Starting phenix.real_space_refine on Sun Jul 27 23:25:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8seb_40409/07_2025/8seb_40409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8seb_40409/07_2025/8seb_40409.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8seb_40409/07_2025/8seb_40409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8seb_40409/07_2025/8seb_40409.map" model { file = "/net/cci-nas-00/data/ceres_data/8seb_40409/07_2025/8seb_40409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8seb_40409/07_2025/8seb_40409.cif" } resolution = 3.24 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= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 36 5.16 5 C 6106 2.51 5 N 1687 2.21 5 O 1779 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9609 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7693 Classifications: {'peptide': 989} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 65, 'TRANS': 923} Chain: "B" Number of atoms: 650 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 650 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 4, 'TRANS': 77} Chain: "C" Number of atoms: 1243 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1243 Classifications: {'peptide': 152} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 133} Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 6.67, per 1000 atoms: 0.69 Number of scatterers: 9609 At special positions: 0 Unit cell: (103.317, 96.6512, 112.482, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 1 15.00 O 1779 8.00 N 1687 7.00 C 6106 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 599 " - pdb=" SG CYS C 86 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.81 Conformation dependent library (CDL) restraints added in 1.2 seconds 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2292 Finding SS restraints... Secondary structure from input PDB file: 51 helices and 9 sheets defined 44.8% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.35 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 removed outlier: 3.731A pdb=" N ARG A 29 " --> pdb=" O PRO A 25 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ILE A 30 " --> pdb=" O ALA A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 55 Processing helix chain 'A' and resid 68 through 72 removed outlier: 3.696A pdb=" N ASP A 71 " --> pdb=" O CYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 83 Processing helix chain 'A' and resid 86 through 99 removed outlier: 3.874A pdb=" N GLU A 93 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N LEU A 94 " --> pdb=" O ALA A 90 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN A 97 " --> pdb=" O GLU A 93 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN A 99 " --> pdb=" O LEU A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 119 Processing helix chain 'A' and resid 128 through 143 Processing helix chain 'A' and resid 198 through 203 Processing helix chain 'A' and resid 232 through 234 No H-bonds generated for 'chain 'A' and resid 232 through 234' Processing helix chain 'A' and resid 266 through 273 removed outlier: 3.885A pdb=" N LEU A 272 " --> pdb=" O ASP A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 305 Processing helix chain 'A' and resid 312 through 326 Processing helix chain 'A' and resid 327 through 331 Processing helix chain 'A' and resid 342 through 353 Processing helix chain 'A' and resid 357 through 378 Processing helix chain 'A' and resid 392 through 395 removed outlier: 3.726A pdb=" N LEU A 395 " --> pdb=" O LEU A 392 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 392 through 395' Processing helix chain 'A' and resid 415 through 423 Processing helix chain 'A' and resid 423 through 432 Processing helix chain 'A' and resid 441 through 455 Processing helix chain 'A' and resid 491 through 504 Processing helix chain 'A' and resid 517 through 521 removed outlier: 3.725A pdb=" N GLU A 521 " --> pdb=" O PRO A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 Processing helix chain 'A' and resid 541 through 556 Processing helix chain 'A' and resid 585 through 593 removed outlier: 4.354A pdb=" N ASP A 593 " --> pdb=" O ALA A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 597 through 604 removed outlier: 4.219A pdb=" N VAL A 601 " --> pdb=" O PRO A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 623 Processing helix chain 'A' and resid 624 through 630 removed outlier: 4.354A pdb=" N GLU A 628 " --> pdb=" O ARG A 624 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 4.318A pdb=" N ALA A 636 " --> pdb=" O HIS A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 644 through 653 removed outlier: 4.042A pdb=" N THR A 650 " --> pdb=" O PRO A 646 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 656 No H-bonds generated for 'chain 'A' and resid 654 through 656' Processing helix chain 'A' and resid 669 through 682 removed outlier: 3.915A pdb=" N HIS A 676 " --> pdb=" O TRP A 672 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N TRP A 677 " --> pdb=" O ALA A 673 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 692 Processing helix chain 'A' and resid 721 through 740 removed outlier: 3.649A pdb=" N LEU A 725 " --> pdb=" O GLN A 721 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 757 removed outlier: 3.634A pdb=" N LEU A 753 " --> pdb=" O ALA A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 761 through 765 removed outlier: 3.832A pdb=" N MET A 765 " --> pdb=" O PRO A 762 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 799 removed outlier: 3.981A pdb=" N GLN A 787 " --> pdb=" O GLY A 783 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS A 788 " --> pdb=" O PRO A 784 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 799 " --> pdb=" O GLU A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 815 removed outlier: 3.503A pdb=" N ASN A 815 " --> pdb=" O ASP A 812 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 812 through 815' Processing helix chain 'A' and resid 816 through 832 removed outlier: 3.684A pdb=" N GLN A 830 " --> pdb=" O SER A 826 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 843 Processing helix chain 'A' and resid 853 through 872 removed outlier: 3.721A pdb=" N LYS A 870 " --> pdb=" O LEU A 866 " (cutoff:3.500A) Processing helix chain 'A' and resid 927 through 940 Processing helix chain 'A' and resid 959 through 967 Processing helix chain 'A' and resid 970 through 980 Processing helix chain 'B' and resid 103 through 116 Processing helix chain 'B' and resid 118 through 120 No H-bonds generated for 'chain 'B' and resid 118 through 120' Processing helix chain 'B' and resid 136 through 141 Processing helix chain 'C' and resid 3 through 16 Processing helix chain 'C' and resid 45 through 49 removed outlier: 3.594A pdb=" N LYS C 49 " --> pdb=" O TYR C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 114 Processing helix chain 'C' and resid 122 through 132 Processing helix chain 'C' and resid 132 through 148 removed outlier: 3.619A pdb=" N PHE C 136 " --> pdb=" O ASN C 132 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.667A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N VAL A 155 " --> pdb=" O ARG A 152 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.667A pdb=" N VAL A 121 " --> pdb=" O ARG A 34 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 166 through 168 Processing sheet with id=AA4, first strand: chain 'A' and resid 226 through 227 removed outlier: 4.168A pdb=" N LEU A 208 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER A 212 " --> pdb=" O ALA A 252 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ALA A 252 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N ILE A 214 " --> pdb=" O GLY A 250 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N GLY A 250 " --> pdb=" O ILE A 214 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLY A 216 " --> pdb=" O LEU A 248 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N LEU A 248 " --> pdb=" O GLY A 216 " (cutoff:3.500A) removed outlier: 9.296A pdb=" N ARG A 249 " --> pdb=" O HIS A 183 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N HIS A 183 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY A 251 " --> pdb=" O ILE A 181 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 236 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 509 through 512 removed outlier: 7.052A pdb=" N LEU A 464 " --> pdb=" O ILE A 510 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N LEU A 512 " --> pdb=" O LEU A 464 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N VAL A 466 " --> pdb=" O LEU A 512 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N LEU A 436 " --> pdb=" O ALA A 536 " (cutoff:3.500A) removed outlier: 7.418A pdb=" N ALA A 538 " --> pdb=" O LEU A 436 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N VAL A 438 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 904 through 906 Processing sheet with id=AA7, first strand: chain 'A' and resid 917 through 920 removed outlier: 6.154A pdb=" N LEU A 917 " --> pdb=" O HIS A1009 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU A1011 " --> pdb=" O LEU A 917 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N VAL A 919 " --> pdb=" O GLU A1011 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 945 " --> pdb=" O SER A 995 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ARG A 944 " --> pdb=" O ALA A 955 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 955 " --> pdb=" O ARG A 944 " (cutoff:3.500A) removed outlier: 7.001A pdb=" N LEU A 946 " --> pdb=" O LEU A 953 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 93 through 98 Processing sheet with id=AA9, first strand: chain 'C' and resid 22 through 27 removed outlier: 5.718A pdb=" N ASN C 24 " --> pdb=" O LEU C 38 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LEU C 38 " --> pdb=" O ASN C 24 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1251 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: 3.89 Time building geometry restraints manager: 3.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2854 1.33 - 1.45: 1466 1.45 - 1.57: 5473 1.57 - 1.69: 4 1.69 - 1.81: 54 Bond restraints: 9851 Sorted by residual: bond pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 1.426 1.621 -0.195 2.00e-02 2.50e+03 9.47e+01 bond pdb=" C1' AMP B 201 " pdb=" C2' AMP B 201 " ideal model delta sigma weight residual 1.524 1.363 0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" C6 AMP B 201 " pdb=" N6 AMP B 201 " ideal model delta sigma weight residual 1.355 1.496 -0.141 2.00e-02 2.50e+03 4.99e+01 bond pdb=" C4' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 1.426 1.292 0.134 2.00e-02 2.50e+03 4.52e+01 bond pdb=" C4 AMP B 201 " pdb=" C5 AMP B 201 " ideal model delta sigma weight residual 1.490 1.373 0.117 2.00e-02 2.50e+03 3.42e+01 ... (remaining 9846 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.59: 13384 3.59 - 7.17: 28 7.17 - 10.76: 3 10.76 - 14.35: 2 14.35 - 17.93: 2 Bond angle restraints: 13419 Sorted by residual: angle pdb=" C2' AMP B 201 " pdb=" C1' AMP B 201 " pdb=" N9 AMP B 201 " ideal model delta sigma weight residual 109.47 127.40 -17.93 3.00e+00 1.11e-01 3.57e+01 angle pdb=" O2P AMP B 201 " pdb=" P AMP B 201 " pdb=" O3P AMP B 201 " ideal model delta sigma weight residual 119.90 105.09 14.81 3.00e+00 1.11e-01 2.44e+01 angle pdb=" N9 AMP B 201 " pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 109.47 96.21 13.26 3.00e+00 1.11e-01 1.96e+01 angle pdb=" O1P AMP B 201 " pdb=" P AMP B 201 " pdb=" O2P AMP B 201 " ideal model delta sigma weight residual 119.60 108.62 10.98 3.00e+00 1.11e-01 1.34e+01 angle pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " pdb=" C4' AMP B 201 " ideal model delta sigma weight residual 111.80 101.81 9.99 3.00e+00 1.11e-01 1.11e+01 ... (remaining 13414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.88: 5801 29.88 - 59.77: 127 59.77 - 89.65: 10 89.65 - 119.54: 0 119.54 - 149.42: 1 Dihedral angle restraints: 5939 sinusoidal: 2399 harmonic: 3540 Sorted by residual: dihedral pdb=" C5' AMP B 201 " pdb=" O5' AMP B 201 " pdb=" P AMP B 201 " pdb=" O3P AMP B 201 " ideal model delta sinusoidal sigma weight residual 300.00 150.58 149.42 1 2.00e+01 2.50e-03 4.47e+01 dihedral pdb=" CA GLN A 923 " pdb=" C GLN A 923 " pdb=" N PRO A 924 " pdb=" CA PRO A 924 " ideal model delta harmonic sigma weight residual 180.00 158.52 21.48 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA ARG A 895 " pdb=" CB ARG A 895 " pdb=" CG ARG A 895 " pdb=" CD ARG A 895 " ideal model delta sinusoidal sigma weight residual -60.00 -118.22 58.22 3 1.50e+01 4.44e-03 9.46e+00 ... (remaining 5936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1052 0.034 - 0.068: 323 0.068 - 0.103: 95 0.103 - 0.137: 25 0.137 - 0.171: 1 Chirality restraints: 1496 Sorted by residual: chirality pdb=" C3' AMP B 201 " pdb=" C2' AMP B 201 " pdb=" C4' AMP B 201 " pdb=" O3' AMP B 201 " both_signs ideal model delta sigma weight residual False -2.51 -2.68 0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CA ILE C 85 " pdb=" N ILE C 85 " pdb=" C ILE C 85 " pdb=" CB ILE C 85 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.83e-01 chirality pdb=" CA ILE A 214 " pdb=" N ILE A 214 " pdb=" C ILE A 214 " pdb=" CB ILE A 214 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 1493 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 645 " -0.035 5.00e-02 4.00e+02 5.35e-02 4.58e+00 pdb=" N PRO A 646 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 646 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 646 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 517 " 0.026 5.00e-02 4.00e+02 3.88e-02 2.41e+00 pdb=" N PRO A 518 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 518 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 518 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 692 " -0.020 5.00e-02 4.00e+02 3.01e-02 1.45e+00 pdb=" N PRO A 693 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 693 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 693 " -0.017 5.00e-02 4.00e+02 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1095 2.75 - 3.29: 9826 3.29 - 3.83: 16019 3.83 - 4.36: 18622 4.36 - 4.90: 32187 Nonbonded interactions: 77749 Sorted by model distance: nonbonded pdb=" OG1 THR A 927 " pdb=" O LEU A 967 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASP A 517 " pdb=" OG1 THR A 519 " model vdw 2.231 3.040 nonbonded pdb=" O THR A 553 " pdb=" NH2 ARG A 916 " model vdw 2.264 3.120 nonbonded pdb=" O GLU A 621 " pdb=" OG SER A 626 " model vdw 2.268 3.040 nonbonded pdb=" OG1 THR C 99 " pdb=" OE1 GLN C 103 " model vdw 2.277 3.040 ... (remaining 77744 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 23.010 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: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.300 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:3.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6961 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 0.195 9853 Z= 0.234 Angle : 0.600 17.935 13421 Z= 0.283 Chirality : 0.038 0.171 1496 Planarity : 0.004 0.053 1762 Dihedral : 12.060 149.425 3644 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.44 % Favored : 95.48 % Rotamer: Outliers : 1.74 % Allowed : 8.02 % Favored : 90.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1217 helix: 1.62 (0.25), residues: 448 sheet: 0.19 (0.39), residues: 182 loop : -0.34 (0.27), residues: 587 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 666 HIS 0.002 0.000 HIS A 817 PHE 0.008 0.001 PHE A 146 TYR 0.007 0.001 TYR A 388 ARG 0.002 0.000 ARG A 204 Details of bonding type rmsd hydrogen bonds : bond 0.18190 ( 432) hydrogen bonds : angle 6.68135 ( 1251) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.76750 ( 2) covalent geometry : bond 0.00439 ( 9851) covalent geometry : angle 0.60035 (13419) Misc. bond : bond 0.08281 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 84 GLU cc_start: 0.7421 (mm-30) cc_final: 0.7078 (mm-30) REVERT: A 177 LEU cc_start: 0.6400 (mm) cc_final: 0.5709 (mt) REVERT: A 224 ASP cc_start: 0.8906 (m-30) cc_final: 0.8695 (p0) REVERT: A 229 HIS cc_start: 0.6930 (t-90) cc_final: 0.6423 (t-90) REVERT: A 256 VAL cc_start: 0.8355 (t) cc_final: 0.7773 (m) REVERT: A 258 ARG cc_start: 0.7278 (ptp-110) cc_final: 0.6752 (mtt-85) REVERT: A 410 LEU cc_start: 0.8792 (mp) cc_final: 0.8499 (mt) REVERT: A 473 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7589 (mm-30) REVERT: A 476 ASN cc_start: 0.7845 (m110) cc_final: 0.7611 (m-40) REVERT: A 490 ARG cc_start: 0.8582 (mtp180) cc_final: 0.8209 (mtm110) REVERT: A 565 SER cc_start: 0.8111 (t) cc_final: 0.7471 (p) REVERT: A 738 MET cc_start: -0.0859 (mtp) cc_final: -0.1281 (mpp) REVERT: A 867 GLU cc_start: 0.7224 (mm-30) cc_final: 0.7018 (mm-30) REVERT: A 988 ARG cc_start: 0.7076 (mmp-170) cc_final: 0.6728 (mmp80) REVERT: B 87 ARG cc_start: 0.7951 (tpp80) cc_final: 0.7732 (tpp80) REVERT: C 26 SER cc_start: 0.7760 (p) cc_final: 0.7399 (t) REVERT: C 67 MET cc_start: 0.7287 (mpp) cc_final: 0.7021 (mpp) REVERT: C 136 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5768 (m-80) outliers start: 18 outliers final: 6 residues processed: 177 average time/residue: 0.2597 time to fit residues: 62.8573 Evaluate side-chains 104 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 97 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 941 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 61 optimal weight: 20.0000 chunk 48 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 10.0000 chunk 70 optimal weight: 20.0000 chunk 109 optimal weight: 3.9990 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 62 HIS A 132 GLN A 288 HIS A 433 GLN A 508 GLN ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 ASN ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.211057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.137327 restraints weight = 12617.466| |-----------------------------------------------------------------------------| r_work (start): 0.3714 rms_B_bonded: 3.95 r_work: 0.3334 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9853 Z= 0.167 Angle : 0.625 7.510 13421 Z= 0.303 Chirality : 0.041 0.184 1496 Planarity : 0.005 0.058 1762 Dihedral : 6.086 121.166 1337 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.40 % Rotamer: Outliers : 2.80 % Allowed : 11.40 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.53 (0.25), residues: 1217 helix: 1.50 (0.24), residues: 457 sheet: 0.03 (0.38), residues: 184 loop : -0.42 (0.27), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 666 HIS 0.010 0.001 HIS A 142 PHE 0.012 0.001 PHE A 146 TYR 0.014 0.001 TYR C 21 ARG 0.007 0.001 ARG A 204 Details of bonding type rmsd hydrogen bonds : bond 0.04151 ( 432) hydrogen bonds : angle 5.41858 ( 1251) SS BOND : bond 0.00227 ( 1) SS BOND : angle 0.42120 ( 2) covalent geometry : bond 0.00388 ( 9851) covalent geometry : angle 0.62538 (13419) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 109 time to evaluate : 2.201 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8402 (mmm) cc_final: 0.7887 (mmm) REVERT: A 84 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7832 (mm-30) REVERT: A 229 HIS cc_start: 0.6814 (t-90) cc_final: 0.6437 (t-90) REVERT: A 256 VAL cc_start: 0.8861 (t) cc_final: 0.8457 (m) REVERT: A 258 ARG cc_start: 0.7578 (ptp-110) cc_final: 0.7182 (mtt-85) REVERT: A 477 LEU cc_start: 0.7767 (pt) cc_final: 0.7509 (pt) REVERT: A 565 SER cc_start: 0.8372 (t) cc_final: 0.7984 (p) REVERT: A 738 MET cc_start: -0.1322 (mtp) cc_final: -0.1825 (mpp) REVERT: A 807 MET cc_start: 0.2594 (tpt) cc_final: 0.2366 (tpt) REVERT: A 988 ARG cc_start: 0.7641 (mmp-170) cc_final: 0.7332 (mmp80) REVERT: B 87 ARG cc_start: 0.8298 (tpp80) cc_final: 0.7983 (tpp80) REVERT: C 26 SER cc_start: 0.7951 (p) cc_final: 0.7555 (t) REVERT: C 54 ARG cc_start: 0.6489 (ttm170) cc_final: 0.6007 (ptm160) REVERT: C 105 LEU cc_start: 0.9042 (mt) cc_final: 0.8722 (pp) REVERT: C 106 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8219 (mt-10) REVERT: C 136 PHE cc_start: 0.6430 (OUTLIER) cc_final: 0.5752 (m-80) outliers start: 29 outliers final: 19 residues processed: 130 average time/residue: 0.3293 time to fit residues: 61.0457 Evaluate side-chains 111 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 91 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 60 optimal weight: 6.9990 chunk 82 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 17 optimal weight: 6.9990 chunk 120 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 0.0870 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.209804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.131510 restraints weight = 12836.430| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 3.34 r_work: 0.3371 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9853 Z= 0.224 Angle : 0.642 6.973 13421 Z= 0.312 Chirality : 0.042 0.158 1496 Planarity : 0.004 0.057 1762 Dihedral : 5.498 63.826 1335 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 3.48 % Allowed : 12.75 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.32 (0.25), residues: 1217 helix: 1.30 (0.24), residues: 462 sheet: -0.27 (0.37), residues: 187 loop : -0.46 (0.27), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 666 HIS 0.006 0.001 HIS A 934 PHE 0.013 0.001 PHE A 146 TYR 0.011 0.001 TYR A1010 ARG 0.007 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.03991 ( 432) hydrogen bonds : angle 5.35077 ( 1251) SS BOND : bond 0.00346 ( 1) SS BOND : angle 0.60729 ( 2) covalent geometry : bond 0.00535 ( 9851) covalent geometry : angle 0.64161 (13419) Misc. bond : bond 0.00105 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 89 time to evaluate : 1.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8369 (mmm) cc_final: 0.7805 (mmm) REVERT: A 84 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7860 (mm-30) REVERT: A 229 HIS cc_start: 0.6796 (t-90) cc_final: 0.6406 (t-90) REVERT: A 256 VAL cc_start: 0.8952 (t) cc_final: 0.8638 (m) REVERT: A 258 ARG cc_start: 0.7544 (ptp-110) cc_final: 0.7145 (mtt-85) REVERT: A 738 MET cc_start: -0.1243 (mtp) cc_final: -0.1730 (mpp) REVERT: A 807 MET cc_start: 0.2631 (tpt) cc_final: 0.2311 (tpt) REVERT: A 988 ARG cc_start: 0.7619 (mmp-170) cc_final: 0.7310 (mmp80) REVERT: B 87 ARG cc_start: 0.8274 (tpp80) cc_final: 0.7912 (tpp80) REVERT: B 107 LEU cc_start: 0.8337 (OUTLIER) cc_final: 0.8122 (tp) REVERT: C 54 ARG cc_start: 0.6422 (ttm170) cc_final: 0.6047 (ptm160) REVERT: C 57 PHE cc_start: 0.7886 (m-80) cc_final: 0.7632 (m-80) REVERT: C 105 LEU cc_start: 0.9078 (mt) cc_final: 0.8775 (pp) REVERT: C 106 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8181 (mt-10) REVERT: C 136 PHE cc_start: 0.6325 (OUTLIER) cc_final: 0.5638 (m-80) outliers start: 36 outliers final: 19 residues processed: 114 average time/residue: 0.3919 time to fit residues: 61.8035 Evaluate side-chains 107 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 160 CYS Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 356 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 583 ARG Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 151 ASN Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 85 optimal weight: 0.9980 chunk 102 optimal weight: 0.0000 chunk 41 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 116 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 117 optimal weight: 20.0000 chunk 61 optimal weight: 0.0270 chunk 38 optimal weight: 0.9990 chunk 55 optimal weight: 0.6980 chunk 78 optimal weight: 10.0000 overall best weight: 0.4642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** 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 = 0.4540 r_free = 0.4540 target = 0.209994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.134778 restraints weight = 12718.300| |-----------------------------------------------------------------------------| r_work (start): 0.3712 rms_B_bonded: 3.46 r_work: 0.3403 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9853 Z= 0.114 Angle : 0.575 10.157 13421 Z= 0.275 Chirality : 0.040 0.184 1496 Planarity : 0.004 0.059 1762 Dihedral : 4.715 51.301 1334 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.44 % Favored : 95.40 % Rotamer: Outliers : 3.29 % Allowed : 13.14 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 1217 helix: 1.47 (0.24), residues: 461 sheet: -0.24 (0.36), residues: 191 loop : -0.43 (0.28), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 666 HIS 0.005 0.001 HIS A 142 PHE 0.012 0.001 PHE C 63 TYR 0.012 0.001 TYR A1010 ARG 0.004 0.000 ARG A 195 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 432) hydrogen bonds : angle 4.98098 ( 1251) SS BOND : bond 0.00190 ( 1) SS BOND : angle 0.31919 ( 2) covalent geometry : bond 0.00260 ( 9851) covalent geometry : angle 0.57543 (13419) Misc. bond : bond 0.00059 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 102 time to evaluate : 0.965 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.8252 (mmm) cc_final: 0.7789 (mmm) REVERT: A 217 MET cc_start: 0.4562 (mpp) cc_final: 0.4001 (mmt) REVERT: A 256 VAL cc_start: 0.8928 (t) cc_final: 0.8600 (m) REVERT: A 258 ARG cc_start: 0.7536 (ptp-110) cc_final: 0.7121 (mtt-85) REVERT: A 480 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: A 503 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.7877 (tt) REVERT: A 565 SER cc_start: 0.8293 (t) cc_final: 0.7895 (p) REVERT: A 643 MET cc_start: -0.0980 (tpt) cc_final: -0.1306 (ttm) REVERT: A 738 MET cc_start: -0.1369 (mtp) cc_final: -0.1824 (mpp) REVERT: A 807 MET cc_start: 0.2604 (tpt) cc_final: 0.2334 (tpt) REVERT: A 988 ARG cc_start: 0.7543 (mmp-170) cc_final: 0.7250 (mmp80) REVERT: B 87 ARG cc_start: 0.8235 (tpp80) cc_final: 0.7903 (tpp80) REVERT: C 54 ARG cc_start: 0.6364 (ttm170) cc_final: 0.6006 (ptt90) REVERT: C 105 LEU cc_start: 0.9083 (mt) cc_final: 0.8795 (pp) REVERT: C 106 GLU cc_start: 0.8446 (mt-10) cc_final: 0.8153 (mt-10) REVERT: C 136 PHE cc_start: 0.6264 (OUTLIER) cc_final: 0.5560 (m-80) outliers start: 34 outliers final: 17 residues processed: 127 average time/residue: 0.2243 time to fit residues: 39.8608 Evaluate side-chains 110 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 90 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 55 ILE Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 97 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 chunk 107 optimal weight: 0.0370 chunk 28 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 HIS ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.209645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.135523 restraints weight = 12685.000| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 3.79 r_work: 0.3398 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9853 Z= 0.116 Angle : 0.567 8.286 13421 Z= 0.271 Chirality : 0.040 0.198 1496 Planarity : 0.004 0.058 1762 Dihedral : 4.559 49.826 1334 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 2.61 % Allowed : 15.27 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.55 (0.25), residues: 1217 helix: 1.53 (0.24), residues: 462 sheet: -0.20 (0.37), residues: 191 loop : -0.36 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 666 HIS 0.004 0.001 HIS C 47 PHE 0.010 0.001 PHE C 63 TYR 0.018 0.001 TYR C 21 ARG 0.006 0.000 ARG A 204 Details of bonding type rmsd hydrogen bonds : bond 0.03143 ( 432) hydrogen bonds : angle 4.87829 ( 1251) SS BOND : bond 0.00213 ( 1) SS BOND : angle 0.32823 ( 2) covalent geometry : bond 0.00269 ( 9851) covalent geometry : angle 0.56752 (13419) Misc. bond : bond 0.00032 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8212 (mmm) cc_final: 0.7785 (mmm) REVERT: A 256 VAL cc_start: 0.8939 (t) cc_final: 0.8660 (m) REVERT: A 258 ARG cc_start: 0.7534 (ptp-110) cc_final: 0.7130 (mtt-85) REVERT: A 480 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7971 (mp10) REVERT: A 503 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.7930 (tt) REVERT: A 565 SER cc_start: 0.8301 (t) cc_final: 0.7903 (p) REVERT: A 643 MET cc_start: -0.0965 (tpt) cc_final: -0.1292 (ttm) REVERT: A 738 MET cc_start: -0.1384 (mtp) cc_final: -0.1831 (mpp) REVERT: A 807 MET cc_start: 0.2671 (tpt) cc_final: 0.2424 (tpt) REVERT: A 988 ARG cc_start: 0.7543 (mmp-170) cc_final: 0.7264 (mmp80) REVERT: B 87 ARG cc_start: 0.8184 (tpp80) cc_final: 0.7896 (tpp80) REVERT: C 54 ARG cc_start: 0.6346 (ttm170) cc_final: 0.6094 (ptm160) REVERT: C 105 LEU cc_start: 0.9127 (mt) cc_final: 0.8838 (pp) REVERT: C 106 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8036 (mt-10) REVERT: C 136 PHE cc_start: 0.6307 (OUTLIER) cc_final: 0.5600 (m-80) outliers start: 27 outliers final: 17 residues processed: 119 average time/residue: 0.2526 time to fit residues: 42.2364 Evaluate side-chains 107 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 87 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 28 optimal weight: 0.6980 chunk 100 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 33 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 HIS ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.209647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134670 restraints weight = 12624.994| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 4.05 r_work: 0.3363 rms_B_bonded: 4.24 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9853 Z= 0.156 Angle : 0.595 8.869 13421 Z= 0.284 Chirality : 0.040 0.175 1496 Planarity : 0.004 0.058 1762 Dihedral : 4.622 48.768 1334 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.65 % Rotamer: Outliers : 2.61 % Allowed : 15.46 % Favored : 81.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 1217 helix: 1.47 (0.24), residues: 462 sheet: -0.28 (0.36), residues: 191 loop : -0.39 (0.28), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 666 HIS 0.004 0.001 HIS C 47 PHE 0.011 0.001 PHE A 146 TYR 0.013 0.001 TYR C 21 ARG 0.006 0.000 ARG A 942 Details of bonding type rmsd hydrogen bonds : bond 0.03254 ( 432) hydrogen bonds : angle 4.90856 ( 1251) SS BOND : bond 0.00253 ( 1) SS BOND : angle 0.39543 ( 2) covalent geometry : bond 0.00373 ( 9851) covalent geometry : angle 0.59479 (13419) Misc. bond : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 94 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8260 (mmm) cc_final: 0.7794 (mmm) REVERT: A 217 MET cc_start: 0.4768 (mpp) cc_final: 0.4010 (mmt) REVERT: A 256 VAL cc_start: 0.8936 (t) cc_final: 0.8650 (m) REVERT: A 258 ARG cc_start: 0.7558 (ptp-110) cc_final: 0.7153 (mtt-85) REVERT: A 503 LEU cc_start: 0.8446 (OUTLIER) cc_final: 0.7960 (tt) REVERT: A 565 SER cc_start: 0.8326 (t) cc_final: 0.7933 (p) REVERT: A 643 MET cc_start: -0.0887 (tpt) cc_final: -0.1197 (ttm) REVERT: A 738 MET cc_start: -0.1160 (mtp) cc_final: -0.1630 (mpp) REVERT: A 807 MET cc_start: 0.2677 (tpt) cc_final: 0.2407 (tpt) REVERT: A 988 ARG cc_start: 0.7528 (mmp-170) cc_final: 0.7247 (mmp80) REVERT: A 1011 GLU cc_start: 0.7447 (mp0) cc_final: 0.7247 (mp0) REVERT: B 87 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7877 (tpp80) REVERT: C 54 ARG cc_start: 0.6342 (ttm170) cc_final: 0.6131 (ptt90) REVERT: C 105 LEU cc_start: 0.9132 (mt) cc_final: 0.8848 (pp) REVERT: C 106 GLU cc_start: 0.8495 (mt-10) cc_final: 0.8077 (mt-10) REVERT: C 136 PHE cc_start: 0.6312 (OUTLIER) cc_final: 0.5642 (m-80) outliers start: 27 outliers final: 22 residues processed: 116 average time/residue: 0.2355 time to fit residues: 37.9523 Evaluate side-chains 115 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 91 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 76 HIS Chi-restraints excluded: chain C residue 136 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 63 optimal weight: 5.9990 chunk 62 optimal weight: 7.9990 chunk 71 optimal weight: 8.9990 chunk 66 optimal weight: 6.9990 chunk 99 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 81 optimal weight: 9.9990 chunk 52 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 108 optimal weight: 9.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** 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 = 0.4539 r_free = 0.4539 target = 0.209216 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.135439 restraints weight = 12747.949| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 4.13 r_work: 0.3358 rms_B_bonded: 4.35 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9853 Z= 0.151 Angle : 0.596 8.294 13421 Z= 0.284 Chirality : 0.040 0.143 1496 Planarity : 0.004 0.057 1762 Dihedral : 4.618 47.492 1334 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.65 % Rotamer: Outliers : 3.00 % Allowed : 15.46 % Favored : 81.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.39 (0.25), residues: 1217 helix: 1.42 (0.24), residues: 469 sheet: -0.41 (0.36), residues: 191 loop : -0.43 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 666 HIS 0.004 0.001 HIS A 142 PHE 0.010 0.001 PHE C 63 TYR 0.010 0.001 TYR A 388 ARG 0.004 0.000 ARG A 204 Details of bonding type rmsd hydrogen bonds : bond 0.03210 ( 432) hydrogen bonds : angle 4.86095 ( 1251) SS BOND : bond 0.00265 ( 1) SS BOND : angle 0.41306 ( 2) covalent geometry : bond 0.00359 ( 9851) covalent geometry : angle 0.59581 (13419) Misc. bond : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 101 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 256 VAL cc_start: 0.8941 (t) cc_final: 0.8665 (m) REVERT: A 258 ARG cc_start: 0.7592 (ptp-110) cc_final: 0.7210 (mtt-85) REVERT: A 503 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.8013 (tt) REVERT: A 565 SER cc_start: 0.8349 (t) cc_final: 0.7966 (p) REVERT: A 738 MET cc_start: -0.1105 (mtp) cc_final: -0.1566 (mpp) REVERT: A 807 MET cc_start: 0.2658 (tpt) cc_final: 0.2442 (tpt) REVERT: A 988 ARG cc_start: 0.7546 (mmp-170) cc_final: 0.7271 (mmp80) REVERT: A 1011 GLU cc_start: 0.7465 (mp0) cc_final: 0.7166 (mp0) REVERT: B 87 ARG cc_start: 0.8251 (tpp80) cc_final: 0.7926 (tpp80) REVERT: C 105 LEU cc_start: 0.9098 (mt) cc_final: 0.8850 (pp) REVERT: C 106 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8076 (mt-10) outliers start: 31 outliers final: 24 residues processed: 126 average time/residue: 0.2729 time to fit residues: 47.5968 Evaluate side-chains 120 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 1.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 92 optimal weight: 0.9980 chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 20.0000 chunk 17 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 107 optimal weight: 0.0870 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 96 optimal weight: 0.0970 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 682 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** 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 = 0.4550 r_free = 0.4550 target = 0.210443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.133810 restraints weight = 12777.114| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 3.55 r_work: 0.3424 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9853 Z= 0.124 Angle : 0.594 9.351 13421 Z= 0.283 Chirality : 0.040 0.254 1496 Planarity : 0.004 0.057 1762 Dihedral : 4.363 36.064 1332 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.11 % Favored : 95.73 % Rotamer: Outliers : 2.71 % Allowed : 16.23 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 1217 helix: 1.52 (0.24), residues: 468 sheet: -0.39 (0.35), residues: 191 loop : -0.41 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 666 HIS 0.004 0.000 HIS A 142 PHE 0.009 0.001 PHE C 63 TYR 0.021 0.001 TYR C 21 ARG 0.009 0.000 ARG A 204 Details of bonding type rmsd hydrogen bonds : bond 0.03029 ( 432) hydrogen bonds : angle 4.76555 ( 1251) SS BOND : bond 0.00204 ( 1) SS BOND : angle 0.33976 ( 2) covalent geometry : bond 0.00291 ( 9851) covalent geometry : angle 0.59431 (13419) Misc. bond : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8442 (mmm) cc_final: 0.7780 (mmm) REVERT: A 256 VAL cc_start: 0.8937 (t) cc_final: 0.8664 (m) REVERT: A 258 ARG cc_start: 0.7564 (ptp-110) cc_final: 0.7154 (mtt-85) REVERT: A 363 MET cc_start: 0.7202 (tpt) cc_final: 0.6789 (tpt) REVERT: A 503 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7950 (tt) REVERT: A 565 SER cc_start: 0.8280 (t) cc_final: 0.7857 (p) REVERT: A 738 MET cc_start: -0.1155 (mtp) cc_final: -0.1615 (mpp) REVERT: A 807 MET cc_start: 0.2660 (tpt) cc_final: 0.2409 (tpt) REVERT: A 988 ARG cc_start: 0.7489 (mmp-170) cc_final: 0.7225 (mmp80) REVERT: A 1011 GLU cc_start: 0.7385 (mp0) cc_final: 0.7071 (mp0) REVERT: B 87 ARG cc_start: 0.8180 (tpp80) cc_final: 0.7859 (tpp80) REVERT: C 105 LEU cc_start: 0.9090 (mt) cc_final: 0.8844 (pp) REVERT: C 106 GLU cc_start: 0.8458 (mt-10) cc_final: 0.8078 (mt-10) outliers start: 28 outliers final: 23 residues processed: 125 average time/residue: 0.2458 time to fit residues: 43.5553 Evaluate side-chains 122 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 98 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 519 THR Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 76 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 16 optimal weight: 8.9990 chunk 110 optimal weight: 0.0270 chunk 118 optimal weight: 3.9990 chunk 112 optimal weight: 0.9980 chunk 108 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 81 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.6042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 HIS A 610 HIS ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 682 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.205516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.128564 restraints weight = 12912.849| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 3.47 r_work: 0.3357 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 9853 Z= 0.221 Angle : 0.663 10.230 13421 Z= 0.319 Chirality : 0.043 0.214 1496 Planarity : 0.004 0.054 1762 Dihedral : 4.709 38.856 1332 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.01 % Favored : 94.82 % Rotamer: Outliers : 3.09 % Allowed : 16.33 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.14 (0.24), residues: 1217 helix: 1.22 (0.24), residues: 469 sheet: -0.55 (0.36), residues: 184 loop : -0.58 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 666 HIS 0.004 0.001 HIS A 554 PHE 0.012 0.001 PHE A 146 TYR 0.020 0.002 TYR C 21 ARG 0.007 0.001 ARG A 204 Details of bonding type rmsd hydrogen bonds : bond 0.03586 ( 432) hydrogen bonds : angle 5.00164 ( 1251) SS BOND : bond 0.00311 ( 1) SS BOND : angle 0.51843 ( 2) covalent geometry : bond 0.00529 ( 9851) covalent geometry : angle 0.66305 (13419) Misc. bond : bond 0.00068 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.980 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8475 (mmm) cc_final: 0.7811 (mmm) REVERT: A 256 VAL cc_start: 0.8943 (t) cc_final: 0.8658 (m) REVERT: A 258 ARG cc_start: 0.7595 (ptp-110) cc_final: 0.7174 (mtt-85) REVERT: A 490 ARG cc_start: 0.8730 (mtp85) cc_final: 0.8249 (mtp85) REVERT: A 503 LEU cc_start: 0.8475 (OUTLIER) cc_final: 0.8023 (tt) REVERT: A 565 SER cc_start: 0.8388 (t) cc_final: 0.7980 (p) REVERT: A 738 MET cc_start: -0.1140 (mtp) cc_final: -0.1599 (mpp) REVERT: A 807 MET cc_start: 0.2686 (tpt) cc_final: 0.2403 (tpt) REVERT: A 988 ARG cc_start: 0.7518 (mmp-170) cc_final: 0.7228 (mmp80) REVERT: A 1011 GLU cc_start: 0.7462 (mp0) cc_final: 0.7123 (mp0) REVERT: C 89 ILE cc_start: 0.8104 (mm) cc_final: 0.7862 (mp) REVERT: C 105 LEU cc_start: 0.9071 (mt) cc_final: 0.8832 (pp) REVERT: C 106 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8061 (mt-10) outliers start: 32 outliers final: 23 residues processed: 123 average time/residue: 0.2189 time to fit residues: 38.3488 Evaluate side-chains 118 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 94 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 864 LEU Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 76 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 90 optimal weight: 0.9980 chunk 53 optimal weight: 0.1980 chunk 93 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 62 optimal weight: 6.9990 chunk 9 optimal weight: 0.6980 chunk 117 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 554 HIS ** A 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.210638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134372 restraints weight = 12638.854| |-----------------------------------------------------------------------------| r_work (start): 0.3674 rms_B_bonded: 3.28 r_work: 0.3430 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9853 Z= 0.133 Angle : 0.627 9.744 13421 Z= 0.296 Chirality : 0.041 0.238 1496 Planarity : 0.004 0.055 1762 Dihedral : 4.486 35.926 1332 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 2.32 % Allowed : 16.81 % Favored : 80.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.24), residues: 1217 helix: 1.42 (0.24), residues: 467 sheet: -0.53 (0.36), residues: 185 loop : -0.48 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 666 HIS 0.007 0.001 HIS C 76 PHE 0.009 0.001 PHE C 63 TYR 0.019 0.001 TYR C 21 ARG 0.005 0.000 ARG A 204 Details of bonding type rmsd hydrogen bonds : bond 0.03141 ( 432) hydrogen bonds : angle 4.79931 ( 1251) SS BOND : bond 0.00245 ( 1) SS BOND : angle 0.31256 ( 2) covalent geometry : bond 0.00311 ( 9851) covalent geometry : angle 0.62724 (13419) Misc. bond : bond 0.00031 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2434 Ramachandran restraints generated. 1217 Oldfield, 0 Emsley, 1217 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8439 (mmm) cc_final: 0.7838 (mmm) REVERT: A 256 VAL cc_start: 0.8939 (t) cc_final: 0.8678 (m) REVERT: A 258 ARG cc_start: 0.7533 (ptp-110) cc_final: 0.7137 (mtt-85) REVERT: A 363 MET cc_start: 0.7316 (tpt) cc_final: 0.6908 (tpt) REVERT: A 490 ARG cc_start: 0.8736 (mtp85) cc_final: 0.8221 (mtp85) REVERT: A 503 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.7959 (tt) REVERT: A 565 SER cc_start: 0.8276 (t) cc_final: 0.7864 (p) REVERT: A 738 MET cc_start: -0.1126 (mtp) cc_final: -0.1597 (mpp) REVERT: A 807 MET cc_start: 0.2550 (tpt) cc_final: 0.2326 (tpt) REVERT: A 988 ARG cc_start: 0.7462 (mmp-170) cc_final: 0.7202 (mmp80) REVERT: A 1011 GLU cc_start: 0.7422 (mp0) cc_final: 0.7031 (mp0) REVERT: B 87 ARG cc_start: 0.8247 (tpp80) cc_final: 0.7917 (tpp80) REVERT: C 89 ILE cc_start: 0.8213 (mm) cc_final: 0.7957 (mp) REVERT: C 105 LEU cc_start: 0.9054 (mt) cc_final: 0.8833 (pp) REVERT: C 106 GLU cc_start: 0.8455 (mt-10) cc_final: 0.8063 (mt-10) outliers start: 24 outliers final: 21 residues processed: 120 average time/residue: 0.2300 time to fit residues: 39.1395 Evaluate side-chains 119 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 194 LEU Chi-restraints excluded: chain A residue 262 VAL Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 361 VAL Chi-restraints excluded: chain A residue 364 LEU Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 593 ASP Chi-restraints excluded: chain A residue 598 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 818 VAL Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 943 VAL Chi-restraints excluded: chain A residue 958 TRP Chi-restraints excluded: chain A residue 972 THR Chi-restraints excluded: chain B residue 82 LEU Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 LEU Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain C residue 76 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 5 optimal weight: 1.9990 chunk 80 optimal weight: 7.9990 chunk 40 optimal weight: 0.9980 chunk 107 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 90 optimal weight: 0.9980 chunk 13 optimal weight: 0.1980 chunk 27 optimal weight: 0.8980 chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.9990 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 634 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 102 GLN ** 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 = 0.4561 r_free = 0.4561 target = 0.212189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.138950 restraints weight = 12717.876| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 3.93 r_work: 0.3383 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9853 Z= 0.143 Angle : 0.616 9.637 13421 Z= 0.290 Chirality : 0.041 0.234 1496 Planarity : 0.004 0.053 1762 Dihedral : 4.430 35.430 1332 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.52 % Favored : 95.32 % Rotamer: Outliers : 2.13 % Allowed : 17.10 % Favored : 80.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.30 % 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: 0.31 (0.24), residues: 1217 helix: 1.41 (0.24), residues: 468 sheet: -0.53 (0.36), residues: 185 loop : -0.49 (0.27), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 666 HIS 0.004 0.001 HIS C 47 PHE 0.010 0.001 PHE C 63 TYR 0.018 0.001 TYR C 21 ARG 0.005 0.000 ARG A 204 Details of bonding type rmsd hydrogen bonds : bond 0.03126 ( 432) hydrogen bonds : angle 4.74452 ( 1251) SS BOND : bond 0.00240 ( 1) SS BOND : angle 0.28758 ( 2) covalent geometry : bond 0.00337 ( 9851) covalent geometry : angle 0.61584 (13419) Misc. bond : bond 0.00038 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7439.09 seconds wall clock time: 134 minutes 8.51 seconds (8048.51 seconds total)