Starting phenix.real_space_refine on Mon Apr 8 23:10:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhg_24460/04_2024/7rhg_24460_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhg_24460/04_2024/7rhg_24460.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhg_24460/04_2024/7rhg_24460.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhg_24460/04_2024/7rhg_24460.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhg_24460/04_2024/7rhg_24460_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7rhg_24460/04_2024/7rhg_24460_updated.pdb" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 4 5.49 5 S 82 5.16 5 C 9625 2.51 5 N 2405 2.21 5 O 2637 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 662": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 703": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 787": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14753 Number of models: 1 Model: "" Number of chains: 8 Chain: "C" Number of atoms: 3689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 450, 3689 Classifications: {'peptide': 450} Link IDs: {'PTRANS': 14, 'TRANS': 435} Chain: "B" Number of atoms: 3542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3542 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 14, 'TRANS': 417} Chain breaks: 1 Chain: "A" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3717 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "D" Number of atoms: 3717 Number of conformers: 1 Conformer: "" Number of residues, atoms: 454, 3717 Classifications: {'peptide': 454} Link IDs: {'PTRANS': 14, 'TRANS': 439} Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Chain: "D" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Classifications: {'RNA': 1} Modifications used: {'rna3p': 1} Time building chain proxies: 8.03, per 1000 atoms: 0.54 Number of scatterers: 14753 At special positions: 0 Unit cell: (97.556, 98.397, 119.422, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 82 16.00 P 4 15.00 O 2637 8.00 N 2405 7.00 C 9625 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: 5.98 Conformation dependent library (CDL) restraints added in 2.8 seconds 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3386 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 68 helices and 9 sheets defined 60.7% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'C' and resid 163 through 188 Proline residue: C 175 - end of helix removed outlier: 3.599A pdb=" N VAL C 183 " --> pdb=" O ASN C 179 " (cutoff:3.500A) removed outlier: 5.810A pdb=" N ILE C 184 " --> pdb=" O TRP C 180 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA C 185 " --> pdb=" O THR C 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 190 through 195 Processing helix chain 'C' and resid 197 through 218 Processing helix chain 'C' and resid 233 through 242 Processing helix chain 'C' and resid 244 through 253 Processing helix chain 'C' and resid 256 through 261 Processing helix chain 'C' and resid 268 through 291 removed outlier: 4.193A pdb=" N ASN C 273 " --> pdb=" O ILE C 270 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ARG C 277 " --> pdb=" O ARG C 274 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N SER C 279 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLU C 289 " --> pdb=" O GLN C 286 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 325 Processing helix chain 'C' and resid 345 through 361 Processing helix chain 'C' and resid 372 through 403 Processing helix chain 'C' and resid 405 through 423 Processing helix chain 'C' and resid 428 through 443 Processing helix chain 'C' and resid 450 through 456 removed outlier: 4.486A pdb=" N TYR C 456 " --> pdb=" O GLU C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 459 through 476 removed outlier: 6.271A pdb=" N ASP C 472 " --> pdb=" O ASN C 468 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N THR C 473 " --> pdb=" O VAL C 469 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS C 476 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing helix chain 'C' and resid 485 through 493 removed outlier: 3.840A pdb=" N VAL C 489 " --> pdb=" O ALA C 485 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 578 through 587 removed outlier: 4.653A pdb=" N GLU C 587 " --> pdb=" O GLU C 583 " (cutoff:3.500A) Processing helix chain 'C' and resid 589 through 604 Processing helix chain 'B' and resid 654 through 679 Proline residue: B 675 - end of helix Processing helix chain 'B' and resid 688 through 708 Processing helix chain 'B' and resid 725 through 734 removed outlier: 3.510A pdb=" N LEU B 733 " --> pdb=" O ARG B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 736 through 743 Processing helix chain 'B' and resid 759 through 767 Proline residue: B 764 - end of helix Processing helix chain 'B' and resid 770 through 782 removed outlier: 3.785A pdb=" N SER B 781 " --> pdb=" O SER B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 816 Processing helix chain 'B' and resid 833 through 843 Processing helix chain 'B' and resid 855 through 886 Processing helix chain 'B' and resid 888 through 906 Processing helix chain 'B' and resid 911 through 928 removed outlier: 3.565A pdb=" N ARG B 916 " --> pdb=" O SER B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 933 through 939 removed outlier: 4.059A pdb=" N VAL B 938 " --> pdb=" O GLU B 935 " (cutoff:3.500A) Processing helix chain 'B' and resid 942 through 959 removed outlier: 6.272A pdb=" N ASN B 955 " --> pdb=" O ASP B 951 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ILE B 956 " --> pdb=" O VAL B 952 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS B 959 " --> pdb=" O ASN B 955 " (cutoff:3.500A) Processing helix chain 'B' and resid 968 through 977 Processing helix chain 'B' and resid 1030 through 1034 Processing helix chain 'B' and resid 1059 through 1065 Processing helix chain 'B' and resid 1070 through 1081 Processing helix chain 'A' and resid 163 through 188 removed outlier: 3.570A pdb=" N LEU A 174 " --> pdb=" O PHE A 170 " (cutoff:3.500A) Proline residue: A 175 - end of helix removed outlier: 3.702A pdb=" N VAL A 183 " --> pdb=" O ASN A 179 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ILE A 184 " --> pdb=" O TRP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 195 Processing helix chain 'A' and resid 197 through 220 Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 244 through 251 Processing helix chain 'A' and resid 257 through 263 removed outlier: 3.550A pdb=" N PHE A 261 " --> pdb=" O LEU A 258 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU A 263 " --> pdb=" O TYR A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 291 removed outlier: 4.168A pdb=" N ASN A 273 " --> pdb=" O ILE A 270 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 277 " --> pdb=" O ARG A 274 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N SER A 279 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLU A 289 " --> pdb=" O GLN A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 325 Processing helix chain 'A' and resid 345 through 360 Processing helix chain 'A' and resid 372 through 403 Processing helix chain 'A' and resid 405 through 424 Processing helix chain 'A' and resid 428 through 443 Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 459 through 474 removed outlier: 6.110A pdb=" N ASP A 472 " --> pdb=" O ASN A 468 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N THR A 473 " --> pdb=" O VAL A 469 " (cutoff:3.500A) Processing helix chain 'A' and resid 485 through 493 Processing helix chain 'A' and resid 578 through 587 removed outlier: 4.859A pdb=" N GLU A 587 " --> pdb=" O GLU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 605 Processing helix chain 'D' and resid 163 through 188 Proline residue: D 175 - end of helix removed outlier: 5.286A pdb=" N ILE D 184 " --> pdb=" O TRP D 180 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA D 185 " --> pdb=" O THR D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 190 through 195 Processing helix chain 'D' and resid 197 through 219 Processing helix chain 'D' and resid 233 through 241 Processing helix chain 'D' and resid 244 through 252 Processing helix chain 'D' and resid 257 through 263 removed outlier: 3.591A pdb=" N PHE D 261 " --> pdb=" O LEU D 258 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N LEU D 263 " --> pdb=" O TYR D 260 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 289 removed outlier: 4.248A pdb=" N ASN D 273 " --> pdb=" O ILE D 270 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG D 277 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N SER D 279 " --> pdb=" O LEU D 276 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N PHE D 282 " --> pdb=" O SER D 279 " (cutoff:3.500A) Processing helix chain 'D' and resid 295 through 325 Processing helix chain 'D' and resid 345 through 360 Processing helix chain 'D' and resid 372 through 403 Processing helix chain 'D' and resid 405 through 423 Processing helix chain 'D' and resid 428 through 443 Processing helix chain 'D' and resid 450 through 456 removed outlier: 3.883A pdb=" N TYR D 456 " --> pdb=" O GLU D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 475 removed outlier: 5.858A pdb=" N ASP D 472 " --> pdb=" O ASN D 468 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N THR D 473 " --> pdb=" O VAL D 469 " (cutoff:3.500A) Processing helix chain 'D' and resid 485 through 493 Processing helix chain 'D' and resid 578 through 587 removed outlier: 4.633A pdb=" N GLU D 587 " --> pdb=" O GLU D 583 " (cutoff:3.500A) Processing helix chain 'D' and resid 589 through 605 Processing sheet with id= A, first strand: chain 'C' and resid 496 through 499 Processing sheet with id= B, first strand: chain 'C' and resid 524 through 527 removed outlier: 4.002A pdb=" N ASN C 564 " --> pdb=" O VAL C 527 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 715 through 717 removed outlier: 3.873A pdb=" N PHE B 715 " --> pdb=" O ILE B 722 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 979 through 983 removed outlier: 6.498A pdb=" N PHE B1055 " --> pdb=" O ILE B1002 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N ILE B1002 " --> pdb=" O PHE B1055 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N LEU B1057 " --> pdb=" O TYR B1000 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N TYR B1000 " --> pdb=" O LEU B1057 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 1046 through 1048 removed outlier: 3.783A pdb=" N VAL B1020 " --> pdb=" O VAL B1009 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N GLY B1011 " --> pdb=" O VAL B1018 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N VAL B1018 " --> pdb=" O GLY B1011 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 496 through 500 removed outlier: 6.653A pdb=" N PHE A 574 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 5.661A pdb=" N ILE A 519 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU A 576 " --> pdb=" O TYR A 517 " (cutoff:3.500A) removed outlier: 5.603A pdb=" N TYR A 517 " --> pdb=" O LEU A 576 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 564 through 567 removed outlier: 3.841A pdb=" N ASN A 564 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 536 " --> pdb=" O VAL A 526 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'D' and resid 496 through 500 removed outlier: 6.549A pdb=" N PHE D 574 " --> pdb=" O ILE D 519 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ILE D 519 " --> pdb=" O PHE D 574 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N LEU D 576 " --> pdb=" O TYR D 517 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N TYR D 517 " --> pdb=" O LEU D 576 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'D' and resid 524 through 527 removed outlier: 3.735A pdb=" N ASN D 564 " --> pdb=" O VAL D 527 " (cutoff:3.500A) 816 hydrogen bonds defined for protein. 2226 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: 4.39 Time building geometry restraints manager: 6.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4540 1.34 - 1.46: 3203 1.46 - 1.58: 7221 1.58 - 1.69: 9 1.69 - 1.81: 138 Bond restraints: 15111 Sorted by residual: bond pdb=" N PRO B 685 " pdb=" CD PRO B 685 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.13e+01 bond pdb=" CB PRO B 685 " pdb=" CG PRO B 685 " ideal model delta sigma weight residual 1.492 1.589 -0.097 5.00e-02 4.00e+02 3.76e+00 bond pdb=" CB THR B 842 " pdb=" CG2 THR B 842 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.52e+00 bond pdb=" CB VAL A 492 " pdb=" CG1 VAL A 492 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.59e+00 bond pdb=" CB VAL A 350 " pdb=" CG1 VAL A 350 " ideal model delta sigma weight residual 1.521 1.477 0.044 3.30e-02 9.18e+02 1.75e+00 ... (remaining 15106 not shown) Histogram of bond angle deviations from ideal: 97.91 - 105.58: 249 105.58 - 113.25: 8237 113.25 - 120.92: 7718 120.92 - 128.59: 4184 128.59 - 136.26: 105 Bond angle restraints: 20493 Sorted by residual: angle pdb=" C ASN B 830 " pdb=" N SER B 831 " pdb=" CA SER B 831 " ideal model delta sigma weight residual 121.54 127.15 -5.61 1.91e+00 2.74e-01 8.62e+00 angle pdb=" C3' CMP C 701 " pdb=" O3' CMP C 701 " pdb=" P CMP C 701 " ideal model delta sigma weight residual 120.50 111.94 8.56 3.00e+00 1.11e-01 8.14e+00 angle pdb=" C3' CMP A 701 " pdb=" O3' CMP A 701 " pdb=" P CMP A 701 " ideal model delta sigma weight residual 120.50 112.10 8.40 3.00e+00 1.11e-01 7.85e+00 angle pdb=" C3' CMP D 701 " pdb=" O3' CMP D 701 " pdb=" P CMP D 701 " ideal model delta sigma weight residual 120.50 112.35 8.15 3.00e+00 1.11e-01 7.38e+00 angle pdb=" C3' CMP B1301 " pdb=" O3' CMP B1301 " pdb=" P CMP B1301 " ideal model delta sigma weight residual 120.50 112.68 7.82 3.00e+00 1.11e-01 6.80e+00 ... (remaining 20488 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.48: 8813 34.48 - 68.96: 118 68.96 - 103.44: 16 103.44 - 137.92: 4 137.92 - 172.39: 8 Dihedral angle restraints: 8959 sinusoidal: 3675 harmonic: 5284 Sorted by residual: dihedral pdb=" C3' CMP C 701 " pdb=" O3' CMP C 701 " pdb=" P CMP C 701 " pdb=" O1P CMP C 701 " ideal model delta sinusoidal sigma weight residual -60.00 112.39 -172.39 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C3' CMP A 701 " pdb=" O3' CMP A 701 " pdb=" P CMP A 701 " pdb=" O1P CMP A 701 " ideal model delta sinusoidal sigma weight residual -60.00 112.38 -172.38 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C3' CMP D 701 " pdb=" O3' CMP D 701 " pdb=" P CMP D 701 " pdb=" O1P CMP D 701 " ideal model delta sinusoidal sigma weight residual -60.00 111.48 -171.48 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 8956 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1461 0.033 - 0.067: 593 0.067 - 0.100: 179 0.100 - 0.133: 50 0.133 - 0.166: 6 Chirality restraints: 2289 Sorted by residual: chirality pdb=" CB VAL B 757 " pdb=" CA VAL B 757 " pdb=" CG1 VAL B 757 " pdb=" CG2 VAL B 757 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 6.92e-01 chirality pdb=" CA ILE A 254 " pdb=" N ILE A 254 " pdb=" C ILE A 254 " pdb=" CB ILE A 254 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.50e-01 chirality pdb=" CA ILE C 254 " pdb=" N ILE C 254 " pdb=" C ILE C 254 " pdb=" CB ILE C 254 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 2286 not shown) Planarity restraints: 2524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 763 " -0.043 5.00e-02 4.00e+02 6.47e-02 6.70e+00 pdb=" N PRO B 764 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 764 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 764 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 339 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO D 340 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 340 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 340 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 382 " -0.016 2.00e-02 2.50e+03 1.48e-02 3.81e+00 pdb=" CG PHE A 382 " 0.034 2.00e-02 2.50e+03 pdb=" CD1 PHE A 382 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 382 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE A 382 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 382 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 382 " -0.002 2.00e-02 2.50e+03 ... (remaining 2521 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 820 2.74 - 3.28: 15311 3.28 - 3.82: 26866 3.82 - 4.36: 31468 4.36 - 4.90: 52915 Nonbonded interactions: 127380 Sorted by model distance: nonbonded pdb=" O THR C 357 " pdb=" OG1 THR C 361 " model vdw 2.196 2.440 nonbonded pdb=" O LEU C 169 " pdb=" OG1 THR C 173 " model vdw 2.221 2.440 nonbonded pdb=" O LEU D 169 " pdb=" OG1 THR D 173 " model vdw 2.241 2.440 nonbonded pdb=" O THR A 357 " pdb=" OG1 THR A 361 " model vdw 2.269 2.440 nonbonded pdb=" OE2 GLU A 515 " pdb=" OH TYR A 517 " model vdw 2.272 2.440 ... (remaining 127375 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 156 through 605 or resid 701)) selection = chain 'C' selection = (chain 'D' and (resid 156 through 605 or resid 701)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 4.270 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: 0.000 Extract box with map and model: 5.720 Check model and map are aligned: 0.200 Set scattering table: 0.140 Process input model: 41.430 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.070 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:14.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 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 : 0.003 0.097 15111 Z= 0.195 Angle : 0.573 8.561 20493 Z= 0.299 Chirality : 0.041 0.166 2289 Planarity : 0.004 0.065 2524 Dihedral : 15.356 172.395 5573 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.74 (0.19), residues: 1780 helix: 0.77 (0.14), residues: 1141 sheet: 0.38 (0.72), residues: 44 loop : 0.20 (0.26), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP D 168 HIS 0.004 0.001 HIS A 312 PHE 0.034 0.001 PHE A 382 TYR 0.017 0.001 TYR B 787 ARG 0.006 0.000 ARG A 407 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 1.757 Fit side-chains REVERT: C 296 ASN cc_start: 0.8505 (m-40) cc_final: 0.8270 (m-40) REVERT: B 1061 ASP cc_start: 0.7803 (m-30) cc_final: 0.7512 (m-30) REVERT: A 281 MET cc_start: 0.8450 (ttp) cc_final: 0.8242 (ttm) REVERT: D 237 ILE cc_start: 0.8421 (mm) cc_final: 0.8182 (mm) REVERT: D 411 GLN cc_start: 0.8169 (tp-100) cc_final: 0.7827 (mm-40) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 1.5207 time to fit residues: 318.1675 Evaluate side-chains 138 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 74 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 91 optimal weight: 0.0020 chunk 72 optimal weight: 0.1980 chunk 139 optimal weight: 0.9990 chunk 53 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 103 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 overall best weight: 0.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 758 ASN B 805 ASN B 864 ASN B1068 HIS A 411 GLN D 243 ASN D 498 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.0788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 15111 Z= 0.129 Angle : 0.454 9.344 20493 Z= 0.237 Chirality : 0.037 0.153 2289 Planarity : 0.004 0.052 2524 Dihedral : 12.264 162.762 2033 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.06 % Allowed : 6.52 % Favored : 92.42 % 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: 1.64 (0.20), residues: 1780 helix: 1.52 (0.15), residues: 1129 sheet: 0.52 (0.69), residues: 44 loop : 0.48 (0.26), residues: 607 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 168 HIS 0.005 0.001 HIS B1068 PHE 0.013 0.001 PHE B 870 TYR 0.010 0.001 TYR D 349 ARG 0.005 0.000 ARG A 514 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 159 time to evaluate : 1.650 Fit side-chains REVERT: C 475 LYS cc_start: 0.8348 (mmtt) cc_final: 0.8093 (mmtt) REVERT: B 770 MET cc_start: 0.7905 (mtt) cc_final: 0.7682 (mtp) REVERT: B 897 MET cc_start: 0.8185 (ttt) cc_final: 0.7915 (ttt) REVERT: B 1061 ASP cc_start: 0.7703 (m-30) cc_final: 0.7467 (m-30) REVERT: D 411 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7856 (mm-40) REVERT: D 490 GLU cc_start: 0.7066 (OUTLIER) cc_final: 0.6837 (mm-30) outliers start: 17 outliers final: 5 residues processed: 169 average time/residue: 1.4395 time to fit residues: 266.3756 Evaluate side-chains 145 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 139 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 89 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 134 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 161 optimal weight: 0.9990 chunk 174 optimal weight: 0.8980 chunk 144 optimal weight: 0.2980 chunk 160 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 chunk 129 optimal weight: 9.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 964 GLN B1053 ASN A 411 GLN D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 15111 Z= 0.138 Angle : 0.443 9.240 20493 Z= 0.230 Chirality : 0.037 0.148 2289 Planarity : 0.003 0.043 2524 Dihedral : 12.216 162.504 2033 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.06 % Allowed : 9.44 % Favored : 89.50 % 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: 1.95 (0.20), residues: 1780 helix: 1.82 (0.15), residues: 1123 sheet: 0.58 (0.67), residues: 43 loop : 0.49 (0.26), residues: 614 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 168 HIS 0.004 0.001 HIS B 803 PHE 0.013 0.001 PHE A 382 TYR 0.022 0.001 TYR B 732 ARG 0.006 0.000 ARG B 778 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 154 time to evaluate : 1.704 Fit side-chains REVERT: B 770 MET cc_start: 0.7911 (mtt) cc_final: 0.7677 (mtp) REVERT: B 897 MET cc_start: 0.8418 (ttt) cc_final: 0.8014 (ttt) REVERT: B 1058 ASP cc_start: 0.8204 (p0) cc_final: 0.7880 (p0) REVERT: B 1061 ASP cc_start: 0.7710 (m-30) cc_final: 0.7421 (m-30) REVERT: D 411 GLN cc_start: 0.8156 (tp-100) cc_final: 0.7880 (mm-40) REVERT: D 490 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6851 (mm-30) outliers start: 17 outliers final: 9 residues processed: 164 average time/residue: 1.3776 time to fit residues: 249.0087 Evaluate side-chains 152 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 142 time to evaluate : 2.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 212 LEU Chi-restraints excluded: chain C residue 294 TYR Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 575 CYS Chi-restraints excluded: chain D residue 590 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 159 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 162 optimal weight: 9.9990 chunk 172 optimal weight: 9.9990 chunk 154 optimal weight: 0.0040 chunk 46 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 overall best weight: 3.6000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 245 GLN B 714 GLN A 411 GLN D 243 ASN D 444 ASN D 498 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 15111 Z= 0.398 Angle : 0.586 10.165 20493 Z= 0.304 Chirality : 0.043 0.153 2289 Planarity : 0.004 0.042 2524 Dihedral : 12.475 168.373 2033 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.61 % Allowed : 10.31 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.20), residues: 1780 helix: 1.37 (0.15), residues: 1131 sheet: 0.66 (0.64), residues: 43 loop : 0.35 (0.26), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 168 HIS 0.006 0.002 HIS B 803 PHE 0.022 0.002 PHE B 872 TYR 0.024 0.002 TYR D 351 ARG 0.005 0.001 ARG C 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 146 time to evaluate : 1.931 Fit side-chains REVERT: C 590 ASP cc_start: 0.6731 (t70) cc_final: 0.6505 (t0) REVERT: B 770 MET cc_start: 0.8130 (mtt) cc_final: 0.7899 (mtp) REVERT: A 409 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7131 (pt0) REVERT: D 490 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6846 (tp30) outliers start: 26 outliers final: 10 residues processed: 165 average time/residue: 1.4728 time to fit residues: 266.7362 Evaluate side-chains 152 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain B residue 648 ILE Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 1083 MET Chi-restraints excluded: chain A residue 409 GLU Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 473 THR Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 97 optimal weight: 6.9990 chunk 2 optimal weight: 0.9980 chunk 128 optimal weight: 7.9990 chunk 70 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 154 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN A 411 GLN D 243 ASN D 498 GLN D 559 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15111 Z= 0.198 Angle : 0.485 8.954 20493 Z= 0.251 Chirality : 0.038 0.144 2289 Planarity : 0.004 0.038 2524 Dihedral : 12.308 163.865 2033 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.74 % Allowed : 11.43 % Favored : 86.83 % 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: 1.72 (0.20), residues: 1780 helix: 1.61 (0.15), residues: 1133 sheet: 0.67 (0.64), residues: 43 loop : 0.45 (0.26), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 168 HIS 0.004 0.001 HIS A 312 PHE 0.015 0.001 PHE B 870 TYR 0.021 0.001 TYR B 732 ARG 0.006 0.000 ARG C 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 143 time to evaluate : 1.801 Fit side-chains REVERT: B 770 MET cc_start: 0.8046 (mtt) cc_final: 0.7809 (mtp) REVERT: B 1060 LYS cc_start: 0.8472 (tppt) cc_final: 0.8098 (ttpp) REVERT: B 1081 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7272 (ppt-90) REVERT: A 553 LYS cc_start: 0.7313 (pttt) cc_final: 0.6828 (pptt) REVERT: D 371 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7520 (mtp-110) REVERT: D 490 GLU cc_start: 0.7130 (OUTLIER) cc_final: 0.6803 (tp30) REVERT: D 594 MET cc_start: 0.7449 (tpp) cc_final: 0.7128 (tpp) outliers start: 28 outliers final: 11 residues processed: 164 average time/residue: 1.5136 time to fit residues: 270.9159 Evaluate side-chains 151 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 137 time to evaluate : 1.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain B residue 1083 MET Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 154 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 101 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 172 optimal weight: 0.0030 chunk 142 optimal weight: 8.9990 chunk 79 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 56 optimal weight: 0.0020 chunk 90 optimal weight: 0.8980 chunk 166 optimal weight: 8.9990 overall best weight: 1.1802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN A 411 GLN D 243 ASN D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.1599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15111 Z= 0.182 Angle : 0.469 7.917 20493 Z= 0.244 Chirality : 0.038 0.141 2289 Planarity : 0.003 0.037 2524 Dihedral : 12.277 163.383 2033 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.74 % Allowed : 11.80 % Favored : 86.46 % 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: 1.87 (0.20), residues: 1780 helix: 1.73 (0.15), residues: 1133 sheet: 0.71 (0.64), residues: 43 loop : 0.51 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 168 HIS 0.004 0.001 HIS A 312 PHE 0.015 0.001 PHE B 870 TYR 0.023 0.001 TYR B 732 ARG 0.007 0.000 ARG C 514 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 147 time to evaluate : 1.697 Fit side-chains REVERT: B 770 MET cc_start: 0.8031 (mtt) cc_final: 0.7806 (mtp) REVERT: B 1058 ASP cc_start: 0.8197 (OUTLIER) cc_final: 0.7952 (p0) REVERT: B 1060 LYS cc_start: 0.8418 (tppt) cc_final: 0.8130 (ttpp) REVERT: B 1081 ARG cc_start: 0.7766 (OUTLIER) cc_final: 0.7296 (ppt-90) REVERT: A 553 LYS cc_start: 0.7302 (pttt) cc_final: 0.6823 (pptt) REVERT: D 371 ARG cc_start: 0.8082 (OUTLIER) cc_final: 0.7495 (mtp-110) REVERT: D 411 GLN cc_start: 0.8194 (tp-100) cc_final: 0.7869 (mm-40) REVERT: D 490 GLU cc_start: 0.7121 (OUTLIER) cc_final: 0.6794 (tp30) REVERT: D 594 MET cc_start: 0.7427 (tpp) cc_final: 0.7064 (tpp) outliers start: 28 outliers final: 14 residues processed: 168 average time/residue: 1.5147 time to fit residues: 277.7904 Evaluate side-chains 153 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 135 time to evaluate : 1.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 521 GLU Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain B residue 1083 MET Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 449 ASP Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 19 optimal weight: 0.9990 chunk 98 optimal weight: 8.9990 chunk 125 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 chunk 144 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 171 optimal weight: 8.9990 chunk 107 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 79 optimal weight: 8.9990 chunk 106 optimal weight: 0.4980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN A 411 GLN D 243 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15111 Z= 0.206 Angle : 0.483 7.452 20493 Z= 0.250 Chirality : 0.038 0.142 2289 Planarity : 0.004 0.039 2524 Dihedral : 12.283 163.655 2033 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.86 % Allowed : 11.99 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.90 (0.20), residues: 1780 helix: 1.74 (0.15), residues: 1133 sheet: 0.82 (0.65), residues: 43 loop : 0.51 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP C 168 HIS 0.005 0.001 HIS A 312 PHE 0.016 0.001 PHE B 870 TYR 0.025 0.001 TYR B 732 ARG 0.007 0.000 ARG B 778 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.746 Fit side-chains REVERT: B 770 MET cc_start: 0.8041 (mtt) cc_final: 0.7821 (mtp) REVERT: B 1058 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7843 (p0) REVERT: B 1060 LYS cc_start: 0.8446 (tppt) cc_final: 0.8127 (ttpp) REVERT: B 1081 ARG cc_start: 0.7772 (OUTLIER) cc_final: 0.7306 (ppt-90) REVERT: A 553 LYS cc_start: 0.7296 (pttt) cc_final: 0.6870 (pptt) REVERT: D 371 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7499 (mtp-110) REVERT: D 411 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7873 (mm-40) REVERT: D 490 GLU cc_start: 0.7134 (OUTLIER) cc_final: 0.6808 (tp30) outliers start: 30 outliers final: 13 residues processed: 159 average time/residue: 1.4982 time to fit residues: 260.4894 Evaluate side-chains 148 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 521 GLU Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 727 ASP Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 68 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 109 optimal weight: 5.9990 chunk 116 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 15 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 chunk 156 optimal weight: 1.9990 chunk 164 optimal weight: 0.9990 overall best weight: 1.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN A 411 GLN A 498 GLN D 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15111 Z= 0.199 Angle : 0.481 7.150 20493 Z= 0.250 Chirality : 0.038 0.142 2289 Planarity : 0.004 0.037 2524 Dihedral : 12.272 163.396 2033 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 1.55 % Allowed : 12.80 % Favored : 85.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.20), residues: 1780 helix: 1.79 (0.15), residues: 1131 sheet: 0.86 (0.65), residues: 43 loop : 0.50 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 168 HIS 0.004 0.001 HIS A 312 PHE 0.015 0.001 PHE B 870 TYR 0.027 0.001 TYR B 732 ARG 0.007 0.000 ARG C 514 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 132 time to evaluate : 1.744 Fit side-chains REVERT: B 1058 ASP cc_start: 0.8129 (OUTLIER) cc_final: 0.7853 (p0) REVERT: B 1060 LYS cc_start: 0.8443 (tppt) cc_final: 0.8128 (ttpp) REVERT: B 1081 ARG cc_start: 0.7847 (OUTLIER) cc_final: 0.7338 (ppt-90) REVERT: A 553 LYS cc_start: 0.7297 (pttt) cc_final: 0.6875 (pptt) REVERT: D 371 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7498 (mtp-110) REVERT: D 411 GLN cc_start: 0.8210 (tp-100) cc_final: 0.7885 (mm-40) REVERT: D 490 GLU cc_start: 0.7150 (OUTLIER) cc_final: 0.6818 (tp30) REVERT: D 594 MET cc_start: 0.7442 (tpp) cc_final: 0.7141 (tpp) REVERT: D 604 MET cc_start: 0.7116 (mmm) cc_final: 0.6747 (mmm) outliers start: 25 outliers final: 13 residues processed: 152 average time/residue: 1.4840 time to fit residues: 247.0452 Evaluate side-chains 148 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 131 time to evaluate : 1.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 521 GLU Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 149 optimal weight: 3.9990 chunk 159 optimal weight: 3.9990 chunk 164 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 69 optimal weight: 5.9990 chunk 125 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 144 optimal weight: 0.9990 chunk 151 optimal weight: 5.9990 chunk 104 optimal weight: 3.9990 chunk 169 optimal weight: 2.9990 overall best weight: 1.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN A 411 GLN A 498 GLN D 243 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8469 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15111 Z= 0.239 Angle : 0.498 7.435 20493 Z= 0.259 Chirality : 0.039 0.142 2289 Planarity : 0.004 0.037 2524 Dihedral : 12.307 164.154 2033 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 1.55 % Allowed : 12.86 % Favored : 85.59 % 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: 1.86 (0.20), residues: 1780 helix: 1.73 (0.15), residues: 1131 sheet: 0.81 (0.65), residues: 43 loop : 0.48 (0.27), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 168 HIS 0.005 0.001 HIS A 312 PHE 0.017 0.001 PHE B 870 TYR 0.031 0.001 TYR B 732 ARG 0.007 0.000 ARG C 514 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 1.649 Fit side-chains REVERT: B 1058 ASP cc_start: 0.8155 (OUTLIER) cc_final: 0.7892 (p0) REVERT: B 1060 LYS cc_start: 0.8448 (tppt) cc_final: 0.8136 (ttpp) REVERT: B 1081 ARG cc_start: 0.7787 (OUTLIER) cc_final: 0.7323 (ppt-90) REVERT: A 553 LYS cc_start: 0.7300 (pttt) cc_final: 0.6878 (pptt) REVERT: D 371 ARG cc_start: 0.8088 (OUTLIER) cc_final: 0.7506 (mtp-110) REVERT: D 411 GLN cc_start: 0.8188 (tp-100) cc_final: 0.7874 (mm-40) REVERT: D 490 GLU cc_start: 0.7151 (OUTLIER) cc_final: 0.6810 (tp30) REVERT: D 496 GLN cc_start: 0.8443 (mm110) cc_final: 0.8226 (mm-40) REVERT: D 594 MET cc_start: 0.7486 (tpp) cc_final: 0.7201 (tpp) REVERT: D 604 MET cc_start: 0.7059 (mmm) cc_final: 0.6672 (mmm) outliers start: 25 outliers final: 15 residues processed: 157 average time/residue: 1.4734 time to fit residues: 252.6080 Evaluate side-chains 153 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 134 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 443 THR Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 521 GLU Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain B residue 720 ASP Chi-restraints excluded: chain B residue 828 VAL Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain A residue 381 ASP Chi-restraints excluded: chain A residue 498 GLN Chi-restraints excluded: chain A residue 529 ASP Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 103 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 117 optimal weight: 8.9990 chunk 177 optimal weight: 0.9980 chunk 163 optimal weight: 4.9990 chunk 141 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 109 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN A 411 GLN A 498 GLN D 243 ASN D 498 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15111 Z= 0.167 Angle : 0.473 8.482 20493 Z= 0.245 Chirality : 0.038 0.143 2289 Planarity : 0.003 0.039 2524 Dihedral : 12.254 162.700 2033 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.30 % Allowed : 13.11 % Favored : 85.59 % 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: 2.00 (0.20), residues: 1780 helix: 1.82 (0.15), residues: 1133 sheet: 0.89 (0.66), residues: 43 loop : 0.56 (0.27), residues: 604 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 168 HIS 0.003 0.001 HIS B 803 PHE 0.013 0.001 PHE C 285 TYR 0.030 0.001 TYR B 732 ARG 0.008 0.000 ARG C 514 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3560 Ramachandran restraints generated. 1780 Oldfield, 0 Emsley, 1780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.802 Fit side-chains REVERT: B 1058 ASP cc_start: 0.8114 (OUTLIER) cc_final: 0.7847 (p0) REVERT: B 1060 LYS cc_start: 0.8423 (tppt) cc_final: 0.8114 (ttpp) REVERT: B 1081 ARG cc_start: 0.7773 (OUTLIER) cc_final: 0.7308 (ppt-90) REVERT: A 553 LYS cc_start: 0.7278 (pttt) cc_final: 0.6869 (pptt) REVERT: D 371 ARG cc_start: 0.8090 (OUTLIER) cc_final: 0.7499 (mtp-110) REVERT: D 411 GLN cc_start: 0.8191 (tp-100) cc_final: 0.7891 (mm-40) REVERT: D 490 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6817 (tp30) REVERT: D 496 GLN cc_start: 0.8435 (mm110) cc_final: 0.8223 (mm-40) REVERT: D 594 MET cc_start: 0.7463 (tpp) cc_final: 0.7161 (tpp) REVERT: D 604 MET cc_start: 0.7036 (mmm) cc_final: 0.6665 (mmm) REVERT: D 605 LYS cc_start: 0.7561 (ttpp) cc_final: 0.6957 (ptpt) outliers start: 21 outliers final: 9 residues processed: 152 average time/residue: 1.5163 time to fit residues: 252.2956 Evaluate side-chains 148 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 135 time to evaluate : 1.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 451 LYS Chi-restraints excluded: chain C residue 532 VAL Chi-restraints excluded: chain C residue 540 ASP Chi-restraints excluded: chain B residue 1058 ASP Chi-restraints excluded: chain B residue 1081 ARG Chi-restraints excluded: chain A residue 281 MET Chi-restraints excluded: chain D residue 194 SER Chi-restraints excluded: chain D residue 371 ARG Chi-restraints excluded: chain D residue 455 LYS Chi-restraints excluded: chain D residue 482 ASP Chi-restraints excluded: chain D residue 490 GLU Chi-restraints excluded: chain D residue 527 VAL Chi-restraints excluded: chain D residue 575 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 43 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 0.2980 chunk 141 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 145 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 8 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 714 GLN A 411 GLN A 498 GLN D 498 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.115257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.092137 restraints weight = 18385.123| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 1.32 r_work: 0.2877 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 15111 Z= 0.161 Angle : 0.469 9.074 20493 Z= 0.243 Chirality : 0.038 0.141 2289 Planarity : 0.003 0.038 2524 Dihedral : 12.239 162.700 2033 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 1.12 % Allowed : 13.48 % Favored : 85.40 % 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: 2.01 (0.20), residues: 1780 helix: 1.84 (0.15), residues: 1145 sheet: 0.92 (0.66), residues: 43 loop : 0.49 (0.27), residues: 592 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 168 HIS 0.003 0.001 HIS B 803 PHE 0.016 0.001 PHE D 423 TYR 0.029 0.001 TYR B 732 ARG 0.007 0.000 ARG C 514 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4933.89 seconds wall clock time: 89 minutes 54.09 seconds (5394.09 seconds total)