Starting phenix.real_space_refine on Wed Feb 14 21:58:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd7_27335/02_2024/8dd7_27335_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd7_27335/02_2024/8dd7_27335.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd7_27335/02_2024/8dd7_27335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd7_27335/02_2024/8dd7_27335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd7_27335/02_2024/8dd7_27335_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd7_27335/02_2024/8dd7_27335_updated.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 66 5.16 5 C 6633 2.51 5 N 1780 2.21 5 O 1889 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 200": "OE1" <-> "OE2" Residue "A GLU 236": "OE1" <-> "OE2" Residue "A GLU 241": "OE1" <-> "OE2" Residue "A TYR 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 1033": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 10370 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4192 Classifications: {'peptide': 516} Link IDs: {'PTRANS': 26, 'TRANS': 489} Chain: "B" Number of atoms: 6125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 759, 6125 Classifications: {'peptide': 759} Link IDs: {'PTRANS': 29, 'TRANS': 729} Chain breaks: 4 Chain: "A" Number of atoms: 53 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 53 Unusual residues: {'FAD': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N CYS A 296 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS A 296 " occ=0.75 Time building chain proxies: 6.18, per 1000 atoms: 0.60 Number of scatterers: 10370 At special positions: 0 Unit cell: (87.72, 99.072, 145.512, 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 66 16.00 P 2 15.00 O 1889 8.00 N 1780 7.00 C 6633 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: 4.37 Conformation dependent library (CDL) restraints added in 1.8 seconds 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2416 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 64 helices and 2 sheets defined 56.9% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.39 Creating SS restraints... Processing helix chain 'A' and resid 21 through 27 Processing helix chain 'A' and resid 54 through 74 Processing helix chain 'A' and resid 88 through 98 Processing helix chain 'A' and resid 112 through 127 removed outlier: 4.745A pdb=" N GLU A 116 " --> pdb=" O ILE A 113 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ASP A 118 " --> pdb=" O ASN A 115 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU A 119 " --> pdb=" O GLU A 116 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 123 " --> pdb=" O SER A 120 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N CYS A 125 " --> pdb=" O ARG A 122 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ARG A 126 " --> pdb=" O SER A 123 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N GLU A 127 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 143 through 150 Processing helix chain 'A' and resid 158 through 168 Processing helix chain 'A' and resid 180 through 182 No H-bonds generated for 'chain 'A' and resid 180 through 182' Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 205 through 208 Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.901A pdb=" N PHE A 217 " --> pdb=" O ASN A 214 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU A 218 " --> pdb=" O MET A 215 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 214 through 218' Processing helix chain 'A' and resid 227 through 245 removed outlier: 3.503A pdb=" N GLU A 236 " --> pdb=" O LEU A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 No H-bonds generated for 'chain 'A' and resid 252 through 255' Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 277 through 293 removed outlier: 3.576A pdb=" N VAL A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 320 removed outlier: 3.670A pdb=" N TRP A 314 " --> pdb=" O GLY A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 347 through 354 Processing helix chain 'A' and resid 361 through 372 Processing helix chain 'A' and resid 378 through 389 removed outlier: 3.511A pdb=" N VAL A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU A 388 " --> pdb=" O VAL A 384 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 407 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 440 through 447 removed outlier: 3.620A pdb=" N LYS A 445 " --> pdb=" O VAL A 441 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 457 Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 477 through 483 removed outlier: 3.621A pdb=" N GLN A 482 " --> pdb=" O GLU A 478 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 516 Processing helix chain 'B' and resid 4 through 17 Proline residue: B 8 - end of helix removed outlier: 3.501A pdb=" N PHE B 14 " --> pdb=" O TYR B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 31 through 43 Processing helix chain 'B' and resid 51 through 59 Processing helix chain 'B' and resid 61 through 72 removed outlier: 4.945A pdb=" N ILE B 67 " --> pdb=" O ARG B 63 " (cutoff:3.500A) Proline residue: B 68 - end of helix Processing helix chain 'B' and resid 76 through 89 Processing helix chain 'B' and resid 93 through 95 No H-bonds generated for 'chain 'B' and resid 93 through 95' Processing helix chain 'B' and resid 99 through 102 No H-bonds generated for 'chain 'B' and resid 99 through 102' Processing helix chain 'B' and resid 106 through 126 Processing helix chain 'B' and resid 129 through 145 Processing helix chain 'B' and resid 151 through 176 Proline residue: B 171 - end of helix removed outlier: 4.201A pdb=" N HIS B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N HIS B 176 " --> pdb=" O GLU B 172 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 201 removed outlier: 4.125A pdb=" N SER B 190 " --> pdb=" O PRO B 186 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLN B 192 " --> pdb=" O GLY B 188 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASN B 193 " --> pdb=" O ILE B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 213 Processing helix chain 'B' and resid 217 through 219 No H-bonds generated for 'chain 'B' and resid 217 through 219' Processing helix chain 'B' and resid 221 through 231 Processing helix chain 'B' and resid 237 through 247 Processing helix chain 'B' and resid 546 through 570 Processing helix chain 'B' and resid 578 through 608 removed outlier: 4.224A pdb=" N ASP B 591 " --> pdb=" O GLU B 587 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR B 597 " --> pdb=" O LEU B 593 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N SER B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 4.495A pdb=" N TYR B 599 " --> pdb=" O LYS B 595 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLU B 603 " --> pdb=" O TYR B 599 " (cutoff:3.500A) Processing helix chain 'B' and resid 618 through 634 removed outlier: 4.126A pdb=" N LYS B 630 " --> pdb=" O THR B 626 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N PHE B 631 " --> pdb=" O TYR B 627 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 641 No H-bonds generated for 'chain 'B' and resid 639 through 641' Processing helix chain 'B' and resid 648 through 668 Processing helix chain 'B' and resid 677 through 702 Processing helix chain 'B' and resid 708 through 722 Processing helix chain 'B' and resid 726 through 736 removed outlier: 4.021A pdb=" N PHE B 731 " --> pdb=" O LEU B 727 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL B 732 " --> pdb=" O ARG B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 745 through 765 Processing helix chain 'B' and resid 776 through 779 No H-bonds generated for 'chain 'B' and resid 776 through 779' Processing helix chain 'B' and resid 787 through 797 removed outlier: 4.430A pdb=" N TYR B 791 " --> pdb=" O GLU B 787 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 795 " --> pdb=" O TYR B 791 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LEU B 796 " --> pdb=" O TYR B 792 " (cutoff:3.500A) Processing helix chain 'B' and resid 799 through 802 No H-bonds generated for 'chain 'B' and resid 799 through 802' Processing helix chain 'B' and resid 807 through 818 removed outlier: 3.688A pdb=" N PHE B 811 " --> pdb=" O ASN B 807 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N THR B 812 " --> pdb=" O ASP B 808 " (cutoff:3.500A) Processing helix chain 'B' and resid 830 through 842 removed outlier: 4.142A pdb=" N LYS B 834 " --> pdb=" O PRO B 830 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR B 835 " --> pdb=" O ILE B 831 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 854 removed outlier: 3.973A pdb=" N ASP B 852 " --> pdb=" O ASP B 848 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N LEU B 853 " --> pdb=" O ASP B 849 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 862 No H-bonds generated for 'chain 'B' and resid 859 through 862' Processing helix chain 'B' and resid 991 through 1002 removed outlier: 3.873A pdb=" N LEU B 998 " --> pdb=" O ILE B 994 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ILE B1000 " --> pdb=" O LEU B 996 " (cutoff:3.500A) Processing helix chain 'B' and resid 1006 through 1017 removed outlier: 3.612A pdb=" N LEU B1011 " --> pdb=" O HIS B1007 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ARG B1013 " --> pdb=" O LEU B1009 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N ILE B1014 " --> pdb=" O TRP B1010 " (cutoff:3.500A) Processing helix chain 'B' and resid 1020 through 1027 Processing helix chain 'B' and resid 1040 through 1046 removed outlier: 4.325A pdb=" N HIS B1044 " --> pdb=" O PRO B1040 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N CYS B1045 " --> pdb=" O VAL B1041 " (cutoff:3.500A) Processing helix chain 'B' and resid 1059 through 1066 removed outlier: 4.584A pdb=" N THR B1064 " --> pdb=" O GLU B1060 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET B1065 " --> pdb=" O GLN B1061 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LEU B1066 " --> pdb=" O SER B1062 " (cutoff:3.500A) Processing helix chain 'B' and resid 1068 through 1076 removed outlier: 4.334A pdb=" N LEU B1073 " --> pdb=" O PRO B1069 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B1074 " --> pdb=" O PHE B1070 " (cutoff:3.500A) Processing helix chain 'B' and resid 1103 through 1107 Processing helix chain 'B' and resid 1210 through 1218 Processing sheet with id= A, first strand: chain 'A' and resid 131 through 135 removed outlier: 7.910A pdb=" N ALA A 6 " --> pdb=" O ARG A 103 " (cutoff:3.500A) removed outlier: 8.854A pdb=" N CYS A 105 " --> pdb=" O ALA A 6 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL A 8 " --> pdb=" O CYS A 105 " (cutoff:3.500A) removed outlier: 8.438A pdb=" N GLU A 107 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 8.398A pdb=" N TRP A 10 " --> pdb=" O GLU A 107 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N ALA A 35 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ILE A 9 " --> pdb=" O ALA A 35 " (cutoff:3.500A) removed outlier: 6.374A pdb=" N ILE A 37 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU A 82 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 18 through 21 removed outlier: 3.736A pdb=" N GLU B 21 " --> pdb=" O THR B 24 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1221 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: 2.62 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3108 1.34 - 1.46: 2250 1.46 - 1.58: 5148 1.58 - 1.70: 4 1.70 - 1.83: 106 Bond restraints: 10616 Sorted by residual: bond pdb=" C4A FAD A 602 " pdb=" C5A FAD A 602 " ideal model delta sigma weight residual 1.386 1.471 -0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" C5X FAD A 602 " pdb=" C9A FAD A 602 " ideal model delta sigma weight residual 1.412 1.492 -0.080 2.00e-02 2.50e+03 1.62e+01 bond pdb=" C5A FAD A 602 " pdb=" C6A FAD A 602 " ideal model delta sigma weight residual 1.407 1.482 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" CA GLN B 573 " pdb=" CB GLN B 573 " ideal model delta sigma weight residual 1.529 1.581 -0.052 1.38e-02 5.25e+03 1.40e+01 bond pdb=" C7 FAD A 602 " pdb=" C8 FAD A 602 " ideal model delta sigma weight residual 1.420 1.488 -0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 10611 not shown) Histogram of bond angle deviations from ideal: 99.29 - 106.65: 339 106.65 - 114.01: 5978 114.01 - 121.37: 5505 121.37 - 128.73: 2476 128.73 - 136.09: 107 Bond angle restraints: 14405 Sorted by residual: angle pdb=" N TRP B 3 " pdb=" CA TRP B 3 " pdb=" C TRP B 3 " ideal model delta sigma weight residual 113.89 103.07 10.82 1.58e+00 4.01e-01 4.69e+01 angle pdb=" N LEU B 998 " pdb=" CA LEU B 998 " pdb=" C LEU B 998 " ideal model delta sigma weight residual 111.36 104.85 6.51 1.09e+00 8.42e-01 3.57e+01 angle pdb=" N LEU B1211 " pdb=" CA LEU B1211 " pdb=" C LEU B1211 " ideal model delta sigma weight residual 111.71 105.25 6.46 1.15e+00 7.56e-01 3.16e+01 angle pdb=" CA LYS B1117 " pdb=" CB LYS B1117 " pdb=" CG LYS B1117 " ideal model delta sigma weight residual 114.10 123.86 -9.76 2.00e+00 2.50e-01 2.38e+01 angle pdb=" CA TRP B1210 " pdb=" CB TRP B1210 " pdb=" CG TRP B1210 " ideal model delta sigma weight residual 113.60 122.15 -8.55 1.90e+00 2.77e-01 2.03e+01 ... (remaining 14400 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 5403 17.85 - 35.70: 722 35.70 - 53.55: 197 53.55 - 71.40: 37 71.40 - 89.25: 16 Dihedral angle restraints: 6375 sinusoidal: 2648 harmonic: 3727 Sorted by residual: dihedral pdb=" CD ARG B1216 " pdb=" NE ARG B1216 " pdb=" CZ ARG B1216 " pdb=" NH1 ARG B1216 " ideal model delta sinusoidal sigma weight residual 0.00 52.13 -52.13 1 1.00e+01 1.00e-02 3.71e+01 dihedral pdb=" CA HIS B1036 " pdb=" C HIS B1036 " pdb=" N ILE B1037 " pdb=" CA ILE B1037 " ideal model delta harmonic sigma weight residual 180.00 -154.22 -25.78 0 5.00e+00 4.00e-02 2.66e+01 dihedral pdb=" CA MET B1065 " pdb=" C MET B1065 " pdb=" N LEU B1066 " pdb=" CA LEU B1066 " ideal model delta harmonic sigma weight residual 180.00 155.66 24.34 0 5.00e+00 4.00e-02 2.37e+01 ... (remaining 6372 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1371 0.068 - 0.136: 202 0.136 - 0.204: 29 0.204 - 0.273: 2 0.273 - 0.341: 1 Chirality restraints: 1605 Sorted by residual: chirality pdb=" CA MET B1038 " pdb=" N MET B1038 " pdb=" C MET B1038 " pdb=" CB MET B1038 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CB THR B 626 " pdb=" CA THR B 626 " pdb=" OG1 THR B 626 " pdb=" CG2 THR B 626 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CB ILE B 642 " pdb=" CA ILE B 642 " pdb=" CG1 ILE B 642 " pdb=" CG2 ILE B 642 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1602 not shown) Planarity restraints: 1827 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B1216 " -0.864 9.50e-02 1.11e+02 3.87e-01 9.11e+01 pdb=" NE ARG B1216 " 0.051 2.00e-02 2.50e+03 pdb=" CZ ARG B1216 " 0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B1216 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG B1216 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B1210 " 0.031 2.00e-02 2.50e+03 1.90e-02 9.00e+00 pdb=" CG TRP B1210 " -0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP B1210 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP B1210 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B1210 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP B1210 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP B1210 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B1210 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B1210 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B1210 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 850 " 0.018 2.00e-02 2.50e+03 1.80e-02 8.12e+00 pdb=" CG TRP B 850 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 850 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP B 850 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 850 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 850 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 850 " 0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 850 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 850 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 850 " 0.002 2.00e-02 2.50e+03 ... (remaining 1824 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 2747 2.80 - 3.32: 10118 3.32 - 3.85: 17690 3.85 - 4.37: 20459 4.37 - 4.90: 33555 Nonbonded interactions: 84569 Sorted by model distance: nonbonded pdb=" OG1 THR B 577 " pdb=" OD1 ASP B 579 " model vdw 2.272 2.440 nonbonded pdb=" O LEU B 209 " pdb=" OG1 THR B 213 " model vdw 2.275 2.440 nonbonded pdb=" O SER B 777 " pdb=" OG1 THR B 781 " model vdw 2.283 2.440 nonbonded pdb=" ND2 ASN B 701 " pdb=" OE1 GLN B 718 " model vdw 2.296 2.520 nonbonded pdb=" O SER B1130 " pdb=" OG SER B1130 " model vdw 2.296 2.440 ... (remaining 84564 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.250 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 30.990 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 10616 Z= 0.299 Angle : 0.944 13.358 14405 Z= 0.513 Chirality : 0.051 0.341 1605 Planarity : 0.011 0.387 1827 Dihedral : 17.626 89.249 3959 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer: Outliers : 0.44 % Allowed : 24.80 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.22), residues: 1263 helix: -1.53 (0.16), residues: 749 sheet: -0.48 (1.04), residues: 35 loop : -1.65 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.002 TRP B1210 HIS 0.006 0.001 HIS B1075 PHE 0.034 0.002 PHE B 811 TYR 0.020 0.001 TYR B1095 ARG 0.006 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 108 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 202 LEU cc_start: 0.8624 (tp) cc_final: 0.8385 (tp) REVERT: A 270 LEU cc_start: 0.8667 (tt) cc_final: 0.8182 (mp) REVERT: B 179 MET cc_start: 0.4316 (ptt) cc_final: 0.4073 (ptt) REVERT: B 185 MET cc_start: 0.6852 (mmm) cc_final: 0.6359 (mmm) REVERT: B 191 MET cc_start: 0.6944 (ttm) cc_final: 0.6744 (ttp) REVERT: B 211 LEU cc_start: 0.8697 (tp) cc_final: 0.8380 (mt) REVERT: B 789 MET cc_start: 0.5516 (mmt) cc_final: 0.4916 (mmm) REVERT: B 813 MET cc_start: 0.6151 (tmm) cc_final: 0.5627 (tmm) REVERT: B 814 MET cc_start: 0.7873 (mmt) cc_final: 0.7371 (mmp) REVERT: B 1075 HIS cc_start: 0.8218 (p90) cc_final: 0.7940 (p-80) outliers start: 5 outliers final: 0 residues processed: 112 average time/residue: 0.2356 time to fit residues: 37.8625 Evaluate side-chains 92 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 51 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 114 optimal weight: 20.0000 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B1036 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10616 Z= 0.212 Angle : 0.614 7.437 14405 Z= 0.311 Chirality : 0.041 0.161 1605 Planarity : 0.005 0.053 1827 Dihedral : 6.388 75.638 1426 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.32 % Allowed : 23.49 % Favored : 73.19 % 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: -1.32 (0.23), residues: 1263 helix: -0.47 (0.18), residues: 779 sheet: -0.61 (1.02), residues: 37 loop : -1.43 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B1210 HIS 0.005 0.001 HIS B1075 PHE 0.028 0.001 PHE B1020 TYR 0.018 0.001 TYR B1095 ARG 0.002 0.000 ARG B 737 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 88 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8432 (OUTLIER) cc_final: 0.8057 (tpp-160) REVERT: B 179 MET cc_start: 0.4747 (ptt) cc_final: 0.4516 (ptt) REVERT: B 191 MET cc_start: 0.7101 (ttm) cc_final: 0.6648 (ttp) REVERT: B 638 ASP cc_start: 0.6503 (OUTLIER) cc_final: 0.6199 (p0) REVERT: B 814 MET cc_start: 0.7960 (mmt) cc_final: 0.7648 (mmp) outliers start: 38 outliers final: 16 residues processed: 120 average time/residue: 0.2360 time to fit residues: 41.2504 Evaluate side-chains 98 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 1.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 1065 MET Chi-restraints excluded: chain B residue 1073 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 123 optimal weight: 20.0000 chunk 102 optimal weight: 0.1980 chunk 113 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS A 480 GLN ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10616 Z= 0.208 Angle : 0.578 8.320 14405 Z= 0.293 Chirality : 0.040 0.197 1605 Planarity : 0.004 0.056 1827 Dihedral : 5.962 85.774 1426 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.76 % Allowed : 23.67 % Favored : 72.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.24), residues: 1263 helix: 0.05 (0.19), residues: 766 sheet: -0.67 (1.03), residues: 37 loop : -1.36 (0.31), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B1210 HIS 0.003 0.001 HIS B1075 PHE 0.027 0.001 PHE B 811 TYR 0.021 0.001 TYR A 90 ARG 0.003 0.000 ARG A 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 80 time to evaluate : 1.307 Fit side-chains REVERT: A 27 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8164 (mm) REVERT: A 58 ARG cc_start: 0.8414 (OUTLIER) cc_final: 0.8057 (tpp-160) REVERT: B 191 MET cc_start: 0.7097 (ttm) cc_final: 0.6713 (ttp) REVERT: B 638 ASP cc_start: 0.6556 (OUTLIER) cc_final: 0.6097 (p0) REVERT: B 734 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6758 (mm) REVERT: B 850 TRP cc_start: 0.5584 (p90) cc_final: 0.5176 (m-90) REVERT: B 1035 ASP cc_start: 0.5795 (OUTLIER) cc_final: 0.5361 (p0) REVERT: B 1073 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7800 (mt) REVERT: B 1102 TYR cc_start: 0.4809 (OUTLIER) cc_final: 0.4289 (p90) outliers start: 43 outliers final: 25 residues processed: 119 average time/residue: 0.2369 time to fit residues: 40.6653 Evaluate side-chains 106 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 74 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 27 LEU Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 58 ARG Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 335 ASP Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 641 HIS Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 853 LEU Chi-restraints excluded: chain B residue 1035 ASP Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1102 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 76 optimal weight: 9.9990 chunk 115 optimal weight: 4.9990 chunk 121 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 109 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 overall best weight: 1.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 480 GLN ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10616 Z= 0.318 Angle : 0.628 8.139 14405 Z= 0.317 Chirality : 0.043 0.307 1605 Planarity : 0.005 0.051 1827 Dihedral : 6.489 89.576 1426 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 5.24 % Allowed : 23.23 % Favored : 71.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.79 (0.24), residues: 1263 helix: 0.05 (0.18), residues: 780 sheet: -0.93 (1.01), residues: 37 loop : -1.37 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 623 HIS 0.004 0.001 HIS A 285 PHE 0.021 0.002 PHE B 811 TYR 0.024 0.002 TYR B 597 ARG 0.004 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 73 time to evaluate : 1.383 Fit side-chains REVERT: B 638 ASP cc_start: 0.6828 (OUTLIER) cc_final: 0.6312 (p0) REVERT: B 714 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7866 (mp) REVERT: B 734 LEU cc_start: 0.7232 (OUTLIER) cc_final: 0.6792 (mm) REVERT: B 789 MET cc_start: 0.6362 (mmt) cc_final: 0.5871 (mmm) REVERT: B 850 TRP cc_start: 0.5778 (p90) cc_final: 0.5071 (m-90) REVERT: B 1102 TYR cc_start: 0.4678 (OUTLIER) cc_final: 0.4133 (p90) outliers start: 60 outliers final: 37 residues processed: 128 average time/residue: 0.2380 time to fit residues: 43.7376 Evaluate side-chains 115 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 74 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 714 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 811 PHE Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 TYR Chi-restraints excluded: chain B residue 1118 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 10.0000 chunk 69 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 90 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 84 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN B 705 HIS ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 10616 Z= 0.323 Angle : 0.621 8.478 14405 Z= 0.312 Chirality : 0.043 0.301 1605 Planarity : 0.004 0.047 1827 Dihedral : 6.697 84.313 1426 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 5.59 % Allowed : 22.79 % Favored : 71.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.66 (0.24), residues: 1263 helix: 0.10 (0.18), residues: 773 sheet: -0.74 (1.04), residues: 35 loop : -1.21 (0.32), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 623 HIS 0.004 0.001 HIS B1075 PHE 0.032 0.002 PHE B 811 TYR 0.024 0.002 TYR B 597 ARG 0.004 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 77 time to evaluate : 1.232 Fit side-chains REVERT: A 34 ILE cc_start: 0.8688 (mm) cc_final: 0.8441 (mt) REVERT: A 99 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8313 (p) REVERT: A 410 ASP cc_start: 0.8477 (OUTLIER) cc_final: 0.8007 (p0) REVERT: A 506 MET cc_start: 0.8915 (mmt) cc_final: 0.8711 (mmt) REVERT: B 191 MET cc_start: 0.7637 (ttm) cc_final: 0.7019 (ttp) REVERT: B 638 ASP cc_start: 0.7042 (OUTLIER) cc_final: 0.6621 (p0) REVERT: B 734 LEU cc_start: 0.7085 (OUTLIER) cc_final: 0.6664 (mm) REVERT: B 789 MET cc_start: 0.6542 (mmt) cc_final: 0.5969 (mmm) REVERT: B 813 MET cc_start: 0.6549 (tpp) cc_final: 0.6014 (ttt) REVERT: B 850 TRP cc_start: 0.5910 (p90) cc_final: 0.5212 (m-90) REVERT: B 1102 TYR cc_start: 0.4974 (OUTLIER) cc_final: 0.4299 (p90) outliers start: 64 outliers final: 40 residues processed: 136 average time/residue: 0.2002 time to fit residues: 40.3932 Evaluate side-chains 118 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 73 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1037 ILE Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 TYR Chi-restraints excluded: chain B residue 1118 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 0.5980 chunk 117 optimal weight: 7.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 713 HIS ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10616 Z= 0.228 Angle : 0.592 15.436 14405 Z= 0.293 Chirality : 0.041 0.267 1605 Planarity : 0.004 0.056 1827 Dihedral : 6.363 80.057 1426 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.78 % Favored : 94.22 % Rotamer: Outliers : 4.89 % Allowed : 23.76 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.24), residues: 1263 helix: 0.33 (0.19), residues: 772 sheet: -0.76 (1.03), residues: 35 loop : -1.15 (0.32), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 623 HIS 0.003 0.001 HIS B 641 PHE 0.026 0.001 PHE B 811 TYR 0.018 0.001 TYR B 597 ARG 0.003 0.000 ARG A 278 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 79 time to evaluate : 1.077 Fit side-chains REVERT: A 34 ILE cc_start: 0.8705 (mm) cc_final: 0.8464 (mt) REVERT: A 410 ASP cc_start: 0.8421 (OUTLIER) cc_final: 0.7899 (p0) REVERT: B 638 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6419 (p0) REVERT: B 734 LEU cc_start: 0.6956 (OUTLIER) cc_final: 0.6503 (mm) REVERT: B 789 MET cc_start: 0.6525 (mmt) cc_final: 0.6073 (mmm) REVERT: B 850 TRP cc_start: 0.5922 (p90) cc_final: 0.5288 (m-90) REVERT: B 1073 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7699 (mt) REVERT: B 1075 HIS cc_start: 0.8375 (OUTLIER) cc_final: 0.8073 (p-80) REVERT: B 1102 TYR cc_start: 0.4897 (OUTLIER) cc_final: 0.4316 (p90) outliers start: 56 outliers final: 41 residues processed: 128 average time/residue: 0.2159 time to fit residues: 40.3397 Evaluate side-chains 122 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 75 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 709 ASP Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1075 HIS Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 TYR Chi-restraints excluded: chain B residue 1118 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 2.9990 chunk 69 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 121 optimal weight: 20.0000 chunk 76 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 0.1980 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10616 Z= 0.192 Angle : 0.576 11.453 14405 Z= 0.284 Chirality : 0.041 0.250 1605 Planarity : 0.004 0.052 1827 Dihedral : 6.151 79.181 1426 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.72 % Allowed : 24.10 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1263 helix: 0.42 (0.19), residues: 777 sheet: -0.78 (1.02), residues: 35 loop : -1.07 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1057 HIS 0.003 0.001 HIS B1044 PHE 0.030 0.001 PHE B 811 TYR 0.015 0.001 TYR B 597 ARG 0.004 0.000 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 78 time to evaluate : 1.174 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8697 (mm) cc_final: 0.8465 (mt) REVERT: A 58 ARG cc_start: 0.8268 (tpp-160) cc_final: 0.8052 (tpp-160) REVERT: A 99 VAL cc_start: 0.8510 (OUTLIER) cc_final: 0.8274 (p) REVERT: A 410 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7792 (p0) REVERT: B 638 ASP cc_start: 0.6925 (OUTLIER) cc_final: 0.6369 (p0) REVERT: B 734 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6517 (mm) REVERT: B 789 MET cc_start: 0.6538 (mmt) cc_final: 0.5952 (mmm) REVERT: B 813 MET cc_start: 0.6583 (tpp) cc_final: 0.6177 (ttt) REVERT: B 850 TRP cc_start: 0.5999 (p90) cc_final: 0.5335 (m-90) REVERT: B 1073 LEU cc_start: 0.8053 (OUTLIER) cc_final: 0.7618 (mt) REVERT: B 1102 TYR cc_start: 0.4855 (OUTLIER) cc_final: 0.4246 (p90) outliers start: 54 outliers final: 45 residues processed: 126 average time/residue: 0.2230 time to fit residues: 40.5711 Evaluate side-chains 126 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 75 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 32 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1075 HIS Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1088 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 TYR Chi-restraints excluded: chain B residue 1118 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10616 Z= 0.231 Angle : 0.591 10.950 14405 Z= 0.292 Chirality : 0.041 0.255 1605 Planarity : 0.004 0.051 1827 Dihedral : 6.191 79.394 1426 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 5.33 % Allowed : 23.58 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.25), residues: 1263 helix: 0.45 (0.19), residues: 782 sheet: -1.19 (0.96), residues: 37 loop : -1.07 (0.33), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1057 HIS 0.005 0.001 HIS B1044 PHE 0.026 0.001 PHE B 811 TYR 0.017 0.001 TYR B 597 ARG 0.004 0.000 ARG A 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 75 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8696 (mm) cc_final: 0.8451 (mt) REVERT: A 58 ARG cc_start: 0.8276 (tpp-160) cc_final: 0.8067 (tpp-160) REVERT: A 99 VAL cc_start: 0.8504 (OUTLIER) cc_final: 0.8266 (p) REVERT: A 256 LEU cc_start: 0.8314 (tt) cc_final: 0.8106 (pp) REVERT: A 357 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.7863 (mp10) REVERT: A 410 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7965 (p0) REVERT: B 191 MET cc_start: 0.7528 (ttm) cc_final: 0.6864 (ttp) REVERT: B 638 ASP cc_start: 0.6916 (OUTLIER) cc_final: 0.6416 (p0) REVERT: B 734 LEU cc_start: 0.6900 (OUTLIER) cc_final: 0.6558 (mm) REVERT: B 789 MET cc_start: 0.6603 (mmt) cc_final: 0.6069 (mmm) REVERT: B 813 MET cc_start: 0.6681 (tpp) cc_final: 0.6144 (ttt) REVERT: B 850 TRP cc_start: 0.5980 (p90) cc_final: 0.5287 (m-90) REVERT: B 1102 TYR cc_start: 0.4902 (OUTLIER) cc_final: 0.4288 (p90) outliers start: 61 outliers final: 48 residues processed: 130 average time/residue: 0.2075 time to fit residues: 39.3418 Evaluate side-chains 129 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 75 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 785 THR Chi-restraints excluded: chain B residue 788 VAL Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1075 HIS Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1088 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 TYR Chi-restraints excluded: chain B residue 1118 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 49 optimal weight: 0.1980 chunk 88 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10616 Z= 0.212 Angle : 0.589 10.739 14405 Z= 0.288 Chirality : 0.041 0.201 1605 Planarity : 0.004 0.050 1827 Dihedral : 6.090 78.620 1426 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 4.98 % Allowed : 24.02 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.25), residues: 1263 helix: 0.49 (0.19), residues: 775 sheet: -1.23 (0.96), residues: 37 loop : -1.00 (0.32), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B1057 HIS 0.007 0.001 HIS B1044 PHE 0.024 0.001 PHE B 811 TYR 0.016 0.001 TYR B 597 ARG 0.003 0.000 ARG B 165 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 76 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 34 ILE cc_start: 0.8697 (mm) cc_final: 0.8457 (mt) REVERT: A 58 ARG cc_start: 0.8282 (tpp-160) cc_final: 0.8068 (tpp-160) REVERT: A 99 VAL cc_start: 0.8490 (OUTLIER) cc_final: 0.8256 (p) REVERT: A 357 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.7862 (mp10) REVERT: A 410 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.7820 (p0) REVERT: B 638 ASP cc_start: 0.6900 (OUTLIER) cc_final: 0.6399 (p0) REVERT: B 734 LEU cc_start: 0.6906 (OUTLIER) cc_final: 0.6550 (mm) REVERT: B 789 MET cc_start: 0.6643 (mmt) cc_final: 0.6107 (mmm) REVERT: B 813 MET cc_start: 0.6844 (tpp) cc_final: 0.6361 (ttt) REVERT: B 850 TRP cc_start: 0.6010 (p90) cc_final: 0.5272 (m-90) REVERT: B 1102 TYR cc_start: 0.5053 (OUTLIER) cc_final: 0.4374 (p90) outliers start: 57 outliers final: 47 residues processed: 128 average time/residue: 0.2272 time to fit residues: 42.7754 Evaluate side-chains 126 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 73 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 196 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain A residue 515 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 2 ASP Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 51 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 131 SER Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1031 VAL Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1075 HIS Chi-restraints excluded: chain B residue 1087 SER Chi-restraints excluded: chain B residue 1088 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.6980 chunk 56 optimal weight: 0.4980 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 0.0040 chunk 115 optimal weight: 7.9990 chunk 99 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.1980 chunk 61 optimal weight: 0.6980 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 9.9990 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.3338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10616 Z= 0.158 Angle : 0.577 13.300 14405 Z= 0.281 Chirality : 0.040 0.153 1605 Planarity : 0.004 0.051 1827 Dihedral : 5.835 78.746 1426 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 4.02 % Allowed : 25.15 % Favored : 70.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.25), residues: 1263 helix: 0.53 (0.19), residues: 779 sheet: -1.12 (0.96), residues: 37 loop : -0.95 (0.33), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 850 HIS 0.005 0.000 HIS B1044 PHE 0.025 0.001 PHE B 811 TYR 0.013 0.001 TYR B 597 ARG 0.004 0.000 ARG B 165 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2526 Ramachandran restraints generated. 1263 Oldfield, 0 Emsley, 1263 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 80 time to evaluate : 1.231 Fit side-chains revert: symmetry clash REVERT: A 58 ARG cc_start: 0.8269 (tpp-160) cc_final: 0.8054 (tpp-160) REVERT: A 99 VAL cc_start: 0.8405 (OUTLIER) cc_final: 0.8188 (p) REVERT: A 357 GLN cc_start: 0.8906 (OUTLIER) cc_final: 0.7919 (mp10) REVERT: A 410 ASP cc_start: 0.8281 (OUTLIER) cc_final: 0.7722 (p0) REVERT: B 638 ASP cc_start: 0.6949 (OUTLIER) cc_final: 0.6549 (p0) REVERT: B 734 LEU cc_start: 0.6872 (OUTLIER) cc_final: 0.6529 (mm) REVERT: B 789 MET cc_start: 0.6753 (mmt) cc_final: 0.6347 (mmm) REVERT: B 813 MET cc_start: 0.6800 (tpp) cc_final: 0.6298 (ttt) REVERT: B 850 TRP cc_start: 0.6011 (p90) cc_final: 0.5256 (m-90) REVERT: B 1102 TYR cc_start: 0.5028 (OUTLIER) cc_final: 0.4458 (p90) outliers start: 46 outliers final: 34 residues processed: 121 average time/residue: 0.2250 time to fit residues: 39.4165 Evaluate side-chains 115 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 75 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 ILE Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 156 LEU Chi-restraints excluded: chain A residue 164 THR Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 285 HIS Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 338 LEU Chi-restraints excluded: chain A residue 357 GLN Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 410 ASP Chi-restraints excluded: chain A residue 426 SER Chi-restraints excluded: chain A residue 446 ARG Chi-restraints excluded: chain B residue 26 VAL Chi-restraints excluded: chain B residue 30 ASN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 121 THR Chi-restraints excluded: chain B residue 150 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 237 VAL Chi-restraints excluded: chain B residue 611 ASN Chi-restraints excluded: chain B residue 638 ASP Chi-restraints excluded: chain B residue 643 ASP Chi-restraints excluded: chain B residue 688 THR Chi-restraints excluded: chain B residue 706 LEU Chi-restraints excluded: chain B residue 734 LEU Chi-restraints excluded: chain B residue 779 HIS Chi-restraints excluded: chain B residue 1023 LEU Chi-restraints excluded: chain B residue 1073 LEU Chi-restraints excluded: chain B residue 1088 ILE Chi-restraints excluded: chain B residue 1100 THR Chi-restraints excluded: chain B residue 1102 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 chunk 14 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.0370 chunk 41 optimal weight: 1.9990 chunk 102 optimal weight: 5.9990 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.5462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 816 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.120357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.084477 restraints weight = 24930.509| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 3.50 r_work: 0.3143 rms_B_bonded: 4.33 restraints_weight: 0.5000 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.79 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10616 Z= 0.169 Angle : 0.593 12.722 14405 Z= 0.288 Chirality : 0.040 0.187 1605 Planarity : 0.004 0.051 1827 Dihedral : 5.763 80.021 1426 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 3.49 % Allowed : 25.59 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1263 helix: 0.59 (0.19), residues: 774 sheet: -1.10 (0.97), residues: 37 loop : -0.92 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 623 HIS 0.008 0.001 HIS A 285 PHE 0.022 0.001 PHE B 811 TYR 0.016 0.001 TYR A 281 ARG 0.003 0.000 ARG B 165 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2282.17 seconds wall clock time: 42 minutes 37.80 seconds (2557.80 seconds total)