Starting phenix.real_space_refine on Sun Apr 7 07:46:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1l_36794/04_2024/8k1l_36794_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1l_36794/04_2024/8k1l_36794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1l_36794/04_2024/8k1l_36794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1l_36794/04_2024/8k1l_36794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1l_36794/04_2024/8k1l_36794_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1l_36794/04_2024/8k1l_36794_updated.pdb" } resolution = 3.44 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= -0.002 sd= 0.037 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: 6 Type Number sf(0) Gaussians Al 1 5.89 5 S 69 5.16 5 C 6420 2.51 5 N 1671 2.21 5 O 1861 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 870": "OD1" <-> "OD2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 984": "NH1" <-> "NH2" Residue "B ASP 93": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10026 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7657 Classifications: {'peptide': 979} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 934} Chain: "B" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2364 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 274} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'ALF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.60, per 1000 atoms: 0.56 Number of scatterers: 10026 At special positions: 0 Unit cell: (88.736, 103.776, 166.192, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 69 16.00 Al 1 13.00 F 4 9.00 O 1861 8.00 N 1671 7.00 C 6420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 177 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 311 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.11 Conformation dependent library (CDL) restraints added in 1.9 seconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 7 sheets defined 41.4% alpha, 8.5% 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 25 through 32 Processing helix chain 'A' and resid 42 through 51 Processing helix chain 'A' and resid 65 through 72 Processing helix chain 'A' and resid 79 through 98 Processing helix chain 'A' and resid 106 through 127 removed outlier: 4.114A pdb=" N TYR A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 137 No H-bonds generated for 'chain 'A' and resid 134 through 137' Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 213 through 215 No H-bonds generated for 'chain 'A' and resid 213 through 215' Processing helix chain 'A' and resid 243 through 252 Processing helix chain 'A' and resid 260 through 283 Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.923A pdb=" N GLY A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 331 removed outlier: 3.589A pdb=" N LYS A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS A 331 " --> pdb=" O ARG A 327 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 344 removed outlier: 3.756A pdb=" N GLU A 342 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 343 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 344 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 404 removed outlier: 4.774A pdb=" N GLU A 397 " --> pdb=" O LYS A 393 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 441 Processing helix chain 'A' and resid 444 through 450 Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 507 through 523 removed outlier: 3.674A pdb=" N MET A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 583 Processing helix chain 'A' and resid 596 through 606 Processing helix chain 'A' and resid 616 through 623 Processing helix chain 'A' and resid 642 through 647 removed outlier: 3.594A pdb=" N ASP A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 659 Processing helix chain 'A' and resid 670 through 683 removed outlier: 3.849A pdb=" N LEU A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N GLN A 683 " --> pdb=" O GLY A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 702 Proline residue: A 698 - end of helix Processing helix chain 'A' and resid 715 through 719 Processing helix chain 'A' and resid 730 through 754 removed outlier: 3.557A pdb=" N THR A 735 " --> pdb=" O SER A 732 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU A 739 " --> pdb=" O GLY A 736 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 742 " --> pdb=" O GLU A 739 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 743 " --> pdb=" O GLY A 740 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE A 744 " --> pdb=" O ARG A 741 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ALA A 752 " --> pdb=" O LYS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 769 Proline residue: A 764 - end of helix Processing helix chain 'A' and resid 779 through 786 removed outlier: 3.507A pdb=" N CYS A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 785 " --> pdb=" O THR A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 789 through 799 Proline residue: A 793 - end of helix removed outlier: 4.494A pdb=" N ALA A 798 " --> pdb=" O ALA A 794 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N TYR A 799 " --> pdb=" O ILE A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 826 Processing helix chain 'A' and resid 829 through 849 removed outlier: 3.520A pdb=" N MET A 833 " --> pdb=" O GLN A 829 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 841 " --> pdb=" O GLY A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 853 through 856 No H-bonds generated for 'chain 'A' and resid 853 through 856' Processing helix chain 'A' and resid 860 through 864 removed outlier: 3.568A pdb=" N GLU A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 860 through 864' Processing helix chain 'A' and resid 881 through 911 removed outlier: 4.186A pdb=" N THR A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 906 " --> pdb=" O VAL A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 917 through 920 No H-bonds generated for 'chain 'A' and resid 917 through 920' Processing helix chain 'A' and resid 925 through 942 Processing helix chain 'A' and resid 965 through 983 Processing helix chain 'A' and resid 989 through 993 Processing helix chain 'B' and resid 60 through 91 removed outlier: 3.851A pdb=" N THR B 91 " --> pdb=" O ILE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 150 Processing helix chain 'B' and resid 154 through 158 removed outlier: 3.854A pdb=" N SER B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 154 through 158' Processing helix chain 'B' and resid 181 through 184 Processing helix chain 'B' and resid 190 through 195 removed outlier: 5.673A pdb=" N PHE B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 241 Processing helix chain 'B' and resid 244 through 247 Processing helix chain 'B' and resid 259 through 263 removed outlier: 4.223A pdb=" N GLU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 259 through 263' Processing sheet with id= A, first strand: chain 'A' and resid 167 through 169 removed outlier: 3.898A pdb=" N GLY A 233 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 234 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP A 179 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 333 through 335 removed outlier: 3.654A pdb=" N ILE A 705 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N THR A 349 " --> pdb=" O ALA A 688 " (cutoff:3.500A) removed outlier: 8.281A pdb=" N THR A 690 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N CYS A 351 " --> pdb=" O THR A 690 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N LYS A 587 " --> pdb=" O ILE A 350 " (cutoff:3.500A) removed outlier: 8.074A pdb=" N SER A 352 " --> pdb=" O LYS A 587 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE A 589 " --> pdb=" O SER A 352 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 363 through 365 removed outlier: 3.511A pdb=" N THR A 364 " --> pdb=" O ILE A 567 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N PHE A 530 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU A 563 " --> pdb=" O LEU A 528 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N LEU A 528 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N SER A 565 " --> pdb=" O ARG A 526 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ARG A 526 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR A 478 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 483 " --> pdb=" O GLN A 466 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 466 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N SER A 455 " --> pdb=" O VAL A 469 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N GLU A 471 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N LYS A 453 " --> pdb=" O GLU A 471 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 367 through 370 removed outlier: 3.609A pdb=" N VAL A 375 " --> pdb=" O MET A 368 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 501 through 504 removed outlier: 6.840A pdb=" N LEU A 558 " --> pdb=" O SER A 494 " (cutoff:3.500A) removed outlier: 5.542A pdb=" N ILE A 496 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N PHE A 560 " --> pdb=" O ILE A 496 " (cutoff:3.500A) removed outlier: 6.034A pdb=" N ILE A 498 " --> pdb=" O PHE A 560 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 112 through 114 Processing sheet with id= G, first strand: chain 'B' and resid 127 through 130 removed outlier: 9.189A pdb=" N ILE B 128 " --> pdb=" O HIS B 330 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N GLU B 332 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 8.661A pdb=" N PHE B 130 " --> pdb=" O GLU B 332 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ARG B 334 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET B 335 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 305 " --> pdb=" O MET B 335 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP B 251 " --> pdb=" O TRP B 314 " (cutoff:3.500A) 354 hydrogen bonds defined for protein. 981 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: 3.17 Time building geometry restraints manager: 4.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2575 1.33 - 1.45: 2001 1.45 - 1.58: 5566 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 10257 Sorted by residual: bond pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" F3 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" F4 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" N ILE A 180 " pdb=" CA ILE A 180 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.39e+00 ... (remaining 10252 not shown) Histogram of bond angle deviations from ideal: 89.83 - 107.85: 421 107.85 - 125.86: 13312 125.86 - 143.88: 164 143.88 - 161.89: 0 161.89 - 179.90: 2 Bond angle restraints: 13899 Sorted by residual: angle pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " pdb=" F2 ALF A1001 " ideal model delta sigma weight residual 108.68 179.90 -71.22 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF A1001 " pdb="AL ALF A1001 " pdb=" F4 ALF A1001 " ideal model delta sigma weight residual 109.63 179.36 -69.73 3.00e+00 1.11e-01 5.40e+02 angle pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " pdb=" F4 ALF A1001 " ideal model delta sigma weight residual 110.21 90.25 19.96 3.00e+00 1.11e-01 4.43e+01 angle pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " pdb=" F3 ALF A1001 " ideal model delta sigma weight residual 109.69 89.90 19.79 3.00e+00 1.11e-01 4.35e+01 angle pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " pdb=" F3 ALF A1001 " ideal model delta sigma weight residual 109.59 90.02 19.57 3.00e+00 1.11e-01 4.26e+01 ... (remaining 13894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 5208 17.13 - 34.27: 722 34.27 - 51.40: 163 51.40 - 68.54: 38 68.54 - 85.67: 8 Dihedral angle restraints: 6139 sinusoidal: 2472 harmonic: 3667 Sorted by residual: dihedral pdb=" CB CYS B 188 " pdb=" SG CYS B 188 " pdb=" SG CYS B 202 " pdb=" CB CYS B 202 " ideal model delta sinusoidal sigma weight residual 93.00 159.64 -66.64 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CA TYR B 280 " pdb=" C TYR B 280 " pdb=" N TYR B 281 " pdb=" CA TYR B 281 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER A 406 " pdb=" C SER A 406 " pdb=" N ARG A 407 " pdb=" CA ARG A 407 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 6136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1239 0.052 - 0.103: 238 0.103 - 0.155: 51 0.155 - 0.206: 9 0.206 - 0.258: 3 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CB ILE A 759 " pdb=" CA ILE A 759 " pdb=" CG1 ILE A 759 " pdb=" CG2 ILE A 759 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A 625 " pdb=" N ILE A 625 " pdb=" C ILE A 625 " pdb=" CB ILE A 625 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU B 76 " pdb=" CB LEU B 76 " pdb=" CD1 LEU B 76 " pdb=" CD2 LEU B 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1537 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 622 " 0.616 9.50e-02 1.11e+02 2.76e-01 4.65e+01 pdb=" NE ARG A 622 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 622 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 622 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 622 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 983 " -0.335 9.50e-02 1.11e+02 1.50e-01 1.38e+01 pdb=" NE ARG A 983 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 983 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 983 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 983 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 175 " -0.237 9.50e-02 1.11e+02 1.06e-01 6.95e+00 pdb=" NE ARG A 175 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 175 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 175 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 175 " -0.008 2.00e-02 2.50e+03 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 198 2.63 - 3.20: 9749 3.20 - 3.77: 15932 3.77 - 4.33: 21885 4.33 - 4.90: 35477 Nonbonded interactions: 83241 Sorted by model distance: nonbonded pdb=" O ALA A 431 " pdb=" CE LYS A 435 " model vdw 2.067 3.440 nonbonded pdb=" OD2 ASP A 353 " pdb=" F2 ALF A1001 " model vdw 2.125 2.390 nonbonded pdb=" O ASP B 227 " pdb=" OD1 ASP B 227 " model vdw 2.146 3.040 nonbonded pdb=" O GLY A 312 " pdb=" OG1 THR A 316 " model vdw 2.179 2.440 nonbonded pdb=" OD1 ASP A 353 " pdb=" F3 ALF A1001 " model vdw 2.179 2.390 ... (remaining 83236 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.610 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: 18.620 Check model and map are aligned: 0.210 Set scattering table: 0.100 Process input model: 29.780 Find NCS groups from input model: 0.420 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 : 0.004 0.101 10257 Z= 0.287 Angle : 1.168 71.224 13899 Z= 0.518 Chirality : 0.046 0.258 1540 Planarity : 0.009 0.276 1786 Dihedral : 16.417 85.672 3774 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.37 % Allowed : 24.06 % Favored : 75.57 % 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: -1.16 (0.24), residues: 1267 helix: -0.05 (0.22), residues: 562 sheet: -1.08 (0.49), residues: 129 loop : -1.36 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 63 HIS 0.008 0.001 HIS B 187 PHE 0.011 0.001 PHE A 989 TYR 0.024 0.001 TYR B 281 ARG 0.004 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 1.116 Fit side-chains REVERT: A 523 MET cc_start: 0.8016 (mpp) cc_final: 0.7549 (pmm) outliers start: 4 outliers final: 3 residues processed: 120 average time/residue: 0.2304 time to fit residues: 39.3694 Evaluate side-chains 115 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 627 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 0.0270 chunk 32 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 overall best weight: 1.1640 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.0729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10257 Z= 0.263 Angle : 0.832 33.539 13899 Z= 0.364 Chirality : 0.042 0.238 1540 Planarity : 0.004 0.039 1786 Dihedral : 4.516 27.212 1373 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 14.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 3.75 % Allowed : 22.42 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.24), residues: 1267 helix: 0.54 (0.22), residues: 559 sheet: -1.00 (0.46), residues: 136 loop : -1.17 (0.27), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 63 HIS 0.003 0.001 HIS B 187 PHE 0.010 0.001 PHE A 839 TYR 0.019 0.001 TYR A 465 ARG 0.006 0.001 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 118 time to evaluate : 1.151 Fit side-chains REVERT: A 465 TYR cc_start: 0.7351 (p90) cc_final: 0.7140 (p90) REVERT: A 531 CYS cc_start: 0.5893 (OUTLIER) cc_final: 0.5583 (m) REVERT: B 56 MET cc_start: 0.7409 (tpt) cc_final: 0.7116 (tpt) outliers start: 41 outliers final: 28 residues processed: 148 average time/residue: 0.2098 time to fit residues: 44.8682 Evaluate side-chains 140 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 111 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 531 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 113 optimal weight: 0.8980 chunk 39 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10257 Z= 0.276 Angle : 0.817 30.714 13899 Z= 0.353 Chirality : 0.042 0.247 1540 Planarity : 0.004 0.043 1786 Dihedral : 4.552 37.751 1373 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 4.76 % Allowed : 21.77 % Favored : 73.47 % 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: -0.46 (0.25), residues: 1267 helix: 0.71 (0.23), residues: 556 sheet: -0.94 (0.46), residues: 136 loop : -1.11 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.003 0.001 HIS B 143 PHE 0.022 0.001 PHE A 980 TYR 0.016 0.001 TYR A 465 ARG 0.004 0.000 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 118 time to evaluate : 1.153 Fit side-chains REVERT: A 135 MET cc_start: 0.8554 (tpp) cc_final: 0.8343 (mmm) REVERT: A 142 MET cc_start: 0.7892 (ppp) cc_final: 0.7630 (ppp) REVERT: B 56 MET cc_start: 0.7365 (tpt) cc_final: 0.7050 (tpt) outliers start: 52 outliers final: 32 residues processed: 160 average time/residue: 0.2078 time to fit residues: 48.3102 Evaluate side-chains 144 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 112 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 87 ILE Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.6980 chunk 86 optimal weight: 0.9980 chunk 59 optimal weight: 0.4980 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 115 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 109 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10257 Z= 0.231 Angle : 0.806 30.349 13899 Z= 0.345 Chirality : 0.041 0.248 1540 Planarity : 0.004 0.043 1786 Dihedral : 4.349 23.779 1372 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.92 % Rotamer: Outliers : 4.67 % Allowed : 22.05 % Favored : 73.28 % 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: -0.37 (0.25), residues: 1267 helix: 0.75 (0.23), residues: 563 sheet: -0.64 (0.48), residues: 124 loop : -1.13 (0.27), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.002 0.001 HIS A 641 PHE 0.010 0.001 PHE A 665 TYR 0.013 0.001 TYR A 768 ARG 0.003 0.000 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 121 time to evaluate : 1.231 Fit side-chains REVERT: A 459 PHE cc_start: 0.2173 (OUTLIER) cc_final: 0.0484 (m-10) REVERT: A 483 LYS cc_start: 0.6737 (pttm) cc_final: 0.6408 (pttm) REVERT: B 55 PHE cc_start: 0.7457 (t80) cc_final: 0.6904 (t80) REVERT: B 56 MET cc_start: 0.7318 (tpt) cc_final: 0.6939 (tpt) outliers start: 51 outliers final: 37 residues processed: 158 average time/residue: 0.2044 time to fit residues: 47.1074 Evaluate side-chains 153 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 115 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 742 LEU Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 1.9990 chunk 69 optimal weight: 0.4980 chunk 1 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 30 optimal weight: 0.5980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10257 Z= 0.323 Angle : 0.830 30.342 13899 Z= 0.358 Chirality : 0.043 0.261 1540 Planarity : 0.004 0.043 1786 Dihedral : 4.463 24.438 1372 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.39 % Favored : 93.45 % Rotamer: Outliers : 5.12 % Allowed : 22.32 % Favored : 72.55 % 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: -0.45 (0.25), residues: 1267 helix: 0.64 (0.23), residues: 567 sheet: -0.64 (0.48), residues: 125 loop : -1.13 (0.27), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS A 641 PHE 0.023 0.001 PHE A 145 TYR 0.017 0.001 TYR A 465 ARG 0.006 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 114 time to evaluate : 1.148 Fit side-chains REVERT: A 52 TYR cc_start: 0.6221 (OUTLIER) cc_final: 0.5438 (p90) REVERT: A 175 ARG cc_start: 0.8485 (OUTLIER) cc_final: 0.6859 (ttp-170) REVERT: A 459 PHE cc_start: 0.2061 (OUTLIER) cc_final: 0.0341 (m-10) REVERT: A 483 LYS cc_start: 0.6876 (pttm) cc_final: 0.6503 (pttm) REVERT: B 56 MET cc_start: 0.7342 (tpt) cc_final: 0.7014 (tpt) outliers start: 56 outliers final: 43 residues processed: 155 average time/residue: 0.2261 time to fit residues: 51.0649 Evaluate side-chains 158 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 112 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 900 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 143 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ASN Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 9.9990 chunk 109 optimal weight: 0.9990 chunk 24 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 121 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10257 Z= 0.190 Angle : 0.794 30.062 13899 Z= 0.336 Chirality : 0.041 0.263 1540 Planarity : 0.004 0.045 1786 Dihedral : 4.261 22.954 1372 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.92 % Rotamer: Outliers : 4.12 % Allowed : 23.33 % Favored : 72.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.25), residues: 1267 helix: 0.85 (0.23), residues: 566 sheet: -0.57 (0.47), residues: 125 loop : -1.10 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 63 HIS 0.002 0.001 HIS A 641 PHE 0.010 0.001 PHE A 665 TYR 0.012 0.001 TYR A 768 ARG 0.003 0.000 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 118 time to evaluate : 1.166 Fit side-chains REVERT: A 52 TYR cc_start: 0.6249 (OUTLIER) cc_final: 0.5485 (p90) REVERT: A 459 PHE cc_start: 0.2016 (OUTLIER) cc_final: 0.0358 (m-10) REVERT: A 483 LYS cc_start: 0.6858 (pttm) cc_final: 0.6514 (pttm) REVERT: A 509 MET cc_start: 0.7282 (mmp) cc_final: 0.7047 (mmp) REVERT: B 55 PHE cc_start: 0.7534 (t80) cc_final: 0.7031 (t80) REVERT: B 56 MET cc_start: 0.7173 (tpt) cc_final: 0.6811 (tpt) outliers start: 45 outliers final: 32 residues processed: 148 average time/residue: 0.2206 time to fit residues: 47.6094 Evaluate side-chains 148 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 114 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 0.9990 chunk 69 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 121 optimal weight: 0.8980 chunk 76 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 75 optimal weight: 0.6980 chunk 48 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.1526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10257 Z= 0.205 Angle : 0.804 30.117 13899 Z= 0.340 Chirality : 0.041 0.260 1540 Planarity : 0.004 0.046 1786 Dihedral : 4.178 21.403 1372 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.00 % Favored : 93.84 % Rotamer: Outliers : 4.67 % Allowed : 22.87 % Favored : 72.46 % 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: -0.21 (0.25), residues: 1267 helix: 0.88 (0.23), residues: 569 sheet: -0.51 (0.50), residues: 115 loop : -1.07 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.027 0.001 PHE A 145 TYR 0.016 0.001 TYR A 465 ARG 0.007 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 118 time to evaluate : 1.046 Fit side-chains REVERT: A 52 TYR cc_start: 0.6289 (OUTLIER) cc_final: 0.5563 (p90) REVERT: A 175 ARG cc_start: 0.8441 (OUTLIER) cc_final: 0.6821 (ttp-170) REVERT: A 459 PHE cc_start: 0.1912 (OUTLIER) cc_final: 0.0237 (m-10) REVERT: A 483 LYS cc_start: 0.6873 (pttm) cc_final: 0.6431 (pttm) REVERT: A 509 MET cc_start: 0.7275 (mmp) cc_final: 0.7062 (mmp) REVERT: A 517 TYR cc_start: 0.8020 (t80) cc_final: 0.7754 (t80) REVERT: B 56 MET cc_start: 0.7157 (tpt) cc_final: 0.6797 (tpt) REVERT: B 209 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8733 (ptpp) outliers start: 51 outliers final: 41 residues processed: 153 average time/residue: 0.2240 time to fit residues: 49.3039 Evaluate side-chains 159 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 114 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 3.9990 chunk 36 optimal weight: 8.9990 chunk 23 optimal weight: 0.2980 chunk 77 optimal weight: 0.3980 chunk 82 optimal weight: 0.9980 chunk 60 optimal weight: 0.1980 chunk 11 optimal weight: 6.9990 chunk 95 optimal weight: 0.9980 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 0.8980 chunk 106 optimal weight: 5.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10257 Z= 0.177 Angle : 0.812 30.024 13899 Z= 0.341 Chirality : 0.041 0.259 1540 Planarity : 0.004 0.046 1786 Dihedral : 4.086 19.353 1372 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.37 % Favored : 94.48 % Rotamer: Outliers : 3.57 % Allowed : 24.52 % Favored : 71.91 % 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: -0.13 (0.25), residues: 1267 helix: 0.96 (0.23), residues: 569 sheet: -0.39 (0.51), residues: 115 loop : -1.06 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.013 0.001 PHE A 410 TYR 0.012 0.001 TYR A 768 ARG 0.003 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 115 time to evaluate : 1.226 Fit side-chains REVERT: A 52 TYR cc_start: 0.6227 (OUTLIER) cc_final: 0.5599 (p90) REVERT: A 175 ARG cc_start: 0.8466 (OUTLIER) cc_final: 0.6852 (ttp-170) REVERT: A 459 PHE cc_start: 0.1938 (OUTLIER) cc_final: 0.0328 (m-10) REVERT: A 483 LYS cc_start: 0.6833 (pttm) cc_final: 0.6453 (pttm) REVERT: A 517 TYR cc_start: 0.7978 (t80) cc_final: 0.7741 (t80) REVERT: B 56 MET cc_start: 0.7145 (tpt) cc_final: 0.6764 (tpt) outliers start: 39 outliers final: 30 residues processed: 143 average time/residue: 0.2238 time to fit residues: 46.0629 Evaluate side-chains 146 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.5980 chunk 116 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 49 optimal weight: 10.0000 chunk 88 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 102 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 112 optimal weight: 0.0670 chunk 74 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10257 Z= 0.187 Angle : 0.814 30.086 13899 Z= 0.341 Chirality : 0.041 0.262 1540 Planarity : 0.004 0.048 1786 Dihedral : 4.006 16.956 1369 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 12.16 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.84 % Favored : 94.00 % Rotamer: Outliers : 3.57 % Allowed : 24.61 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.25), residues: 1267 helix: 1.02 (0.23), residues: 569 sheet: -0.34 (0.51), residues: 115 loop : -1.02 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.030 0.001 PHE A 145 TYR 0.015 0.001 TYR A 465 ARG 0.009 0.000 ARG A 633 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 115 time to evaluate : 1.098 Fit side-chains revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6245 (OUTLIER) cc_final: 0.5668 (p90) REVERT: A 459 PHE cc_start: 0.1870 (OUTLIER) cc_final: 0.0283 (m-10) REVERT: A 483 LYS cc_start: 0.6845 (pttm) cc_final: 0.6397 (pttm) REVERT: B 56 MET cc_start: 0.7132 (tpt) cc_final: 0.6754 (tpt) outliers start: 39 outliers final: 33 residues processed: 143 average time/residue: 0.2242 time to fit residues: 46.0305 Evaluate side-chains 149 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 83 optimal weight: 3.9990 chunk 125 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 3.9990 chunk 77 optimal weight: 2.9990 chunk 61 optimal weight: 0.0170 chunk 79 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.8822 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10257 Z= 0.213 Angle : 0.819 30.121 13899 Z= 0.345 Chirality : 0.041 0.262 1540 Planarity : 0.004 0.047 1786 Dihedral : 4.027 17.105 1369 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.60 % Favored : 94.24 % Rotamer: Outliers : 3.66 % Allowed : 24.52 % Favored : 71.82 % 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: -0.09 (0.25), residues: 1267 helix: 0.98 (0.23), residues: 569 sheet: -0.33 (0.51), residues: 115 loop : -1.03 (0.27), residues: 583 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.007 0.001 PHE A 896 TYR 0.012 0.001 TYR A 768 ARG 0.009 0.000 ARG A 633 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 114 time to evaluate : 1.243 Fit side-chains revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6298 (OUTLIER) cc_final: 0.5734 (p90) REVERT: A 459 PHE cc_start: 0.1554 (OUTLIER) cc_final: -0.0037 (m-10) REVERT: A 483 LYS cc_start: 0.6925 (pttm) cc_final: 0.6555 (pttm) REVERT: A 517 TYR cc_start: 0.7712 (t80) cc_final: 0.7438 (t80) REVERT: B 55 PHE cc_start: 0.7529 (t80) cc_final: 0.7147 (t80) REVERT: B 56 MET cc_start: 0.7100 (tpt) cc_final: 0.6754 (tpt) outliers start: 40 outliers final: 34 residues processed: 143 average time/residue: 0.2251 time to fit residues: 47.1779 Evaluate side-chains 150 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 114 time to evaluate : 1.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 301 MET Chi-restraints excluded: chain A residue 441 THR Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 773 LEU Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 109 ASN Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.6980 chunk 92 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 102 optimal weight: 0.0000 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.4980 chunk 87 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.129283 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095385 restraints weight = 19020.744| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.51 r_work: 0.3235 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10257 Z= 0.174 Angle : 0.816 30.024 13899 Z= 0.342 Chirality : 0.041 0.260 1540 Planarity : 0.004 0.049 1786 Dihedral : 3.958 16.362 1369 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.45 % Favored : 94.40 % Rotamer: Outliers : 3.48 % Allowed : 24.79 % Favored : 71.73 % 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: -0.01 (0.25), residues: 1267 helix: 1.05 (0.23), residues: 570 sheet: -0.28 (0.50), residues: 115 loop : -1.00 (0.27), residues: 582 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.008 0.001 PHE A 410 TYR 0.015 0.001 TYR A 465 ARG 0.009 0.000 ARG A 633 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2631.75 seconds wall clock time: 48 minutes 59.72 seconds (2939.72 seconds total)