outlier: 4.396A pdb=" N HIS A 292 " --> pdb=" O PHE A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 297 through 316 Processing helix chain 'A' and resid 324 through 336 Processing helix chain 'A' and resid 345 through 378 removed outlier: 4.136A pdb=" N LEU A 377 " --> pdb=" O THR A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 406 removed outlier: 4.491A pdb=" N PHE A 386 " --> pdb=" O LYS A 382 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N TYR A 387 " --> pdb=" O MET A 383 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE A 390 " --> pdb=" O PHE A 386 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG A 399 " --> pdb=" O ILE A 395 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY A 400 " --> pdb=" O THR A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 427 Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 453 through 480 removed outlier: 3.826A pdb=" N ALA A 471 " --> pdb=" O LEU A 467 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR A 472 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN A 475 " --> pdb=" O ALA A 471 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N THR A 476 " --> pdb=" O THR A 472 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 514 removed outlier: 3.723A pdb=" N SER A 514 " --> pdb=" O ASN A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 528 No H-bonds generated for 'chain 'A' and resid 525 through 528' Processing helix chain 'A' and resid 576 through 600 Processing helix chain 'A' and resid 606 through 620 Processing helix chain 'A' and resid 635 through 638 No H-bonds generated for 'chain 'A' and resid 635 through 638' Processing helix chain 'A' and resid 643 through 653 Processing helix chain 'A' and resid 669 through 676 Processing helix chain 'A' and resid 678 through 702 removed outlier: 4.223A 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 724 through 751 removed outlier: 3.590A pdb=" N ARG A 733 " --> pdb=" O GLU A 729 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE A 734 " --> pdb=" O ASP A 730 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL A 741 " --> pdb=" O TYR A 737 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 760 removed outlier: 3.592A pdb=" N TYR A 758 " --> pdb=" O GLY A 755 " (cutoff:3.500A) Processing helix chain 'A' and resid 764 through 776 removed outlier: 3.519A pdb=" N ILE A 770 " --> pdb=" O ASP A 767 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LEU A 775 " --> pdb=" O VAL A 772 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 857 removed outlier: 3.533A pdb=" N THR A 814 " --> pdb=" O LEU A 811 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS A 815 " --> pdb=" O ARG A 812 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ILE A 818 " --> pdb=" O LYS A 815 " (cutoff:3.500A) Proline residue: A 819 - end of helix removed outlier: 3.519A pdb=" N GLU A 849 " --> pdb=" O GLY A 846 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A 855 " --> pdb=" O LYS A 852 " (cutoff:3.500A) Processing helix chain 'A' and resid 862 through 888 removed outlier: 3.530A pdb=" N GLY A 874 " --> pdb=" O ILE A 870 " (cutoff:3.500A) Processing helix chain 'A' and resid 890 through 918 removed outlier: 3.740A pdb=" N VAL A 894 " --> pdb=" O PRO A 890 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER A 895 " --> pdb=" O GLY A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 943 removed outlier: 3.679A 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 961 through 963 No H-bonds generated for 'chain 'A' and resid 961 through 963' Processing helix chain 'A' and resid 967 through 976 removed outlier: 3.924A pdb=" N ARG A 976 " --> pdb=" O PHE A 972 " (cutoff:3.500A) Processing helix chain 'A' and resid 1044 through 1049 Processing helix chain 'A' and resid 1070 through 1079 Processing helix chain 'A' and resid 1086 through 1106 Proline residue: A1101 - end of helix removed outlier: 4.231A pdb=" N MET A1104 " --> pdb=" O THR A1100 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU A1105 " --> pdb=" O PRO A1101 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN A1106 " --> pdb=" O LEU A1102 " (cutoff:3.500A) Processing helix chain 'A' and resid 1116 through 1123 Processing helix chain 'B' and resid 78 through 94 Processing helix chain 'B' and resid 102 through 119 Processing helix chain 'B' and resid 121 through 131 removed outlier: 3.833A pdb=" N HIS B 126 " --> pdb=" O LEU B 122 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N ASP B 129 " --> pdb=" O GLU B 125 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N VAL B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 removed outlier: 3.525A pdb=" N LEU B 139 " --> pdb=" O PRO B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 152 Processing helix chain 'B' and resid 156 through 188 removed outlier: 5.810A pdb=" N SER B 164 " --> pdb=" O MET B 160 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLN B 165 " --> pdb=" O ARG B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 195 through 206 Processing helix chain 'B' and resid 211 through 220 Processing helix chain 'B' and resid 224 through 253 Processing helix chain 'B' and resid 261 through 292 removed outlier: 3.563A pdb=" N LEU B 266 " --> pdb=" O GLY B 262 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA B 274 " --> pdb=" O GLN B 270 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N GLY B 275 " --> pdb=" O VAL B 271 " (cutoff:3.500A) Proline residue: B 276 - end of helix removed outlier: 4.396A pdb=" N HIS B 292 " --> pdb=" O PHE B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 316 Processing helix chain 'B' and resid 324 through 336 Processing helix chain 'B' and resid 345 through 378 removed outlier: 4.137A pdb=" N LEU B 377 " --> pdb=" O THR B 373 " (cutoff:3.500A) Processing helix chain 'B' and resid 382 through 406 removed outlier: 4.491A pdb=" N PHE B 386 " --> pdb=" O LYS B 382 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N TYR B 387 " --> pdb=" O MET B 383 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ILE B 390 " --> pdb=" O PHE B 386 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ARG B 399 " --> pdb=" O ILE B 395 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY B 400 " --> pdb=" O THR B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 427 Processing helix chain 'B' and resid 433 through 445 Processing helix chain 'B' and resid 453 through 480 removed outlier: 3.826A pdb=" N ALA B 471 " --> pdb=" O LEU B 467 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N THR B 472 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N GLN B 475 " --> pdb=" O ALA B 471 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N THR B 476 " --> pdb=" O THR B 472 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 513 Processing helix chain 'B' and resid 525 through 528 No H-bonds generated for 'chain 'B' and resid 525 through 528' Processing helix chain 'B' and resid 576 through 600 Processing helix chain 'B' and resid 606 through 620 Processing helix chain 'B' and resid 635 through 638 No H-bonds generated for 'chain 'B' and resid 635 through 638' Processing helix chain 'B' and resid 643 through 653 Processing helix chain 'B' and resid 669 through 676 Processing helix chain 'B' and resid 678 through 702 removed outlier: 4.223A 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 724 through 751 removed outlier: 3.590A pdb=" N ARG B 733 " --> pdb=" O GLU B 729 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE B 734 " --> pdb=" O ASP B 730 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL B 741 " --> pdb=" O TYR B 737 " (cutoff:3.500A) Processing helix chain 'B' and resid 755 through 760 removed outlier: 3.592A pdb=" N TYR B 758 " --> pdb=" O GLY B 755 " (cutoff:3.500A) Processing helix chain 'B' and resid 764 through 776 removed outlier: 3.520A pdb=" N ILE B 770 " --> pdb=" O ASP B 767 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU B 775 " --> pdb=" O VAL B 772 " (cutoff:3.500A) Processing helix chain 'B' and resid 803 through 857 removed outlier: 3.533A pdb=" N THR B 814 " --> pdb=" O LEU B 811 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LYS B 815 " --> pdb=" O ARG B 812 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE B 818 " --> pdb=" O LYS B 815 " (cutoff:3.500A) Proline residue: B 819 - end of helix removed outlier: 3.520A pdb=" N GLU B 849 " --> pdb=" O GLY B 846 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP B 855 " --> pdb=" O LYS B 852 " (cutoff:3.500A) Processing helix chain 'B' and resid 862 through 888 removed outlier: 3.531A pdb=" N GLY B 874 " --> pdb=" O ILE B 870 " (cutoff:3.500A) Processing helix chain 'B' and resid 890 through 918 removed outlier: 3.740A pdb=" N VAL B 894 " --> pdb=" O PRO B 890 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N SER B 895 " --> pdb=" O GLY B 891 " (cutoff:3.500A) Processing helix chain 'B' and resid 924 through 943 removed outlier: 3.679A 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 961 through 963 No H-bonds generated for 'chain 'B' and resid 961 through 963' Processing helix chain 'B' and resid 967 through 976 removed outlier: 3.925A pdb=" N ARG B 976 " --> pdb=" O PHE B 972 " (cutoff:3.500A) Processing helix chain 'B' and resid 1044 through 1049 Processing helix chain 'B' and resid 1070 through 1079 Processing helix chain 'B' and resid 1086 through 1106 Proline residue: B1101 - end of helix removed outlier: 4.231A pdb=" N MET B1104 " --> pdb=" O THR B1100 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLU B1105 " --> pdb=" O PRO B1101 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN B1106 " --> pdb=" O LEU B1102 " (cutoff:3.500A) Processing helix chain 'B' and resid 1116 through 1123 Processing sheet with id= A, first strand: chain 'A' and resid 978 through 982 removed outlier: 3.566A pdb=" N SER A1003 " --> pdb=" O GLN A1064 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N TYR A1066 " --> pdb=" O ILE A1001 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ILE A1001 " --> pdb=" O TYR A1066 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 1032 through 1036 Processing sheet with id= C, first strand: chain 'A' and resid 1125 through 1127 removed outlier: 4.422A pdb=" N LEU A1186 " --> pdb=" O VAL A1127 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ASN A1149 " --> pdb=" O ARG A1185 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N PHE A1187 " --> pdb=" O LEU A1147 " (cutoff:3.500A) removed outlier: 5.586A pdb=" N LEU A1147 " --> pdb=" O PHE A1187 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 978 through 982 removed outlier: 3.566A pdb=" N SER B1003 " --> pdb=" O GLN B1064 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N TYR B1066 " --> pdb=" O ILE B1001 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N ILE B1001 " --> pdb=" O TYR B1066 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 1032 through 1036 Processing sheet with id= F, first strand: chain 'B' and resid 1125 through 1127 removed outlier: 4.510A pdb=" N LEU B1186 " --> pdb=" O VAL B1127 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN B1149 " --> pdb=" O ARG B1185 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE B1187 " --> pdb=" O LEU B1147 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LEU B1147 " --> pdb=" O PHE B1187 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 1135 through 1137 1002 hydrogen bonds defined for protein. 2646 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: 5.64 Time building geometry restraints manager: 7.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 2659 1.31 - 1.44: 4279 1.44 - 1.57: 9932 1.57 - 1.70: 6 1.70 - 1.82: 158 Bond restraints: 17034 Sorted by residual: bond pdb=" C LEU B1086 " pdb=" N GLU B1087 " ideal model delta sigma weight residual 1.334 1.436 -0.102 1.27e-02 6.20e+03 6.45e+01 bond pdb=" C GLU B 847 " pdb=" N GLU B 848 " ideal model delta sigma weight residual 1.334 1.255 0.079 1.27e-02 6.20e+03 3.87e+01 bond pdb=" C GLU A 847 " pdb=" N GLU A 848 " ideal model delta sigma weight residual 1.334 1.256 0.078 1.27e-02 6.20e+03 3.78e+01 bond pdb=" C ARG A 499 " pdb=" N ARG A 500 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.27e-02 6.20e+03 2.61e+01 bond pdb=" C ARG B 499 " pdb=" N ARG B 500 " ideal model delta sigma weight residual 1.334 1.399 -0.065 1.27e-02 6.20e+03 2.61e+01 ... (remaining 17029 not shown) Histogram of bond angle deviations from ideal: 99.28 - 110.03: 2278 110.03 - 120.78: 15879 120.78 - 131.53: 4879 131.53 - 142.28: 32 142.28 - 153.02: 2 Bond angle restraints: 23070 Sorted by residual: angle pdb=" C39 CPL A1401 " pdb=" C40 CPL A1401 " pdb=" C41 CPL A1401 " ideal model delta sigma weight residual 127.51 153.02 -25.51 3.00e+00 1.11e-01 7.23e+01 angle pdb=" C39 CPL B1401 " pdb=" C40 CPL B1401 " pdb=" C41 CPL B1401 " ideal model delta sigma weight residual 127.51 152.99 -25.48 3.00e+00 1.11e-01 7.21e+01 angle pdb=" O LEU B1086 " pdb=" C LEU B1086 " pdb=" N GLU B1087 " ideal model delta sigma weight residual 122.12 128.95 -6.83 1.06e+00 8.90e-01 4.15e+01 angle pdb=" O GLU B1087 " pdb=" C GLU B1087 " pdb=" N TYR B1088 " ideal model delta sigma weight residual 122.07 128.45 -6.38 1.03e+00 9.43e-01 3.84e+01 angle pdb=" CA LEU B1086 " pdb=" C LEU B1086 " pdb=" N GLU B1087 " ideal model delta sigma weight residual 117.30 110.42 6.88 1.16e+00 7.43e-01 3.52e+01 ... (remaining 23065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.72: 9521 30.72 - 61.45: 654 61.45 - 92.17: 37 92.17 - 122.89: 0 122.89 - 153.61: 6 Dihedral angle restraints: 10218 sinusoidal: 4100 harmonic: 6118 Sorted by residual: dihedral pdb=" C33 CPL B1401 " pdb=" C31 CPL B1401 " pdb=" C32 CPL B1401 " pdb=" O2 CPL B1401 " ideal model delta sinusoidal sigma weight residual 171.65 -34.74 -153.61 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C33 CPL A1401 " pdb=" C31 CPL A1401 " pdb=" C32 CPL A1401 " pdb=" O2 CPL A1401 " ideal model delta sinusoidal sigma weight residual 171.65 -34.74 -153.61 1 3.00e+01 1.11e-03 2.02e+01 dihedral pdb=" C3 CPL B1401 " pdb=" C1 CPL B1401 " pdb=" C2 CPL B1401 " pdb=" O3P CPL B1401 " ideal model delta sinusoidal sigma weight residual 72.09 -73.31 145.40 1 3.00e+01 1.11e-03 1.94e+01 ... (remaining 10215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 2053 0.048 - 0.096: 506 0.096 - 0.144: 148 0.144 - 0.192: 43 0.192 - 0.240: 12 Chirality restraints: 2762 Sorted by residual: chirality pdb=" C2 CPL B1401 " pdb=" C1 CPL B1401 " pdb=" C3 CPL B1401 " pdb=" O2 CPL B1401 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" C2 CPL A1401 " pdb=" C1 CPL A1401 " pdb=" C3 CPL A1401 " pdb=" O2 CPL A1401 " both_signs ideal model delta sigma weight residual False -2.32 -2.55 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE A 734 " pdb=" N ILE A 734 " pdb=" C ILE A 734 " pdb=" CB ILE A 734 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 2759 not shown) Planarity restraints: 2828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR B 641 " -0.059 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO B 642 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 642 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO B 642 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 641 " 0.059 5.00e-02 4.00e+02 8.91e-02 1.27e+01 pdb=" N PRO A 642 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 642 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 642 " 0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 732 " -0.014 2.00e-02 2.50e+03 2.88e-02 8.28e+00 pdb=" C LEU B 732 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU B 732 " -0.019 2.00e-02 2.50e+03 pdb=" N ARG B 733 " -0.017 2.00e-02 2.50e+03 ... (remaining 2825 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 495 2.71 - 3.25: 17754 3.25 - 3.80: 27012 3.80 - 4.35: 30894 4.35 - 4.90: 52797 Nonbonded interactions: 128952 Sorted by model distance: nonbonded pdb=" N GLU A1071 " pdb=" OE1 GLU A1071 " model vdw 2.157 2.520 nonbonded pdb=" N GLU B1071 " pdb=" OE1 GLU B1071 " model vdw 2.158 2.520 nonbonded pdb=" N GLU A 346 " pdb=" OE1 GLU A 346 " model vdw 2.227 2.520 nonbonded pdb=" N GLU B 346 " pdb=" OE1 GLU B 346 " model vdw 2.227 2.520 nonbonded pdb=" N GLU A 531 " pdb=" OE1 GLU A 531 " model vdw 2.233 2.520 ... (remaining 128947 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: 2.970 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: 9.100 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 46.260 Find NCS groups from input model: 1.120 Set up NCS constraints: 0.100 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 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 : 0.006 0.123 17034 Z= 0.363 Angle : 0.902 25.515 23070 Z= 0.507 Chirality : 0.050 0.240 2762 Planarity : 0.005 0.089 2828 Dihedral : 19.192 153.613 6254 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.80 % Favored : 94.10 % Rotamer: Outliers : 2.99 % Allowed : 33.96 % Favored : 63.05 % 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: 1.04 (0.19), residues: 2086 helix: 1.84 (0.14), residues: 1354 sheet: 1.45 (0.64), residues: 54 loop : -1.87 (0.24), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 643 HIS 0.006 0.001 HIS B1172 PHE 0.014 0.001 PHE A 598 TYR 0.029 0.001 TYR B 758 ARG 0.004 0.000 ARG B 585 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 220 time to evaluate : 1.754 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 678 MET cc_start: 0.7124 (pmm) cc_final: 0.6851 (pmm) REVERT: A 758 TYR cc_start: 0.8985 (t80) cc_final: 0.8773 (t80) REVERT: A 900 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8191 (mt0) REVERT: A 967 MET cc_start: 0.8986 (mmm) cc_final: 0.8483 (mpp) REVERT: A 986 GLU cc_start: 0.7840 (mm-30) cc_final: 0.7546 (mt-10) REVERT: A 1109 PHE cc_start: 0.8651 (m-80) cc_final: 0.7919 (m-80) REVERT: A 1172 HIS cc_start: 0.6138 (OUTLIER) cc_final: 0.5791 (m-70) REVERT: B 205 MET cc_start: 0.8712 (mtm) cc_final: 0.8504 (mtm) REVERT: B 477 LEU cc_start: 0.9464 (tp) cc_final: 0.9261 (tp) REVERT: B 967 MET cc_start: 0.8807 (mmm) cc_final: 0.8600 (mmm) REVERT: B 1109 PHE cc_start: 0.8616 (m-80) cc_final: 0.8117 (m-80) outliers start: 54 outliers final: 11 residues processed: 257 average time/residue: 0.3041 time to fit residues: 115.3194 Evaluate side-chains 188 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 175 time to evaluate : 1.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 801 LEU Chi-restraints excluded: chain A residue 808 LEU Chi-restraints excluded: chain A residue 849 GLU Chi-restraints excluded: chain A residue 900 GLN Chi-restraints excluded: chain A residue 915 GLU Chi-restraints excluded: chain A residue 1119 LEU Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain B residue 801 LEU Chi-restraints excluded: chain B residue 808 LEU Chi-restraints excluded: chain B residue 915 GLU Chi-restraints excluded: chain B residue 1119 LEU Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 2.9990 chunk 159 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 107 optimal weight: 2.9990 chunk 85 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 100 optimal weight: 0.0870 chunk 122 optimal weight: 0.7980 chunk 190 optimal weight: 6.9990 overall best weight: 1.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 136 HIS ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 691 ASN A 736 ASN A1120 HIS B 136 HIS B 691 ASN B 736 ASN B1120 HIS ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17034 Z= 0.239 Angle : 0.587 8.244 23070 Z= 0.300 Chirality : 0.039 0.204 2762 Planarity : 0.005 0.080 2828 Dihedral : 11.136 144.086 2371 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 4.15 % Allowed : 31.42 % Favored : 64.44 % 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: 1.34 (0.19), residues: 2086 helix: 1.94 (0.14), residues: 1360 sheet: 1.06 (0.61), residues: 58 loop : -1.43 (0.24), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 635 HIS 0.003 0.001 HIS B 757 PHE 0.019 0.001 PHE B 769 TYR 0.035 0.001 TYR B 758 ARG 0.006 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 171 time to evaluate : 1.963 Fit side-chains revert: symmetry clash REVERT: A 94 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8989 (tt) REVERT: A 382 LYS cc_start: 0.7039 (OUTLIER) cc_final: 0.6312 (ptpp) REVERT: A 585 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8638 (ttm110) REVERT: A 662 MET cc_start: 0.7224 (mpp) cc_final: 0.6901 (tpt) REVERT: A 857 MET cc_start: 0.8394 (tmm) cc_final: 0.6804 (tmm) REVERT: A 925 MET cc_start: 0.8513 (ppp) cc_final: 0.8127 (ppp) REVERT: A 967 MET cc_start: 0.8965 (mmm) cc_final: 0.8478 (mpp) REVERT: A 1172 HIS cc_start: 0.6379 (OUTLIER) cc_final: 0.6034 (m-70) REVERT: B 382 LYS cc_start: 0.7096 (OUTLIER) cc_final: 0.6312 (ptpp) REVERT: B 579 MET cc_start: 0.7941 (mmm) cc_final: 0.7739 (mmp) REVERT: B 662 MET cc_start: 0.6906 (mpp) cc_final: 0.6658 (tpt) REVERT: B 855 ASP cc_start: 0.8971 (t0) cc_final: 0.8751 (p0) REVERT: B 857 MET cc_start: 0.8428 (tmm) cc_final: 0.8220 (tmm) REVERT: B 925 MET cc_start: 0.8491 (ppp) cc_final: 0.8091 (ppp) REVERT: B 967 MET cc_start: 0.8817 (mmm) cc_final: 0.8608 (mmm) outliers start: 75 outliers final: 25 residues processed: 229 average time/residue: 0.2613 time to fit residues: 94.4548 Evaluate side-chains 183 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 153 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 585 ARG Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 401 MET Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 105 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 158 optimal weight: 7.9990 chunk 129 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 191 optimal weight: 7.9990 chunk 206 optimal weight: 20.0000 chunk 170 optimal weight: 9.9990 chunk 189 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 677 HIS ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 702 GLN A 764 ASN ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17034 Z= 0.270 Angle : 0.565 7.068 23070 Z= 0.292 Chirality : 0.039 0.157 2762 Planarity : 0.005 0.078 2828 Dihedral : 10.396 144.321 2347 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.70 % Favored : 95.21 % Rotamer: Outliers : 3.87 % Allowed : 30.92 % Favored : 65.21 % 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: 1.37 (0.19), residues: 2086 helix: 1.95 (0.14), residues: 1364 sheet: 1.14 (0.60), residues: 58 loop : -1.39 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 635 HIS 0.002 0.001 HIS B1120 PHE 0.018 0.001 PHE B 769 TYR 0.030 0.001 TYR A 758 ARG 0.005 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 165 time to evaluate : 1.787 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 382 LYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6283 (ptpp) REVERT: A 662 MET cc_start: 0.7301 (mpp) cc_final: 0.6995 (tpt) REVERT: A 685 ASN cc_start: 0.8132 (m-40) cc_final: 0.7672 (p0) REVERT: A 966 ASP cc_start: 0.8769 (OUTLIER) cc_final: 0.8257 (p0) REVERT: A 967 MET cc_start: 0.8917 (mmm) cc_final: 0.8440 (mpp) REVERT: A 1172 HIS cc_start: 0.6450 (OUTLIER) cc_final: 0.5999 (m170) REVERT: B 382 LYS cc_start: 0.7027 (OUTLIER) cc_final: 0.6283 (ptpp) REVERT: B 579 MET cc_start: 0.8080 (mmm) cc_final: 0.7754 (mmp) REVERT: B 662 MET cc_start: 0.7178 (mpp) cc_final: 0.6926 (tpt) REVERT: B 685 ASN cc_start: 0.8011 (m-40) cc_final: 0.7593 (p0) REVERT: B 855 ASP cc_start: 0.8973 (t0) cc_final: 0.8723 (p0) REVERT: B 967 MET cc_start: 0.8827 (mmm) cc_final: 0.8574 (mmm) outliers start: 70 outliers final: 40 residues processed: 227 average time/residue: 0.2401 time to fit residues: 87.5230 Evaluate side-chains 194 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 150 time to evaluate : 1.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 188 LEU Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 776 VAL Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 966 ASP Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 776 VAL Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1148 ILE Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 188 optimal weight: 1.9990 chunk 143 optimal weight: 0.0170 chunk 99 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 91 optimal weight: 6.9990 chunk 128 optimal weight: 0.8980 chunk 191 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 181 optimal weight: 3.9990 chunk 54 optimal weight: 5.9990 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 702 GLN ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17034 Z= 0.198 Angle : 0.533 7.268 23070 Z= 0.272 Chirality : 0.038 0.138 2762 Planarity : 0.004 0.078 2828 Dihedral : 10.161 143.757 2347 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 4.31 % Allowed : 30.31 % Favored : 65.38 % 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: 1.44 (0.19), residues: 2086 helix: 1.99 (0.14), residues: 1370 sheet: 1.39 (0.60), residues: 58 loop : -1.39 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 635 HIS 0.005 0.001 HIS A 600 PHE 0.018 0.001 PHE A1109 TYR 0.014 0.001 TYR A 758 ARG 0.004 0.000 ARG A 903 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 160 time to evaluate : 1.790 Fit side-chains revert: symmetry clash REVERT: A 382 LYS cc_start: 0.6970 (OUTLIER) cc_final: 0.6214 (ptpp) REVERT: A 662 MET cc_start: 0.7331 (mpp) cc_final: 0.7127 (tpt) REVERT: A 685 ASN cc_start: 0.8171 (m-40) cc_final: 0.7704 (p0) REVERT: A 737 TYR cc_start: 0.7347 (OUTLIER) cc_final: 0.7053 (m-80) REVERT: A 855 ASP cc_start: 0.8994 (t0) cc_final: 0.8650 (p0) REVERT: A 857 MET cc_start: 0.8284 (tmm) cc_final: 0.7812 (tmm) REVERT: A 967 MET cc_start: 0.8891 (mmm) cc_final: 0.8624 (mmm) REVERT: A 1107 MET cc_start: 0.6636 (tmm) cc_final: 0.6409 (ppp) REVERT: A 1172 HIS cc_start: 0.6415 (OUTLIER) cc_final: 0.5995 (m170) REVERT: B 685 ASN cc_start: 0.8019 (m-40) cc_final: 0.7582 (p0) REVERT: B 737 TYR cc_start: 0.7071 (OUTLIER) cc_final: 0.6775 (m-80) REVERT: B 855 ASP cc_start: 0.8971 (t70) cc_final: 0.8686 (p0) REVERT: B 967 MET cc_start: 0.8774 (mmm) cc_final: 0.8570 (mmm) REVERT: B 1104 MET cc_start: 0.8669 (mmp) cc_final: 0.8293 (mmt) REVERT: B 1107 MET cc_start: 0.6630 (tmm) cc_final: 0.6372 (ppp) REVERT: B 1169 ARG cc_start: 0.6648 (OUTLIER) cc_final: 0.6193 (ttt-90) outliers start: 78 outliers final: 49 residues processed: 226 average time/residue: 0.2387 time to fit residues: 87.4717 Evaluate side-chains 206 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 152 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 208 THR Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 425 MET Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 208 THR Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 677 HIS Chi-restraints excluded: chain B residue 737 TYR Chi-restraints excluded: chain B residue 779 ILE Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1169 ARG Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 169 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 151 optimal weight: 4.9990 chunk 83 optimal weight: 0.9980 chunk 173 optimal weight: 4.9990 chunk 140 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 182 optimal weight: 3.9990 chunk 51 optimal weight: 0.4980 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 736 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 17034 Z= 0.390 Angle : 0.621 6.998 23070 Z= 0.320 Chirality : 0.041 0.188 2762 Planarity : 0.005 0.079 2828 Dihedral : 10.152 144.677 2347 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.23 % Favored : 94.68 % Rotamer: Outliers : 5.92 % Allowed : 29.15 % Favored : 64.93 % 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: 1.23 (0.19), residues: 2086 helix: 1.80 (0.14), residues: 1374 sheet: 1.27 (0.61), residues: 58 loop : -1.42 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 635 HIS 0.007 0.001 HIS A 600 PHE 0.019 0.002 PHE B 769 TYR 0.015 0.001 TYR A 312 ARG 0.003 0.000 ARG B 856 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 154 time to evaluate : 1.918 Fit side-chains revert: symmetry clash REVERT: A 302 THR cc_start: 0.9365 (OUTLIER) cc_final: 0.9162 (p) REVERT: A 382 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6302 (ptpp) REVERT: A 641 TYR cc_start: 0.7764 (t80) cc_final: 0.7549 (t80) REVERT: A 685 ASN cc_start: 0.8109 (m-40) cc_final: 0.7633 (p0) REVERT: A 737 TYR cc_start: 0.7573 (OUTLIER) cc_final: 0.7342 (m-10) REVERT: A 855 ASP cc_start: 0.9044 (t0) cc_final: 0.8722 (p0) REVERT: A 857 MET cc_start: 0.8316 (tmm) cc_final: 0.7903 (tmm) REVERT: A 967 MET cc_start: 0.8867 (mmm) cc_final: 0.8620 (mmm) REVERT: A 1107 MET cc_start: 0.6902 (tmm) cc_final: 0.6670 (ppp) REVERT: A 1172 HIS cc_start: 0.6575 (OUTLIER) cc_final: 0.6145 (m170) REVERT: B 302 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9224 (p) REVERT: B 382 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6566 (ptpp) REVERT: B 578 MET cc_start: 0.8058 (mpp) cc_final: 0.7772 (mpp) REVERT: B 685 ASN cc_start: 0.8049 (m-40) cc_final: 0.7591 (p0) REVERT: B 737 TYR cc_start: 0.7113 (OUTLIER) cc_final: 0.6854 (m-80) REVERT: B 855 ASP cc_start: 0.9022 (t70) cc_final: 0.8715 (p0) REVERT: B 924 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7949 (tm-30) REVERT: B 967 MET cc_start: 0.8806 (mmm) cc_final: 0.8604 (mmm) REVERT: B 1104 MET cc_start: 0.8757 (mmp) cc_final: 0.8480 (mmt) REVERT: B 1107 MET cc_start: 0.7009 (tmm) cc_final: 0.6749 (ppp) REVERT: B 1169 ARG cc_start: 0.6610 (OUTLIER) cc_final: 0.6063 (ttt-90) outliers start: 107 outliers final: 62 residues processed: 247 average time/residue: 0.2492 time to fit residues: 98.9736 Evaluate side-chains 213 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 143 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 CYS Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 220 LEU Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 302 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 867 LEU Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 934 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 1002 VAL Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1148 ILE Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 85 CYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain B residue 205 MET Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 302 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 677 HIS Chi-restraints excluded: chain B residue 737 TYR Chi-restraints excluded: chain B residue 813 LEU Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 867 LEU Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 934 VAL Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1148 ILE Chi-restraints excluded: chain B residue 1169 ARG Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 68 optimal weight: 10.0000 chunk 182 optimal weight: 0.8980 chunk 40 optimal weight: 0.6980 chunk 119 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 203 optimal weight: 7.9990 chunk 168 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 106 optimal weight: 0.9990 overall best weight: 0.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 736 ASN ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 17034 Z= 0.168 Angle : 0.540 7.653 23070 Z= 0.275 Chirality : 0.038 0.149 2762 Planarity : 0.004 0.091 2828 Dihedral : 10.038 144.633 2347 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.65 % Favored : 95.30 % Rotamer: Outliers : 4.04 % Allowed : 30.81 % Favored : 65.15 % 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: 1.42 (0.19), residues: 2086 helix: 1.95 (0.14), residues: 1376 sheet: 1.91 (0.63), residues: 54 loop : -1.41 (0.25), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 635 HIS 0.002 0.001 HIS B 600 PHE 0.021 0.001 PHE B1109 TYR 0.025 0.001 TYR B 641 ARG 0.006 0.000 ARG B 573 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 159 time to evaluate : 1.852 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.9023 (pm20) cc_final: 0.8590 (pm20) REVERT: A 678 MET cc_start: 0.7557 (pmm) cc_final: 0.7102 (pmm) REVERT: A 685 ASN cc_start: 0.8128 (m-40) cc_final: 0.7900 (m-40) REVERT: A 737 TYR cc_start: 0.7411 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: A 855 ASP cc_start: 0.9035 (t0) cc_final: 0.8686 (p0) REVERT: A 967 MET cc_start: 0.8773 (mmm) cc_final: 0.8550 (mmm) REVERT: A 1172 HIS cc_start: 0.6469 (OUTLIER) cc_final: 0.6068 (m170) REVERT: B 346 GLU cc_start: 0.9081 (pm20) cc_final: 0.8650 (pm20) REVERT: B 382 LYS cc_start: 0.7028 (OUTLIER) cc_final: 0.6221 (ptpp) REVERT: B 685 ASN cc_start: 0.8094 (m-40) cc_final: 0.7645 (p0) REVERT: B 737 TYR cc_start: 0.7021 (OUTLIER) cc_final: 0.6813 (m-80) REVERT: B 855 ASP cc_start: 0.8977 (t70) cc_final: 0.8740 (p0) REVERT: B 924 GLU cc_start: 0.8129 (tm-30) cc_final: 0.7809 (tm-30) REVERT: B 967 MET cc_start: 0.8755 (mmm) cc_final: 0.8550 (mmm) REVERT: B 1104 MET cc_start: 0.8814 (mmp) cc_final: 0.8545 (mmt) REVERT: B 1107 MET cc_start: 0.6711 (tmm) cc_final: 0.6408 (ppp) REVERT: B 1169 ARG cc_start: 0.6751 (OUTLIER) cc_final: 0.6244 (ttt-90) outliers start: 73 outliers final: 39 residues processed: 217 average time/residue: 0.2596 time to fit residues: 89.6137 Evaluate side-chains 191 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 147 time to evaluate : 1.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 644 LEU Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 382 LYS Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 635 TRP Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 677 HIS Chi-restraints excluded: chain B residue 737 TYR Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1169 ARG Chi-restraints excluded: chain B residue 1176 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 195 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 148 optimal weight: 0.6980 chunk 114 optimal weight: 1.9990 chunk 171 optimal weight: 0.0040 chunk 113 optimal weight: 4.9990 chunk 202 optimal weight: 3.9990 chunk 126 optimal weight: 0.9990 chunk 123 optimal weight: 0.6980 chunk 93 optimal weight: 3.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 17034 Z= 0.155 Angle : 0.533 8.383 23070 Z= 0.270 Chirality : 0.038 0.168 2762 Planarity : 0.004 0.091 2828 Dihedral : 9.898 143.318 2346 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.79 % Favored : 95.21 % Rotamer: Outliers : 2.93 % Allowed : 31.80 % Favored : 65.27 % 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: 1.52 (0.19), residues: 2086 helix: 2.07 (0.14), residues: 1372 sheet: 1.75 (0.63), residues: 58 loop : -1.46 (0.26), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 635 HIS 0.004 0.000 HIS A 600 PHE 0.021 0.001 PHE B 769 TYR 0.040 0.001 TYR A 641 ARG 0.002 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 156 time to evaluate : 1.890 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8948 (pm20) cc_final: 0.8578 (pm20) REVERT: A 675 CYS cc_start: 0.7437 (OUTLIER) cc_final: 0.6895 (p) REVERT: A 685 ASN cc_start: 0.8142 (m-40) cc_final: 0.7932 (m-40) REVERT: A 737 TYR cc_start: 0.7409 (OUTLIER) cc_final: 0.7207 (m-80) REVERT: A 855 ASP cc_start: 0.9002 (t0) cc_final: 0.8664 (p0) REVERT: A 857 MET cc_start: 0.8316 (tmm) cc_final: 0.8007 (tmm) REVERT: A 967 MET cc_start: 0.8774 (mmm) cc_final: 0.8566 (mmm) REVERT: A 1172 HIS cc_start: 0.6473 (OUTLIER) cc_final: 0.6067 (m170) REVERT: B 346 GLU cc_start: 0.9043 (pm20) cc_final: 0.8641 (pm20) REVERT: B 685 ASN cc_start: 0.8112 (m-40) cc_final: 0.7901 (m-40) REVERT: B 855 ASP cc_start: 0.8992 (t70) cc_final: 0.8709 (p0) REVERT: B 911 GLU cc_start: 0.9036 (tp30) cc_final: 0.8825 (tt0) REVERT: B 924 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 967 MET cc_start: 0.8757 (mmm) cc_final: 0.8383 (mmm) REVERT: B 1104 MET cc_start: 0.8832 (mmp) cc_final: 0.8582 (mmt) REVERT: B 1107 MET cc_start: 0.6563 (tmm) cc_final: 0.6242 (ppp) REVERT: B 1169 ARG cc_start: 0.6660 (OUTLIER) cc_final: 0.6106 (ttt-90) outliers start: 53 outliers final: 38 residues processed: 197 average time/residue: 0.2529 time to fit residues: 81.2150 Evaluate side-chains 193 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 2.038 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 635 TRP Chi-restraints excluded: chain B residue 677 HIS Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1169 ARG Chi-restraints excluded: chain B residue 1176 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 125 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 120 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 39 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 137 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 159 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17034 Z= 0.169 Angle : 0.530 8.765 23070 Z= 0.268 Chirality : 0.038 0.179 2762 Planarity : 0.004 0.089 2828 Dihedral : 9.752 142.666 2346 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.48 % Allowed : 31.08 % Favored : 65.43 % 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: 1.57 (0.19), residues: 2086 helix: 2.11 (0.14), residues: 1374 sheet: 1.83 (0.65), residues: 58 loop : -1.45 (0.26), residues: 654 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 635 HIS 0.003 0.000 HIS A 600 PHE 0.021 0.001 PHE A 769 TYR 0.026 0.001 TYR A 641 ARG 0.002 0.000 ARG B 903 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 157 time to evaluate : 1.906 Fit side-chains revert: symmetry clash REVERT: A 224 LYS cc_start: 0.9100 (pptt) cc_final: 0.8845 (pptt) REVERT: A 346 GLU cc_start: 0.8929 (pm20) cc_final: 0.8571 (pm20) REVERT: A 675 CYS cc_start: 0.7365 (OUTLIER) cc_final: 0.6825 (p) REVERT: A 685 ASN cc_start: 0.8186 (m-40) cc_final: 0.7986 (m-40) REVERT: A 737 TYR cc_start: 0.7417 (OUTLIER) cc_final: 0.7203 (m-80) REVERT: A 855 ASP cc_start: 0.9021 (t0) cc_final: 0.8698 (p0) REVERT: A 967 MET cc_start: 0.8744 (mmm) cc_final: 0.8345 (mmm) REVERT: A 1172 HIS cc_start: 0.6495 (OUTLIER) cc_final: 0.6077 (m170) REVERT: B 346 GLU cc_start: 0.9041 (pm20) cc_final: 0.8657 (pm20) REVERT: B 685 ASN cc_start: 0.8119 (m-40) cc_final: 0.7896 (m-40) REVERT: B 855 ASP cc_start: 0.8988 (t70) cc_final: 0.8726 (p0) REVERT: B 924 GLU cc_start: 0.8066 (tm-30) cc_final: 0.7780 (tm-30) REVERT: B 967 MET cc_start: 0.8764 (mmm) cc_final: 0.8392 (mmm) REVERT: B 1104 MET cc_start: 0.8837 (mmp) cc_final: 0.8597 (mmt) REVERT: B 1107 MET cc_start: 0.6643 (tmm) cc_final: 0.6293 (ppp) REVERT: B 1169 ARG cc_start: 0.6662 (OUTLIER) cc_final: 0.6147 (ttt-90) outliers start: 63 outliers final: 48 residues processed: 212 average time/residue: 0.2455 time to fit residues: 84.5626 Evaluate side-chains 206 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 154 time to evaluate : 1.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 260 THR Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 322 SER Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 737 TYR Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 850 VAL Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 909 SER Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 983 ASP Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1063 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain A residue 1188 VAL Chi-restraints excluded: chain B residue 246 ASN Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 322 SER Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 677 HIS Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 850 VAL Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 909 SER Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1063 VAL Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1161 ILE Chi-restraints excluded: chain B residue 1169 ARG Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 193 optimal weight: 7.9990 chunk 176 optimal weight: 0.0980 chunk 188 optimal weight: 0.0170 chunk 113 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 148 optimal weight: 0.6980 chunk 57 optimal weight: 8.9990 chunk 170 optimal weight: 0.0270 chunk 178 optimal weight: 0.1980 chunk 187 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 overall best weight: 0.1076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.2738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 17034 Z= 0.142 Angle : 0.542 10.595 23070 Z= 0.269 Chirality : 0.037 0.182 2762 Planarity : 0.004 0.090 2828 Dihedral : 9.492 141.273 2346 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.16 % Allowed : 32.13 % Favored : 65.71 % 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: 1.59 (0.19), residues: 2086 helix: 2.16 (0.14), residues: 1360 sheet: 1.98 (0.65), residues: 58 loop : -1.47 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 635 HIS 0.003 0.000 HIS A 600 PHE 0.020 0.001 PHE A 769 TYR 0.021 0.001 TYR A 641 ARG 0.004 0.000 ARG B 812 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 171 time to evaluate : 1.958 Fit side-chains REVERT: A 346 GLU cc_start: 0.8925 (pm20) cc_final: 0.8654 (pm20) REVERT: A 675 CYS cc_start: 0.7227 (OUTLIER) cc_final: 0.6663 (p) REVERT: A 855 ASP cc_start: 0.8979 (t0) cc_final: 0.8735 (p0) REVERT: A 967 MET cc_start: 0.8746 (mmm) cc_final: 0.8358 (mmm) REVERT: A 1172 HIS cc_start: 0.6412 (OUTLIER) cc_final: 0.6016 (m170) REVERT: B 346 GLU cc_start: 0.8997 (pm20) cc_final: 0.8662 (pm20) REVERT: B 685 ASN cc_start: 0.8182 (m-40) cc_final: 0.7950 (m-40) REVERT: B 855 ASP cc_start: 0.8982 (t70) cc_final: 0.8761 (p0) REVERT: B 924 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7602 (tm-30) REVERT: B 967 MET cc_start: 0.8736 (mmm) cc_final: 0.8381 (mmm) REVERT: B 1104 MET cc_start: 0.8833 (mmp) cc_final: 0.8594 (mmt) REVERT: B 1107 MET cc_start: 0.6453 (tmm) cc_final: 0.6115 (ppp) REVERT: B 1169 ARG cc_start: 0.6574 (OUTLIER) cc_final: 0.6130 (ttt-90) outliers start: 39 outliers final: 29 residues processed: 200 average time/residue: 0.2433 time to fit residues: 79.4641 Evaluate side-chains 193 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 161 time to evaluate : 1.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 373 THR Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 635 TRP Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 373 THR Chi-restraints excluded: chain B residue 575 PHE Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1169 ARG Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 199 optimal weight: 0.0980 chunk 121 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 138 optimal weight: 4.9990 chunk 209 optimal weight: 7.9990 chunk 192 optimal weight: 0.2980 chunk 166 optimal weight: 4.9990 chunk 17 optimal weight: 0.7980 chunk 128 optimal weight: 1.9990 chunk 102 optimal weight: 7.9990 chunk 132 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 17034 Z= 0.158 Angle : 0.544 9.749 23070 Z= 0.270 Chirality : 0.038 0.263 2762 Planarity : 0.004 0.088 2828 Dihedral : 9.354 139.933 2346 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 1.83 % Allowed : 32.80 % Favored : 65.38 % 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: 1.67 (0.19), residues: 2086 helix: 2.18 (0.14), residues: 1370 sheet: 1.91 (0.65), residues: 58 loop : -1.38 (0.25), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 635 HIS 0.002 0.000 HIS A1172 PHE 0.021 0.001 PHE B 769 TYR 0.022 0.001 TYR A 641 ARG 0.003 0.000 ARG B 585 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4172 Ramachandran restraints generated. 2086 Oldfield, 0 Emsley, 2086 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 2.081 Fit side-chains revert: symmetry clash REVERT: A 346 GLU cc_start: 0.8905 (pm20) cc_final: 0.8622 (pm20) REVERT: A 675 CYS cc_start: 0.7275 (OUTLIER) cc_final: 0.6710 (p) REVERT: A 855 ASP cc_start: 0.8998 (t0) cc_final: 0.8791 (p0) REVERT: A 967 MET cc_start: 0.8752 (mmm) cc_final: 0.8362 (mmm) REVERT: A 1172 HIS cc_start: 0.6477 (OUTLIER) cc_final: 0.6067 (m170) REVERT: B 346 GLU cc_start: 0.8993 (pm20) cc_final: 0.8653 (pm20) REVERT: B 685 ASN cc_start: 0.8192 (m-40) cc_final: 0.7961 (m-40) REVERT: B 855 ASP cc_start: 0.8994 (t70) cc_final: 0.8771 (p0) REVERT: B 924 GLU cc_start: 0.7937 (tm-30) cc_final: 0.7649 (tm-30) REVERT: B 967 MET cc_start: 0.8745 (mmm) cc_final: 0.8390 (mmm) REVERT: B 1104 MET cc_start: 0.8845 (mmp) cc_final: 0.8617 (mmt) REVERT: B 1107 MET cc_start: 0.6466 (tmm) cc_final: 0.6120 (ppp) REVERT: B 1169 ARG cc_start: 0.6586 (OUTLIER) cc_final: 0.6142 (ttt-90) outliers start: 33 outliers final: 28 residues processed: 192 average time/residue: 0.2433 time to fit residues: 76.0975 Evaluate side-chains 191 residues out of total 1808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ASP Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 321 VAL Chi-restraints excluded: chain A residue 525 ILE Chi-restraints excluded: chain A residue 675 CYS Chi-restraints excluded: chain A residue 690 LEU Chi-restraints excluded: chain A residue 817 LEU Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 963 LEU Chi-restraints excluded: chain A residue 1057 VAL Chi-restraints excluded: chain A residue 1117 VAL Chi-restraints excluded: chain A residue 1172 HIS Chi-restraints excluded: chain A residue 1176 PHE Chi-restraints excluded: chain A residue 1178 TYR Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 319 LEU Chi-restraints excluded: chain B residue 321 VAL Chi-restraints excluded: chain B residue 577 ASP Chi-restraints excluded: chain B residue 677 HIS Chi-restraints excluded: chain B residue 817 LEU Chi-restraints excluded: chain B residue 858 VAL Chi-restraints excluded: chain B residue 956 LEU Chi-restraints excluded: chain B residue 963 LEU Chi-restraints excluded: chain B residue 983 ASP Chi-restraints excluded: chain B residue 1002 VAL Chi-restraints excluded: chain B residue 1057 VAL Chi-restraints excluded: chain B residue 1117 VAL Chi-restraints excluded: chain B residue 1169 ARG Chi-restraints excluded: chain B residue 1176 PHE Chi-restraints excluded: chain B residue 1188 VAL Chi-restraints excluded: chain B residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 210 random chunks: chunk 177 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 46 optimal weight: 0.0980 chunk 166 optimal weight: 20.0000 chunk 69 optimal weight: 0.0870 chunk 171 optimal weight: 0.0370 chunk 21 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 146 optimal weight: 0.0270 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B1172 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.109757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.075277 restraints weight = 45029.599| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 3.51 r_work: 0.3050 rms_B_bonded: 4.30 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 17034 Z= 0.141 Angle : 0.550 9.694 23070 Z= 0.271 Chirality : 0.037 0.192 2762 Planarity : 0.004 0.089 2828 Dihedral : 9.209 138.981 2346 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.88 % Allowed : 32.85 % Favored : 65.27 % 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: 1.61 (0.19), residues: 2086 helix: 2.20 (0.14), residues: 1350 sheet: 2.00 (0.66), residues: 58 loop : -1.47 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 635 HIS 0.002 0.000 HIS A 981 PHE 0.020 0.001 PHE B 769 TYR 0.021 0.001 TYR A 641 ARG 0.002 0.000 ARG B 812 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3386.63 seconds wall clock time: 62 minutes 51.34 seconds (3771.34 seconds total)