Starting phenix.real_space_refine on Sat Dec 9 06:59:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd7_27335/12_2023/8dd7_27335_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd7_27335/12_2023/8dd7_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_27335/12_2023/8dd7_27335.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd7_27335/12_2023/8dd7_27335.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd7_27335/12_2023/8dd7_27335_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dd7_27335/12_2023/8dd7_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-1.21rc1-5172/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: 6.09, per 1000 atoms: 0.59 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: 3.77 Conformation dependent library (CDL) restraints added in 1.9 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: 2.41 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: 2.65 Time building geometry restraints manager: 4.15 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: 1.490 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: 6.240 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 30.950 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.040 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:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.940 ------------------------------------------------------------------------------- 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 : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 0 residues processed: 112 average time/residue: 0.2382 time to fit residues: 38.5994 Evaluate side-chains 90 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 1.235 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.7766 ------------------------------------------------------------------------------- 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: 6.9990 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 B1036 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10616 Z= 0.210 Angle : 0.613 8.054 14405 Z= 0.309 Chirality : 0.041 0.162 1605 Planarity : 0.005 0.050 1827 Dihedral : 6.276 75.724 1426 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 11.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 3.84 % Allowed : 22.79 % Favored : 73.36 % 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: -1.29 (0.23), residues: 1263 helix: -0.44 (0.18), residues: 773 sheet: -0.67 (1.02), residues: 37 loop : -1.43 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B1210 HIS 0.004 0.001 HIS A 285 PHE 0.019 0.001 PHE B1020 TYR 0.018 0.001 TYR B1095 ARG 0.004 0.000 ARG A 271 *********************** 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 136 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 92 time to evaluate : 1.260 Fit side-chains revert: symmetry clash outliers start: 44 outliers final: 18 residues processed: 130 average time/residue: 0.2455 time to fit residues: 45.9678 Evaluate side-chains 100 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 1.295 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.1007 time to fit residues: 5.0352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 31 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 123 optimal weight: 30.0000 chunk 102 optimal weight: 10.0000 chunk 113 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 91 optimal weight: 6.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS ** B 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN ** 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: 0.7769 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.058 10616 Z= 0.512 Angle : 0.780 10.941 14405 Z= 0.392 Chirality : 0.048 0.350 1605 Planarity : 0.006 0.067 1827 Dihedral : 7.298 87.401 1426 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 17.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 4.02 % Allowed : 23.49 % Favored : 72.49 % 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: -1.31 (0.23), residues: 1263 helix: -0.43 (0.18), residues: 777 sheet: -0.80 (1.03), residues: 35 loop : -1.46 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP B1210 HIS 0.005 0.001 HIS B 779 PHE 0.028 0.003 PHE B 621 TYR 0.033 0.003 TYR B 597 ARG 0.008 0.001 ARG A 278 *********************** 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: 46 poor density : 77 time to evaluate : 1.140 Fit side-chains outliers start: 46 outliers final: 23 residues processed: 119 average time/residue: 0.2371 time to fit residues: 40.7771 Evaluate side-chains 97 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 74 time to evaluate : 1.306 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.1254 time to fit residues: 6.6976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 6.9990 chunk 86 optimal weight: 0.2980 chunk 59 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 54 optimal weight: 0.5980 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 6.9990 chunk 60 optimal weight: 0.0270 chunk 109 optimal weight: 0.0370 chunk 32 optimal weight: 0.4980 overall best weight: 0.2916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 705 HIS B 782 GLN ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 993 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10616 Z= 0.159 Angle : 0.571 8.542 14405 Z= 0.290 Chirality : 0.040 0.237 1605 Planarity : 0.004 0.054 1827 Dihedral : 6.586 79.530 1426 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.66 % Allowed : 24.63 % Favored : 73.71 % 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: -0.67 (0.24), residues: 1263 helix: 0.11 (0.18), residues: 778 sheet: -0.83 (1.00), residues: 35 loop : -1.26 (0.32), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 623 HIS 0.004 0.001 HIS B 574 PHE 0.028 0.001 PHE A 217 TYR 0.022 0.001 TYR B1102 ARG 0.002 0.000 ARG B 715 *********************** 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 98 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 1.361 Fit side-chains outliers start: 19 outliers final: 9 residues processed: 96 average time/residue: 0.2368 time to fit residues: 33.2486 Evaluate side-chains 82 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 73 time to evaluate : 1.214 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.1012 time to fit residues: 3.3530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 6.9990 chunk 1 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 4.9990 chunk 103 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 109 optimal weight: 0.8980 chunk 30 optimal weight: 3.9990 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 166 GLN A 260 HIS A 480 GLN B 241 GLN B 713 HIS B 782 GLN ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.072 10616 Z= 0.613 Angle : 0.803 11.133 14405 Z= 0.402 Chirality : 0.050 0.240 1605 Planarity : 0.006 0.078 1827 Dihedral : 7.068 70.240 1426 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 3.32 % Allowed : 24.54 % Favored : 72.14 % 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: -1.31 (0.23), residues: 1263 helix: -0.37 (0.18), residues: 779 sheet: -1.14 (0.98), residues: 35 loop : -1.56 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP B 623 HIS 0.009 0.001 HIS A 285 PHE 0.028 0.003 PHE B 621 TYR 0.029 0.003 TYR B 597 ARG 0.007 0.001 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 112 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 74 time to evaluate : 1.291 Fit side-chains outliers start: 38 outliers final: 17 residues processed: 106 average time/residue: 0.2134 time to fit residues: 33.7560 Evaluate side-chains 87 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 1.244 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 0 residues processed: 17 average time/residue: 0.1003 time to fit residues: 4.8964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 121 optimal weight: 0.0570 chunk 101 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 10 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- 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: 0.7704 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10616 Z= 0.185 Angle : 0.597 15.404 14405 Z= 0.296 Chirality : 0.041 0.307 1605 Planarity : 0.004 0.050 1827 Dihedral : 6.733 82.942 1426 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 2.18 % Allowed : 24.80 % Favored : 73.01 % 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: -0.56 (0.24), residues: 1263 helix: 0.23 (0.19), residues: 774 sheet: -1.21 (0.95), residues: 35 loop : -1.23 (0.32), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 623 HIS 0.003 0.001 HIS B1036 PHE 0.017 0.001 PHE B 811 TYR 0.018 0.001 TYR B 597 ARG 0.002 0.000 ARG A 294 *********************** 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 100 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 75 time to evaluate : 1.281 Fit side-chains outliers start: 25 outliers final: 6 residues processed: 96 average time/residue: 0.2296 time to fit residues: 32.7398 Evaluate side-chains 76 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 70 time to evaluate : 1.269 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1028 time to fit residues: 2.8639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.7980 chunk 69 optimal weight: 8.9990 chunk 89 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 102 optimal weight: 0.0970 chunk 121 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 56 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN A 480 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10616 Z= 0.213 Angle : 0.606 13.935 14405 Z= 0.299 Chirality : 0.042 0.276 1605 Planarity : 0.004 0.062 1827 Dihedral : 6.440 77.067 1426 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 0.96 % Allowed : 26.38 % Favored : 72.66 % 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: -0.42 (0.24), residues: 1263 helix: 0.37 (0.19), residues: 776 sheet: -1.23 (0.94), residues: 35 loop : -1.23 (0.32), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 850 HIS 0.003 0.001 HIS B1044 PHE 0.016 0.001 PHE B 811 TYR 0.016 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 82 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 71 time to evaluate : 1.275 Fit side-chains outliers start: 11 outliers final: 3 residues processed: 81 average time/residue: 0.2224 time to fit residues: 27.1494 Evaluate side-chains 74 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 1.291 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1057 time to fit residues: 2.3121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 11 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 110 optimal weight: 0.3980 chunk 116 optimal weight: 0.4980 chunk 106 optimal weight: 2.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS B 226 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 782 GLN ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10616 Z= 0.170 Angle : 0.584 12.557 14405 Z= 0.286 Chirality : 0.041 0.294 1605 Planarity : 0.004 0.060 1827 Dihedral : 6.381 81.575 1426 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.79 % Allowed : 26.64 % 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: -0.29 (0.25), residues: 1263 helix: 0.46 (0.19), residues: 782 sheet: -1.13 (0.95), residues: 35 loop : -1.17 (0.32), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 850 HIS 0.007 0.001 HIS B1044 PHE 0.019 0.001 PHE B 811 TYR 0.014 0.001 TYR B 597 ARG 0.004 0.000 ARG B 165 *********************** 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 90 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 1.277 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 89 average time/residue: 0.2524 time to fit residues: 32.4442 Evaluate side-chains 78 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 1.309 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2640 time to fit residues: 2.7435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 10.0000 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 112 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 119 optimal weight: 5.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 HIS B 226 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10616 Z= 0.285 Angle : 0.637 12.565 14405 Z= 0.312 Chirality : 0.043 0.344 1605 Planarity : 0.004 0.055 1827 Dihedral : 6.314 71.611 1426 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 0.44 % Allowed : 27.34 % Favored : 72.23 % 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: -0.33 (0.25), residues: 1263 helix: 0.42 (0.19), residues: 785 sheet: -1.08 (0.96), residues: 35 loop : -1.18 (0.32), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 850 HIS 0.005 0.001 HIS B1044 PHE 0.015 0.002 PHE B 811 TYR 0.018 0.002 TYR B 597 ARG 0.005 0.000 ARG A 12 *********************** 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 79 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 1.258 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 2 residues processed: 76 average time/residue: 0.2304 time to fit residues: 26.2801 Evaluate side-chains 75 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 73 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1082 time to fit residues: 2.0891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 83 optimal weight: 1.9990 chunk 125 optimal weight: 9.9990 chunk 115 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 0.1980 chunk 79 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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: 0.7705 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10616 Z= 0.213 Angle : 0.609 12.646 14405 Z= 0.296 Chirality : 0.042 0.302 1605 Planarity : 0.004 0.055 1827 Dihedral : 6.262 74.207 1426 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 0.26 % Allowed : 27.60 % Favored : 72.14 % 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: -0.22 (0.25), residues: 1263 helix: 0.51 (0.19), residues: 783 sheet: -1.06 (0.96), residues: 35 loop : -1.13 (0.32), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 623 HIS 0.006 0.001 HIS B1044 PHE 0.014 0.001 PHE B 811 TYR 0.018 0.001 TYR B 597 ARG 0.005 0.000 ARG A 12 ********************** 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 77 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 74 time to evaluate : 1.254 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 76 average time/residue: 0.2588 time to fit residues: 28.9248 Evaluate side-chains 74 residues out of total 1145 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 71 time to evaluate : 1.153 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1139 time to fit residues: 2.2823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.7980 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.0570 chunk 41 optimal weight: 0.7980 chunk 102 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 226 GLN ** B 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 755 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.119701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.080936 restraints weight = 24923.808| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.80 r_work: 0.3165 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.78 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.3651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10616 Z= 0.182 Angle : 0.601 12.231 14405 Z= 0.290 Chirality : 0.041 0.281 1605 Planarity : 0.004 0.055 1827 Dihedral : 6.211 75.742 1426 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 0.17 % Allowed : 27.69 % Favored : 72.14 % 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: -0.16 (0.25), residues: 1263 helix: 0.59 (0.19), residues: 779 sheet: -1.00 (0.96), residues: 35 loop : -1.18 (0.32), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 623 HIS 0.005 0.001 HIS B1044 PHE 0.015 0.001 PHE B 811 TYR 0.019 0.001 TYR B1102 ARG 0.005 0.000 ARG A 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2231.13 seconds wall clock time: 41 minutes 30.45 seconds (2490.45 seconds total)