Starting phenix.real_space_refine on Thu Mar 14 14:45:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0x_28782/03_2024/8f0x_28782.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0x_28782/03_2024/8f0x_28782.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0x_28782/03_2024/8f0x_28782.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0x_28782/03_2024/8f0x_28782.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0x_28782/03_2024/8f0x_28782.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f0x_28782/03_2024/8f0x_28782.pdb" } resolution = 3.21 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= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 334 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 5588 2.51 5 N 1441 2.21 5 O 1679 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 83": "OE1" <-> "OE2" Residue "A ASP 136": "OD1" <-> "OD2" Residue "A PHE 163": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 183": "OE1" <-> "OE2" Residue "A TYR 210": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 242": "OD1" <-> "OD2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 370": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 378": "OE1" <-> "OE2" Residue "A ASP 476": "OD1" <-> "OD2" Residue "A ASP 496": "OD1" <-> "OD2" Residue "A GLU 516": "OE1" <-> "OE2" Residue "A ASP 518": "OD1" <-> "OD2" Residue "A ASP 543": "OD1" <-> "OD2" Residue "A GLU 546": "OE1" <-> "OE2" Residue "A ASP 547": "OD1" <-> "OD2" Residue "A GLU 572": "OE1" <-> "OE2" Residue "A TYR 617": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 693": "OE1" <-> "OE2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A ASP 801": "OD1" <-> "OD2" Residue "A GLU 823": "OE1" <-> "OE2" Residue "A TYR 880": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 890": "OE1" <-> "OE2" Residue "B TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 73": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8743 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 928, 7395 Classifications: {'peptide': 928} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 901} Chain breaks: 2 Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 646 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 3, 'TRANS': 79} Chain: "C" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 702 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Time building chain proxies: 4.97, per 1000 atoms: 0.57 Number of scatterers: 8743 At special positions: 0 Unit cell: (87.897, 94.251, 114.901, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1679 8.00 N 1441 7.00 C 5588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.04 Conformation dependent library (CDL) restraints added in 2.7 seconds 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 4 sheets defined 83.5% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 2 through 12 Processing helix chain 'A' and resid 14 through 46 removed outlier: 3.506A pdb=" N SER A 31 " --> pdb=" O GLN A 27 " (cutoff:3.500A) removed outlier: 8.245A pdb=" N SER A 34 " --> pdb=" O ASP A 30 " (cutoff:3.500A) removed outlier: 7.127A pdb=" N GLN A 35 " --> pdb=" O SER A 31 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 69 removed outlier: 3.794A pdb=" N LYS A 63 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 100 removed outlier: 3.591A pdb=" N LEU A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 123 removed outlier: 3.664A pdb=" N CYS A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VAL A 121 " --> pdb=" O GLN A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 143 through 158 removed outlier: 4.020A pdb=" N MET A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N ASP A 155 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 5.242A pdb=" N ASP A 156 " --> pdb=" O GLU A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 Processing helix chain 'A' and resid 167 through 182 Processing helix chain 'A' and resid 186 through 206 removed outlier: 3.903A pdb=" N SER A 206 " --> pdb=" O LEU A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 235 removed outlier: 3.518A pdb=" N THR A 235 " --> pdb=" O GLY A 231 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 263 Processing helix chain 'A' and resid 265 through 269 removed outlier: 3.569A pdb=" N PHE A 269 " --> pdb=" O ARG A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 292 Processing helix chain 'A' and resid 303 through 321 removed outlier: 3.996A pdb=" N TYR A 313 " --> pdb=" O ASP A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.678A pdb=" N ILE A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 355 Processing helix chain 'A' and resid 355 through 364 removed outlier: 3.940A pdb=" N PHE A 359 " --> pdb=" O ASP A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 383 Processing helix chain 'A' and resid 384 through 403 removed outlier: 4.052A pdb=" N LEU A 390 " --> pdb=" O PRO A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 421 removed outlier: 4.405A pdb=" N GLU A 410 " --> pdb=" O TYR A 406 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N SER A 411 " --> pdb=" O SER A 407 " (cutoff:3.500A) Processing helix chain 'A' and resid 428 through 448 removed outlier: 4.148A pdb=" N ASP A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN A 433 " --> pdb=" O GLU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 470 Proline residue: A 464 - end of helix Processing helix chain 'A' and resid 476 through 494 removed outlier: 3.537A pdb=" N LEU A 480 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 515 removed outlier: 3.815A pdb=" N PHE A 514 " --> pdb=" O TYR A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 542 Proline residue: A 523 - end of helix removed outlier: 3.531A pdb=" N SER A 527 " --> pdb=" O PRO A 523 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER A 542 " --> pdb=" O ASN A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 547 through 562 Processing helix chain 'A' and resid 570 through 588 removed outlier: 3.946A pdb=" N ASP A 588 " --> pdb=" O ILE A 584 " (cutoff:3.500A) Processing helix chain 'A' and resid 591 through 605 Processing helix chain 'A' and resid 610 through 632 Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 633 through 636 Processing helix chain 'A' and resid 640 through 656 Processing helix chain 'A' and resid 664 through 682 removed outlier: 4.036A pdb=" N ASN A 668 " --> pdb=" O PRO A 664 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLU A 673 " --> pdb=" O GLN A 669 " (cutoff:3.500A) Proline residue: A 674 - end of helix Processing helix chain 'A' and resid 684 through 702 Processing helix chain 'A' and resid 703 through 708 Processing helix chain 'A' and resid 710 through 723 removed outlier: 4.101A pdb=" N SER A 723 " --> pdb=" O GLU A 719 " (cutoff:3.500A) Processing helix chain 'A' and resid 733 through 745 Processing helix chain 'A' and resid 745 through 750 removed outlier: 3.596A pdb=" N GLN A 750 " --> pdb=" O SER A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 767 Processing helix chain 'A' and resid 769 through 787 removed outlier: 3.806A pdb=" N VAL A 779 " --> pdb=" O ASN A 775 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU A 780 " --> pdb=" O LEU A 776 " (cutoff:3.500A) Processing helix chain 'A' and resid 787 through 798 Processing helix chain 'A' and resid 805 through 817 Processing helix chain 'A' and resid 818 through 820 No H-bonds generated for 'chain 'A' and resid 818 through 820' Processing helix chain 'A' and resid 822 through 840 Processing helix chain 'A' and resid 841 through 846 removed outlier: 3.527A pdb=" N LYS A 846 " --> pdb=" O LYS A 842 " (cutoff:3.500A) Processing helix chain 'A' and resid 863 through 867 Processing helix chain 'A' and resid 879 through 895 Processing helix chain 'A' and resid 964 through 978 Processing helix chain 'A' and resid 980 through 982 No H-bonds generated for 'chain 'A' and resid 980 through 982' Processing helix chain 'A' and resid 983 through 991 Processing helix chain 'A' and resid 992 through 1000 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 27 through 38 Processing helix chain 'B' and resid 46 through 74 removed outlier: 4.231A pdb=" N VAL B 50 " --> pdb=" O SER B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 Processing helix chain 'B' and resid 91 through 99 Processing helix chain 'C' and resid 40 through 52 removed outlier: 3.572A pdb=" N LYS C 46 " --> pdb=" O SER C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 86 Processing helix chain 'C' and resid 87 through 89 No H-bonds generated for 'chain 'C' and resid 87 through 89' Processing helix chain 'C' and resid 93 through 105 Processing helix chain 'C' and resid 107 through 124 removed outlier: 3.534A pdb=" N SER C 115 " --> pdb=" O LYS C 111 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 799 through 800 Processing sheet with id=AA2, first strand: chain 'A' and resid 848 through 854 removed outlier: 5.184A pdb=" N ASN A 850 " --> pdb=" O VAL A 877 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL A 877 " --> pdb=" O ASN A 850 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ASN A 852 " --> pdb=" O VAL A 875 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ARG A 873 " --> pdb=" O ILE A 854 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 43 through 44 removed outlier: 7.126A pdb=" N ARG B 43 " --> pdb=" O ILE C 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 78 through 79 637 hydrogen bonds defined for protein. 1896 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.82 Time building geometry restraints manager: 3.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 1583 1.33 - 1.45: 2076 1.45 - 1.57: 5168 1.57 - 1.69: 0 1.69 - 1.81: 53 Bond restraints: 8880 Sorted by residual: bond pdb=" N VAL A 965 " pdb=" CA VAL A 965 " ideal model delta sigma weight residual 1.462 1.499 -0.037 1.18e-02 7.18e+03 9.89e+00 bond pdb=" CA SER A 251 " pdb=" CB SER A 251 " ideal model delta sigma weight residual 1.530 1.483 0.047 1.56e-02 4.11e+03 9.01e+00 bond pdb=" N ILE A 884 " pdb=" CA ILE A 884 " ideal model delta sigma weight residual 1.460 1.495 -0.035 1.19e-02 7.06e+03 8.66e+00 bond pdb=" N VAL A 82 " pdb=" CA VAL A 82 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.25e-02 6.40e+03 8.66e+00 bond pdb=" N ILE A 252 " pdb=" CA ILE A 252 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.64e+00 ... (remaining 8875 not shown) Histogram of bond angle deviations from ideal: 98.74 - 105.78: 130 105.78 - 112.82: 4932 112.82 - 119.86: 2912 119.86 - 126.89: 3990 126.89 - 133.93: 61 Bond angle restraints: 12025 Sorted by residual: angle pdb=" N VAL A 258 " pdb=" CA VAL A 258 " pdb=" C VAL A 258 " ideal model delta sigma weight residual 112.35 106.73 5.62 1.41e+00 5.03e-01 1.59e+01 angle pdb=" N SER C 115 " pdb=" CA SER C 115 " pdb=" C SER C 115 " ideal model delta sigma weight residual 111.07 106.87 4.20 1.07e+00 8.73e-01 1.54e+01 angle pdb=" CA ILE C 97 " pdb=" C ILE C 97 " pdb=" O ILE C 97 " ideal model delta sigma weight residual 121.17 117.02 4.15 1.06e+00 8.90e-01 1.54e+01 angle pdb=" N VAL A 966 " pdb=" CA VAL A 966 " pdb=" C VAL A 966 " ideal model delta sigma weight residual 110.42 106.66 3.76 9.60e-01 1.09e+00 1.53e+01 angle pdb=" CA VAL C 69 " pdb=" C VAL C 69 " pdb=" O VAL C 69 " ideal model delta sigma weight residual 121.27 117.26 4.01 1.04e+00 9.25e-01 1.48e+01 ... (remaining 12020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5006 17.99 - 35.98: 364 35.98 - 53.97: 63 53.97 - 71.96: 16 71.96 - 89.95: 5 Dihedral angle restraints: 5454 sinusoidal: 2181 harmonic: 3273 Sorted by residual: dihedral pdb=" CA ALA C 85 " pdb=" C ALA C 85 " pdb=" N TYR C 86 " pdb=" CA TYR C 86 " ideal model delta harmonic sigma weight residual 180.00 163.16 16.84 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA ASP A 476 " pdb=" CB ASP A 476 " pdb=" CG ASP A 476 " pdb=" OD1 ASP A 476 " ideal model delta sinusoidal sigma weight residual -30.00 -87.77 57.77 1 2.00e+01 2.50e-03 1.12e+01 dihedral pdb=" CA MET A 1 " pdb=" C MET A 1 " pdb=" N ASP A 2 " pdb=" CA ASP A 2 " ideal model delta harmonic sigma weight residual 180.00 -163.31 -16.69 0 5.00e+00 4.00e-02 1.11e+01 ... (remaining 5451 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1116 0.042 - 0.085: 230 0.085 - 0.127: 69 0.127 - 0.169: 21 0.169 - 0.212: 7 Chirality restraints: 1443 Sorted by residual: chirality pdb=" CA ILE C 72 " pdb=" N ILE C 72 " pdb=" C ILE C 72 " pdb=" CB ILE C 72 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA VAL A 258 " pdb=" N VAL A 258 " pdb=" C VAL A 258 " pdb=" CB VAL A 258 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 9.66e-01 chirality pdb=" CA ILE C 76 " pdb=" N ILE C 76 " pdb=" C ILE C 76 " pdb=" CB ILE C 76 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 1440 not shown) Planarity restraints: 1522 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 373 " 0.016 2.00e-02 2.50e+03 3.11e-02 9.64e+00 pdb=" C ARG A 373 " -0.054 2.00e-02 2.50e+03 pdb=" O ARG A 373 " 0.020 2.00e-02 2.50e+03 pdb=" N ASP A 374 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL C 114 " -0.015 2.00e-02 2.50e+03 3.10e-02 9.61e+00 pdb=" C VAL C 114 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL C 114 " -0.020 2.00e-02 2.50e+03 pdb=" N SER C 115 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU C 105 " -0.025 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO C 106 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 106 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 106 " -0.021 5.00e-02 4.00e+02 ... (remaining 1519 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1428 2.76 - 3.29: 9391 3.29 - 3.83: 14030 3.83 - 4.36: 17806 4.36 - 4.90: 30711 Nonbonded interactions: 73366 Sorted by model distance: nonbonded pdb=" OG SER B 19 " pdb=" O PHE B 26 " model vdw 2.221 2.440 nonbonded pdb=" O ASN A 422 " pdb=" NZ LYS A 469 " model vdw 2.226 2.520 nonbonded pdb=" OD1 ASP A 14 " pdb=" OG1 THR A 17 " model vdw 2.250 2.440 nonbonded pdb=" NZ LYS A 657 " pdb=" O GLY A 661 " model vdw 2.291 2.520 nonbonded pdb=" OD2 ASP A 841 " pdb=" NH2 ARG A 843 " model vdw 2.301 2.520 ... (remaining 73361 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: 3.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 14.930 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 26.360 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 0.047 8880 Z= 0.264 Angle : 0.647 5.965 12025 Z= 0.470 Chirality : 0.043 0.212 1443 Planarity : 0.004 0.052 1522 Dihedral : 13.349 89.950 3310 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.50 % Allowed : 0.40 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 0.47 (0.25), residues: 1091 helix: 0.49 (0.18), residues: 864 sheet: None (None), residues: 0 loop : 0.13 (0.40), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 127 HIS 0.003 0.001 HIS C 52 PHE 0.012 0.001 PHE C 68 TYR 0.010 0.001 TYR C 86 ARG 0.011 0.000 ARG A 755 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 102 time to evaluate : 0.890 Fit side-chains REVERT: A 309 ASP cc_start: 0.7675 (m-30) cc_final: 0.7212 (m-30) REVERT: A 425 GLU cc_start: 0.7194 (tp30) cc_final: 0.6950 (mm-30) REVERT: A 579 HIS cc_start: 0.8401 (t-90) cc_final: 0.8014 (t-170) REVERT: A 766 LYS cc_start: 0.7691 (mtpp) cc_final: 0.7244 (ttmt) outliers start: 5 outliers final: 0 residues processed: 105 average time/residue: 0.2523 time to fit residues: 35.4684 Evaluate side-chains 87 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 ASN A 563 ASN A 774 GLN A 835 ASN A 840 ASN A 967 GLN B 74 ASN C 87 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8880 Z= 0.205 Angle : 0.500 8.636 12025 Z= 0.267 Chirality : 0.037 0.119 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.832 18.190 1171 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.70 % Allowed : 5.01 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 1.84 (0.25), residues: 1091 helix: 1.50 (0.17), residues: 882 sheet: None (None), residues: 0 loop : 0.31 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 69 HIS 0.003 0.001 HIS A 568 PHE 0.026 0.002 PHE A 837 TYR 0.020 0.002 TYR C 86 ARG 0.005 0.001 ARG A 755 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 0.915 Fit side-chains REVERT: A 309 ASP cc_start: 0.7392 (m-30) cc_final: 0.7033 (m-30) REVERT: A 425 GLU cc_start: 0.7295 (tp30) cc_final: 0.7082 (mm-30) REVERT: A 440 LYS cc_start: 0.7816 (mtpt) cc_final: 0.7556 (mtpp) REVERT: A 627 ASN cc_start: 0.6979 (m110) cc_final: 0.6400 (m110) REVERT: A 859 ASP cc_start: 0.7461 (t0) cc_final: 0.7144 (t0) REVERT: B 74 ASN cc_start: 0.7335 (OUTLIER) cc_final: 0.7123 (m-40) outliers start: 7 outliers final: 1 residues processed: 113 average time/residue: 0.2232 time to fit residues: 34.8103 Evaluate side-chains 96 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain B residue 74 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 107 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 33 optimal weight: 0.0770 chunk 79 optimal weight: 6.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 GLN A 549 ASN A 563 ASN A 613 ASN B 74 ASN C 59 GLN C 87 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8880 Z= 0.190 Angle : 0.456 8.916 12025 Z= 0.243 Chirality : 0.036 0.120 1443 Planarity : 0.004 0.047 1522 Dihedral : 3.696 18.028 1171 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.00 % Allowed : 5.81 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.37 (0.25), residues: 1091 helix: 1.88 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.36 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 69 HIS 0.003 0.001 HIS C 52 PHE 0.023 0.001 PHE A 837 TYR 0.016 0.001 TYR C 86 ARG 0.004 0.000 ARG A 755 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 110 time to evaluate : 0.971 Fit side-chains revert: symmetry clash REVERT: A 309 ASP cc_start: 0.7394 (m-30) cc_final: 0.7052 (m-30) REVERT: A 425 GLU cc_start: 0.7303 (tp30) cc_final: 0.7103 (mm-30) REVERT: A 611 MET cc_start: 0.6425 (mmm) cc_final: 0.6133 (mmm) REVERT: A 702 THR cc_start: 0.8975 (OUTLIER) cc_final: 0.8770 (t) REVERT: A 840 ASN cc_start: 0.7577 (t0) cc_final: 0.7321 (t0) REVERT: A 859 ASP cc_start: 0.7381 (t0) cc_final: 0.7052 (t0) REVERT: B 74 ASN cc_start: 0.7353 (OUTLIER) cc_final: 0.7101 (m-40) outliers start: 10 outliers final: 5 residues processed: 117 average time/residue: 0.2340 time to fit residues: 37.5430 Evaluate side-chains 109 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 102 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 74 optimal weight: 0.0170 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 94 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 87 optimal weight: 0.8980 overall best weight: 0.6018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 74 ASN C 59 GLN C 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8880 Z= 0.178 Angle : 0.446 9.619 12025 Z= 0.237 Chirality : 0.036 0.121 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.626 17.528 1171 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 0.70 % Allowed : 7.72 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.62 (0.25), residues: 1091 helix: 2.09 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.30 (0.42), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 127 HIS 0.003 0.001 HIS C 52 PHE 0.021 0.001 PHE A 837 TYR 0.015 0.001 TYR C 45 ARG 0.003 0.000 ARG A 755 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 106 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7540 (tp40) cc_final: 0.6868 (tt0) REVERT: A 309 ASP cc_start: 0.7383 (m-30) cc_final: 0.7046 (m-30) REVERT: A 411 SER cc_start: 0.8047 (t) cc_final: 0.7700 (p) REVERT: A 516 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7442 (mm-30) REVERT: A 611 MET cc_start: 0.6442 (mmm) cc_final: 0.6119 (mmm) REVERT: A 702 THR cc_start: 0.8997 (OUTLIER) cc_final: 0.8780 (t) REVERT: A 859 ASP cc_start: 0.7333 (t0) cc_final: 0.7021 (t0) REVERT: B 74 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.7031 (t160) outliers start: 7 outliers final: 4 residues processed: 110 average time/residue: 0.2434 time to fit residues: 36.9173 Evaluate side-chains 109 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 103 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.4980 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 5.9990 chunk 26 optimal weight: 0.0470 chunk 35 optimal weight: 1.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN B 39 ASN B 74 ASN C 59 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8880 Z= 0.179 Angle : 0.444 10.226 12025 Z= 0.233 Chirality : 0.035 0.120 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.568 17.586 1171 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.00 % Allowed : 8.32 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.72 (0.25), residues: 1091 helix: 2.18 (0.17), residues: 884 sheet: None (None), residues: 0 loop : 0.23 (0.41), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 127 HIS 0.003 0.001 HIS A 568 PHE 0.015 0.001 PHE A 249 TYR 0.012 0.001 TYR C 86 ARG 0.003 0.000 ARG A 971 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7521 (tp40) cc_final: 0.6870 (tt0) REVERT: A 309 ASP cc_start: 0.7398 (m-30) cc_final: 0.7066 (m-30) REVERT: A 516 GLU cc_start: 0.7829 (mt-10) cc_final: 0.7447 (mm-30) REVERT: A 702 THR cc_start: 0.8977 (OUTLIER) cc_final: 0.8745 (t) REVERT: A 719 GLU cc_start: 0.6548 (mt-10) cc_final: 0.6329 (mt-10) REVERT: A 859 ASP cc_start: 0.7298 (t0) cc_final: 0.6977 (t0) REVERT: B 74 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.7056 (t160) REVERT: C 42 SER cc_start: 0.8061 (t) cc_final: 0.7709 (p) outliers start: 10 outliers final: 5 residues processed: 111 average time/residue: 0.2324 time to fit residues: 35.3961 Evaluate side-chains 107 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 100 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 702 THR Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 105 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 101 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 549 ASN ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 579 HIS A 845 GLN B 74 ASN C 59 GLN C 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8880 Z= 0.181 Angle : 0.453 10.493 12025 Z= 0.239 Chirality : 0.036 0.141 1443 Planarity : 0.004 0.044 1522 Dihedral : 3.546 16.919 1171 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.00 % Allowed : 8.92 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.87 (0.25), residues: 1091 helix: 2.28 (0.17), residues: 879 sheet: None (None), residues: 0 loop : 0.33 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 127 HIS 0.003 0.001 HIS A 568 PHE 0.014 0.001 PHE A 249 TYR 0.011 0.001 TYR C 86 ARG 0.002 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 103 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7513 (tp40) cc_final: 0.6875 (tt0) REVERT: A 309 ASP cc_start: 0.7396 (m-30) cc_final: 0.7065 (m-30) REVERT: A 516 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7443 (mm-30) REVERT: A 611 MET cc_start: 0.6436 (mmm) cc_final: 0.5733 (mmm) REVERT: A 719 GLU cc_start: 0.6523 (mt-10) cc_final: 0.6271 (mt-10) REVERT: B 74 ASN cc_start: 0.7376 (OUTLIER) cc_final: 0.6426 (t0) REVERT: C 42 SER cc_start: 0.8073 (t) cc_final: 0.7739 (p) outliers start: 10 outliers final: 6 residues processed: 110 average time/residue: 0.2305 time to fit residues: 35.1503 Evaluate side-chains 108 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 101 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 845 GLN Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 58 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.5980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 563 ASN A 774 GLN A 840 ASN A 845 GLN B 74 ASN C 59 GLN C 87 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7508 moved from start: 0.2541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8880 Z= 0.239 Angle : 0.483 11.068 12025 Z= 0.252 Chirality : 0.037 0.122 1443 Planarity : 0.004 0.046 1522 Dihedral : 3.609 17.981 1171 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.50 % Allowed : 8.92 % Favored : 89.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.69 (0.25), residues: 1091 helix: 2.16 (0.17), residues: 881 sheet: None (None), residues: 0 loop : 0.25 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP A 69 HIS 0.004 0.001 HIS A 568 PHE 0.015 0.001 PHE A 249 TYR 0.011 0.001 TYR C 86 ARG 0.003 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 100 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7515 (tp40) cc_final: 0.6901 (tt0) REVERT: A 309 ASP cc_start: 0.7464 (m-30) cc_final: 0.7113 (m-30) REVERT: A 516 GLU cc_start: 0.7825 (mt-10) cc_final: 0.7461 (mm-30) REVERT: A 611 MET cc_start: 0.6426 (mmm) cc_final: 0.5759 (mmm) REVERT: A 719 GLU cc_start: 0.6551 (mt-10) cc_final: 0.6274 (mt-10) REVERT: B 74 ASN cc_start: 0.7386 (OUTLIER) cc_final: 0.7081 (t160) REVERT: C 42 SER cc_start: 0.8108 (t) cc_final: 0.7788 (p) outliers start: 15 outliers final: 11 residues processed: 110 average time/residue: 0.2233 time to fit residues: 34.3907 Evaluate side-chains 112 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 100 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain A residue 774 GLN Chi-restraints excluded: chain A residue 845 GLN Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 20 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 91 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 563 ASN A 840 ASN C 59 GLN C 87 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7511 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8880 Z= 0.233 Angle : 0.483 11.446 12025 Z= 0.251 Chirality : 0.037 0.122 1443 Planarity : 0.004 0.046 1522 Dihedral : 3.628 18.117 1171 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.30 % Allowed : 9.42 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.68 (0.24), residues: 1091 helix: 2.17 (0.17), residues: 879 sheet: None (None), residues: 0 loop : 0.15 (0.39), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 813 HIS 0.004 0.001 HIS A 568 PHE 0.015 0.001 PHE A 249 TYR 0.011 0.001 TYR C 86 ARG 0.002 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7506 (tp40) cc_final: 0.6905 (tt0) REVERT: A 309 ASP cc_start: 0.7486 (m-30) cc_final: 0.7142 (m-30) REVERT: A 516 GLU cc_start: 0.7820 (mt-10) cc_final: 0.7456 (mm-30) REVERT: A 611 MET cc_start: 0.6415 (mmm) cc_final: 0.5735 (mmm) REVERT: A 719 GLU cc_start: 0.6536 (mt-10) cc_final: 0.6250 (mt-10) REVERT: C 42 SER cc_start: 0.8120 (t) cc_final: 0.7820 (p) outliers start: 13 outliers final: 9 residues processed: 111 average time/residue: 0.2264 time to fit residues: 34.8106 Evaluate side-chains 109 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 100 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain B residue 77 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 4.9990 chunk 100 optimal weight: 0.9990 chunk 58 optimal weight: 0.6980 chunk 42 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 5.9990 chunk 64 optimal weight: 0.6980 chunk 103 optimal weight: 0.6980 chunk 63 optimal weight: 2.9990 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 81 ASN A 563 ASN B 74 ASN C 87 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7489 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8880 Z= 0.190 Angle : 0.467 11.532 12025 Z= 0.244 Chirality : 0.036 0.168 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.549 17.503 1171 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.37 % Favored : 98.63 % Rotamer: Outliers : 1.30 % Allowed : 9.72 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.82 (0.25), residues: 1091 helix: 2.27 (0.17), residues: 881 sheet: None (None), residues: 0 loop : 0.21 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 28 HIS 0.004 0.001 HIS A 568 PHE 0.014 0.001 PHE A 249 TYR 0.010 0.001 TYR C 45 ARG 0.004 0.000 ARG B 72 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.979 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7491 (tp40) cc_final: 0.6883 (tt0) REVERT: A 309 ASP cc_start: 0.7446 (m-30) cc_final: 0.7114 (m-30) REVERT: A 516 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7434 (mm-30) REVERT: A 611 MET cc_start: 0.6394 (mmm) cc_final: 0.5729 (mmm) REVERT: A 719 GLU cc_start: 0.6514 (mt-10) cc_final: 0.6228 (mt-10) REVERT: B 74 ASN cc_start: 0.7413 (OUTLIER) cc_final: 0.6371 (t0) REVERT: C 42 SER cc_start: 0.8099 (t) cc_final: 0.7815 (p) outliers start: 13 outliers final: 10 residues processed: 111 average time/residue: 0.2133 time to fit residues: 32.8503 Evaluate side-chains 109 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 563 ASN Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 770 ILE Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 99 optimal weight: 0.0170 chunk 86 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 0.1980 chunk 53 optimal weight: 7.9990 chunk 68 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 563 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 845 GLN B 74 ASN C 87 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8880 Z= 0.148 Angle : 0.454 11.279 12025 Z= 0.239 Chirality : 0.035 0.195 1443 Planarity : 0.004 0.043 1522 Dihedral : 3.472 16.698 1171 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Rotamer: Outliers : 1.30 % Allowed : 9.52 % Favored : 89.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 3.02 (0.25), residues: 1091 helix: 2.41 (0.17), residues: 881 sheet: None (None), residues: 0 loop : 0.21 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 69 HIS 0.004 0.001 HIS C 52 PHE 0.013 0.001 PHE A 249 TYR 0.011 0.001 TYR C 45 ARG 0.004 0.000 ARG B 72 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2182 Ramachandran restraints generated. 1091 Oldfield, 0 Emsley, 1091 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 102 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 GLN cc_start: 0.7485 (tp40) cc_final: 0.6891 (tt0) REVERT: A 411 SER cc_start: 0.7991 (t) cc_final: 0.7702 (p) REVERT: A 516 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7411 (mm-30) REVERT: A 611 MET cc_start: 0.6377 (mmm) cc_final: 0.5737 (mmm) REVERT: A 719 GLU cc_start: 0.6476 (mt-10) cc_final: 0.6191 (mt-10) REVERT: B 74 ASN cc_start: 0.7394 (OUTLIER) cc_final: 0.6504 (t0) REVERT: C 42 SER cc_start: 0.8093 (t) cc_final: 0.7807 (p) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.2104 time to fit residues: 32.5743 Evaluate side-chains 111 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 ILE Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 358 THR Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 653 PHE Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 845 GLN Chi-restraints excluded: chain B residue 74 ASN Chi-restraints excluded: chain B residue 77 THR Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 126 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 86 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 76 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 840 ASN A 845 GLN B 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.187356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.149735 restraints weight = 8174.060| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.80 r_work: 0.3523 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3355 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8880 Z= 0.210 Angle : 0.475 11.541 12025 Z= 0.249 Chirality : 0.037 0.229 1443 Planarity : 0.004 0.045 1522 Dihedral : 3.517 16.842 1171 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % Rotamer: Outliers : 1.10 % Allowed : 10.02 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: 2.88 (0.24), residues: 1091 helix: 2.33 (0.17), residues: 880 sheet: None (None), residues: 0 loop : 0.10 (0.39), residues: 211 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 127 HIS 0.004 0.001 HIS A 568 PHE 0.014 0.001 PHE A 249 TYR 0.010 0.001 TYR C 86 ARG 0.004 0.000 ARG B 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2184.28 seconds wall clock time: 39 minutes 56.71 seconds (2396.71 seconds total)