Starting phenix.real_space_refine on Fri Feb 14 05:16:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8seb_40409/02_2025/8seb_40409.cif Found real_map, /net/cci-nas-00/data/ceres_data/8seb_40409/02_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_40409/02_2025/8seb_40409.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8seb_40409/02_2025/8seb_40409.map" model { file = "/net/cci-nas-00/data/ceres_data/8seb_40409/02_2025/8seb_40409.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8seb_40409/02_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-5592/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 Classifications: {'RNA': 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: 2.65 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: 1.34 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: 3.65 Time building geometry restraints manager: 3.05 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 1.415 1.621 -0.206 1.50e-02 4.44e+03 1.88e+02 bond pdb=" C1' AMP B 201 " pdb=" C2' AMP B 201 " ideal model delta sigma weight residual 1.526 1.363 0.163 1.50e-02 4.44e+03 1.18e+02 bond pdb=" C4' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 1.454 1.292 0.162 1.50e-02 4.44e+03 1.17e+02 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=" 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 - 2.96: 13359 2.96 - 5.93: 51 5.93 - 8.89: 5 8.89 - 11.85: 1 11.85 - 14.81: 3 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 114.00 127.40 -13.40 1.50e+00 4.44e-01 7.99e+01 angle pdb=" N9 AMP B 201 " pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " ideal model delta sigma weight residual 108.20 96.21 11.99 1.50e+00 4.44e-01 6.39e+01 angle pdb=" C1' AMP B 201 " pdb=" O4' AMP B 201 " pdb=" C4' AMP B 201 " ideal model delta sigma weight residual 109.70 101.81 7.89 1.00e+00 1.00e+00 6.22e+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=" C3' AMP B 201 " pdb=" C4' AMP B 201 " pdb=" C5' AMP B 201 " ideal model delta sigma weight residual 115.20 109.40 5.80 1.50e+00 4.44e-01 1.50e+01 ... (remaining 13414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.88: 5800 29.88 - 59.77: 128 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=" C1' AMP B 201 " pdb=" C4' AMP B 201 " pdb=" O4' AMP B 201 " pdb=" C5' AMP B 201 " ideal model delta sinusoidal sigma weight residual -123.00 -156.55 33.55 1 8.00e+00 1.56e-02 2.50e+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 ... (remaining 5936 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 855 0.025 - 0.050: 407 0.050 - 0.074: 123 0.074 - 0.099: 77 0.099 - 0.124: 34 Chirality restraints: 1496 Sorted by residual: 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=" C2' AMP B 201 " pdb=" C1' AMP B 201 " pdb=" C3' AMP B 201 " pdb=" O2' AMP B 201 " both_signs ideal model delta sigma weight residual False -2.52 -2.40 -0.12 2.00e-01 2.50e+01 3.75e-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: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.690 Find NCS groups from input model: 0.110 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:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.950 ------------------------------------------------------------------------------- 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 : 0.005 0.206 9851 Z= 0.320 Angle : 0.583 14.813 13419 Z= 0.305 Chirality : 0.037 0.124 1496 Planarity : 0.004 0.053 1762 Dihedral : 12.083 149.425 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 *********************** 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 : 1.064 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: 0.2439 time to fit residues: 58.7717 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 : 1.013 ------------------------------------------------------------------------------- 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 157 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4558 r_free = 0.4558 target = 0.210989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.139486 restraints weight = 12613.169| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 3.77 r_work: 0.3373 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.1435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9851 Z= 0.262 Angle : 0.615 7.060 13419 Z= 0.302 Chirality : 0.041 0.191 1496 Planarity : 0.005 0.057 1762 Dihedral : 6.424 124.798 1337 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.19 % Favored : 95.65 % Rotamer: Outliers : 2.90 % Allowed : 11.40 % Favored : 85.70 % 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: 0.54 (0.25), residues: 1217 helix: 1.51 (0.24), residues: 457 sheet: 0.04 (0.38), residues: 184 loop : -0.41 (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 0.012 0.001 ARG A 204 *********************** 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 139 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8377 (mmm) cc_final: 0.7809 (mmm) REVERT: A 84 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7758 (mm-30) REVERT: A 229 HIS cc_start: 0.6732 (t-90) cc_final: 0.6398 (t-90) REVERT: A 256 VAL cc_start: 0.8835 (t) cc_final: 0.8425 (m) REVERT: A 258 ARG cc_start: 0.7493 (ptp-110) cc_final: 0.7089 (mtt-85) REVERT: A 468 ASP cc_start: 0.8005 (t0) cc_final: 0.7737 (t0) REVERT: A 470 ASP cc_start: 0.8245 (t0) cc_final: 0.7853 (t0) REVERT: A 565 SER cc_start: 0.8357 (t) cc_final: 0.7950 (p) REVERT: A 738 MET cc_start: -0.1272 (mtp) cc_final: -0.1769 (mpp) REVERT: A 807 MET cc_start: 0.2591 (tpt) cc_final: 0.2376 (tpt) REVERT: A 988 ARG cc_start: 0.7614 (mmp-170) cc_final: 0.7306 (mmp80) REVERT: B 87 ARG cc_start: 0.8228 (tpp80) cc_final: 0.7893 (tpp80) REVERT: C 26 SER cc_start: 0.7986 (p) cc_final: 0.7591 (t) REVERT: C 54 ARG cc_start: 0.6492 (ttm170) cc_final: 0.5967 (ptm160) REVERT: C 105 LEU cc_start: 0.9028 (mt) cc_final: 0.8706 (pp) REVERT: C 106 GLU cc_start: 0.8474 (mt-10) cc_final: 0.8227 (mt-10) REVERT: C 136 PHE cc_start: 0.6426 (OUTLIER) cc_final: 0.5755 (m-80) outliers start: 30 outliers final: 19 residues processed: 131 average time/residue: 0.2668 time to fit residues: 47.6110 Evaluate side-chains 112 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 1.193 ------------------------------------------------------------------------------- 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 638 THR Chi-restraints excluded: chain A residue 872 VAL Chi-restraints excluded: chain A residue 893 LEU Chi-restraints excluded: chain A residue 941 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: 8.9990 chunk 66 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 120 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 49 optimal weight: 0.0570 chunk 13 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 HIS A 554 HIS ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 109 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.208674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.134728 restraints weight = 12826.842| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 3.43 r_work: 0.3334 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9851 Z= 0.394 Angle : 0.661 6.882 13419 Z= 0.325 Chirality : 0.043 0.163 1496 Planarity : 0.005 0.057 1762 Dihedral : 6.334 87.606 1337 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.77 % Favored : 95.07 % Rotamer: Outliers : 3.38 % Allowed : 12.37 % Favored : 84.25 % 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: 0.18 (0.24), residues: 1217 helix: 1.18 (0.24), residues: 461 sheet: -0.25 (0.36), residues: 190 loop : -0.58 (0.27), residues: 566 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 0.014 0.002 PHE A 881 TYR 0.012 0.002 TYR A 388 ARG 0.008 0.001 ARG A 204 *********************** 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 130 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8433 (mmm) cc_final: 0.7829 (mmm) REVERT: A 84 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7859 (mm-30) REVERT: A 229 HIS cc_start: 0.6699 (t-90) cc_final: 0.6294 (t-90) REVERT: A 256 VAL cc_start: 0.8943 (t) cc_final: 0.8623 (m) REVERT: A 258 ARG cc_start: 0.7575 (ptp-110) cc_final: 0.7161 (mtt-85) REVERT: A 468 ASP cc_start: 0.8006 (t0) cc_final: 0.7765 (t70) REVERT: A 470 ASP cc_start: 0.8269 (t0) cc_final: 0.7923 (t0) REVERT: A 738 MET cc_start: -0.1219 (mtp) cc_final: -0.1694 (mpp) REVERT: A 807 MET cc_start: 0.2626 (tpt) cc_final: 0.2356 (tpt) REVERT: A 988 ARG cc_start: 0.7660 (mmp-170) cc_final: 0.7344 (mmp80) REVERT: B 87 ARG cc_start: 0.8305 (tpp80) cc_final: 0.7934 (tpp80) REVERT: B 107 LEU cc_start: 0.8362 (OUTLIER) cc_final: 0.8087 (tp) REVERT: C 54 ARG cc_start: 0.6395 (ttm170) cc_final: 0.6036 (ptm160) REVERT: C 57 PHE cc_start: 0.7945 (m-80) cc_final: 0.7730 (m-80) REVERT: C 105 LEU cc_start: 0.9075 (mt) cc_final: 0.8769 (pp) REVERT: C 106 GLU cc_start: 0.8478 (mt-10) cc_final: 0.8163 (mt-10) REVERT: C 136 PHE cc_start: 0.6290 (OUTLIER) cc_final: 0.5610 (m-80) outliers start: 35 outliers final: 21 residues processed: 118 average time/residue: 0.2579 time to fit residues: 41.9170 Evaluate side-chains 111 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.061 ------------------------------------------------------------------------------- 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 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 480 GLN 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 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 107 LEU Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 151 ASN 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: 0.5980 chunk 102 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 116 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 chunk 117 optimal weight: 0.1980 chunk 61 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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** ** B 109 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 = 0.4523 r_free = 0.4523 target = 0.209060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135692 restraints weight = 12621.716| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 3.98 r_work: 0.3384 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9851 Z= 0.192 Angle : 0.576 8.425 13419 Z= 0.278 Chirality : 0.040 0.182 1496 Planarity : 0.004 0.058 1762 Dihedral : 5.574 60.176 1334 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.35 % Favored : 95.48 % Rotamer: Outliers : 3.29 % Allowed : 13.33 % Favored : 83.38 % 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: 0.35 (0.25), residues: 1217 helix: 1.41 (0.24), residues: 461 sheet: -0.29 (0.36), residues: 191 loop : -0.50 (0.27), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 666 HIS 0.004 0.001 HIS A 691 PHE 0.012 0.001 PHE C 63 TYR 0.012 0.001 TYR A1010 ARG 0.006 0.000 ARG A 942 *********************** 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 133 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.8283 (mmm) cc_final: 0.7802 (mmm) REVERT: A 217 MET cc_start: 0.4678 (mpp) cc_final: 0.4078 (mmt) REVERT: A 256 VAL cc_start: 0.8937 (t) cc_final: 0.8618 (m) REVERT: A 258 ARG cc_start: 0.7544 (ptp-110) cc_final: 0.7116 (mtt-85) REVERT: A 410 LEU cc_start: 0.8379 (OUTLIER) cc_final: 0.8173 (mt) REVERT: A 470 ASP cc_start: 0.8233 (t0) cc_final: 0.7922 (t0) REVERT: A 480 GLN cc_start: 0.8377 (OUTLIER) cc_final: 0.8004 (mp10) REVERT: A 503 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.7918 (tt) REVERT: A 565 SER cc_start: 0.8304 (t) cc_final: 0.7906 (p) REVERT: A 738 MET cc_start: -0.1359 (mtp) cc_final: -0.1806 (mpp) REVERT: A 807 MET cc_start: 0.2608 (tpt) cc_final: 0.2346 (tpt) REVERT: A 867 GLU cc_start: 0.7870 (mm-30) cc_final: 0.7645 (mm-30) REVERT: A 988 ARG cc_start: 0.7566 (mmp-170) cc_final: 0.7280 (mmp80) REVERT: B 87 ARG cc_start: 0.8224 (tpp80) cc_final: 0.7922 (tpp80) REVERT: C 54 ARG cc_start: 0.6362 (ttm170) cc_final: 0.6011 (ptt90) REVERT: C 57 PHE cc_start: 0.7891 (m-80) cc_final: 0.7566 (m-80) REVERT: C 105 LEU cc_start: 0.9088 (mt) cc_final: 0.8828 (pp) REVERT: C 106 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8185 (mt-10) REVERT: C 136 PHE cc_start: 0.6258 (OUTLIER) cc_final: 0.5568 (m-80) outliers start: 34 outliers final: 19 residues processed: 124 average time/residue: 0.2367 time to fit residues: 41.0009 Evaluate side-chains 109 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 410 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 941 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 B residue 125 THR Chi-restraints excluded: chain B residue 135 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: 0.9990 chunk 16 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 107 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7520 ------------------------------------------------------------------------------- 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 = 0.4521 r_free = 0.4521 target = 0.208799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.131793 restraints weight = 12616.661| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.66 r_work: 0.3387 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9851 Z= 0.214 Angle : 0.579 8.279 13419 Z= 0.278 Chirality : 0.040 0.260 1496 Planarity : 0.004 0.058 1762 Dihedral : 5.192 49.544 1334 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.27 % Favored : 95.56 % Rotamer: Outliers : 3.38 % Allowed : 14.20 % Favored : 82.42 % 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: 0.38 (0.25), residues: 1217 helix: 1.43 (0.24), residues: 461 sheet: -0.30 (0.36), residues: 191 loop : -0.47 (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 C 47 PHE 0.011 0.001 PHE C 63 TYR 0.018 0.001 TYR C 21 ARG 0.006 0.000 ARG A 204 *********************** 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 125 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 90 time to evaluate : 1.026 Fit side-chains revert: symmetry clash REVERT: A 54 MET cc_start: 0.8257 (mmm) cc_final: 0.7811 (mmm) REVERT: A 256 VAL cc_start: 0.8906 (t) cc_final: 0.8619 (m) REVERT: A 258 ARG cc_start: 0.7558 (ptp-110) cc_final: 0.7145 (mtt-85) REVERT: A 480 GLN cc_start: 0.8367 (OUTLIER) cc_final: 0.7941 (mp10) REVERT: A 503 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7921 (tt) REVERT: A 565 SER cc_start: 0.8342 (t) cc_final: 0.7944 (p) REVERT: A 738 MET cc_start: -0.1273 (mtp) cc_final: -0.1729 (mpp) REVERT: A 807 MET cc_start: 0.2610 (tpt) cc_final: 0.2337 (tpt) REVERT: A 988 ARG cc_start: 0.7539 (mmp-170) cc_final: 0.7250 (mmp80) REVERT: B 87 ARG cc_start: 0.8223 (tpp80) cc_final: 0.7926 (tpp80) REVERT: C 54 ARG cc_start: 0.6390 (ttm170) cc_final: 0.6110 (ptm160) REVERT: C 57 PHE cc_start: 0.7909 (m-80) cc_final: 0.7662 (m-80) REVERT: C 105 LEU cc_start: 0.9140 (mt) cc_final: 0.8836 (pp) REVERT: C 106 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8101 (mt-10) REVERT: C 136 PHE cc_start: 0.6279 (OUTLIER) cc_final: 0.5539 (m-80) outliers start: 35 outliers final: 18 residues processed: 116 average time/residue: 0.2250 time to fit residues: 36.9977 Evaluate side-chains 104 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 575 MET 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 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 B residue 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 125 THR 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: 0.8980 chunk 100 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 65 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 108 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 83 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 554 HIS A 610 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.206375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.128868 restraints weight = 12692.557| |-----------------------------------------------------------------------------| r_work (start): 0.3618 rms_B_bonded: 3.50 r_work: 0.3366 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 9851 Z= 0.307 Angle : 0.620 8.109 13419 Z= 0.299 Chirality : 0.041 0.164 1496 Planarity : 0.004 0.056 1762 Dihedral : 5.191 48.505 1334 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.60 % Favored : 95.23 % Rotamer: Outliers : 2.90 % Allowed : 15.27 % Favored : 81.84 % 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: 0.22 (0.24), residues: 1217 helix: 1.26 (0.24), residues: 469 sheet: -0.46 (0.36), residues: 191 loop : -0.52 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 666 HIS 0.004 0.001 HIS C 47 PHE 0.012 0.001 PHE A 146 TYR 0.012 0.001 TYR C 21 ARG 0.005 0.000 ARG A 204 *********************** 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 123 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 217 MET cc_start: 0.4897 (mpp) cc_final: 0.4105 (mmt) REVERT: A 256 VAL cc_start: 0.8954 (t) cc_final: 0.8686 (m) REVERT: A 258 ARG cc_start: 0.7599 (ptp-110) cc_final: 0.7195 (mtt-85) REVERT: A 503 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8048 (tt) REVERT: A 565 SER cc_start: 0.8367 (t) cc_final: 0.7976 (p) REVERT: A 738 MET cc_start: -0.1197 (mtp) cc_final: -0.1647 (mpp) REVERT: A 807 MET cc_start: 0.2613 (tpt) cc_final: 0.2350 (tpt) REVERT: A 988 ARG cc_start: 0.7548 (mmp-170) cc_final: 0.7252 (mmp80) REVERT: A 1011 GLU cc_start: 0.7541 (mp0) cc_final: 0.7296 (mp0) REVERT: B 87 ARG cc_start: 0.8297 (tpp80) cc_final: 0.7983 (tpp80) REVERT: C 54 ARG cc_start: 0.6433 (ttm170) cc_final: 0.6159 (ptm160) REVERT: C 57 PHE cc_start: 0.8028 (m-80) cc_final: 0.7790 (m-80) REVERT: C 105 LEU cc_start: 0.9137 (mt) cc_final: 0.8883 (pp) REVERT: C 106 GLU cc_start: 0.8472 (mt-10) cc_final: 0.8060 (mt-10) REVERT: C 136 PHE cc_start: 0.6273 (OUTLIER) cc_final: 0.5600 (m-80) outliers start: 30 outliers final: 22 residues processed: 119 average time/residue: 0.2242 time to fit residues: 38.1319 Evaluate side-chains 112 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 88 time to evaluate : 1.109 ------------------------------------------------------------------------------- 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 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 364 LEU Chi-restraints excluded: chain A residue 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 575 MET 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 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 88 ASN Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 124 LEU Chi-restraints excluded: chain B residue 125 THR Chi-restraints excluded: chain B residue 151 ASN 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: 7.9990 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 20.0000 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 1.9990 chunk 101 optimal weight: 0.6980 chunk 81 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 85 optimal weight: 0.5980 chunk 108 optimal weight: 10.0000 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 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** B 151 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.208243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.137254 restraints weight = 12810.507| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 3.66 r_work: 0.3409 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9851 Z= 0.205 Angle : 0.590 9.088 13419 Z= 0.283 Chirality : 0.040 0.165 1496 Planarity : 0.004 0.057 1762 Dihedral : 5.041 47.495 1334 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.94 % Favored : 95.89 % Rotamer: Outliers : 3.38 % Allowed : 14.98 % Favored : 81.64 % 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: 1.39 (0.24), residues: 469 sheet: -0.43 (0.36), residues: 191 loop : -0.51 (0.27), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 666 HIS 0.004 0.000 HIS C 47 PHE 0.009 0.001 PHE C 63 TYR 0.011 0.001 TYR A1010 ARG 0.004 0.000 ARG A 204 *********************** 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: 35 poor density : 97 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8463 (mmm) cc_final: 0.7807 (mmm) REVERT: A 256 VAL cc_start: 0.8954 (t) cc_final: 0.8707 (m) REVERT: A 258 ARG cc_start: 0.7556 (ptp-110) cc_final: 0.7177 (mtt-85) REVERT: A 480 GLN cc_start: 0.8385 (OUTLIER) cc_final: 0.8012 (mp10) REVERT: A 503 LEU cc_start: 0.8471 (OUTLIER) cc_final: 0.7999 (tt) REVERT: A 565 SER cc_start: 0.8322 (t) cc_final: 0.7924 (p) REVERT: A 738 MET cc_start: -0.1179 (mtp) cc_final: -0.1626 (mpp) REVERT: A 807 MET cc_start: 0.2609 (tpt) cc_final: 0.2370 (tpt) REVERT: A 988 ARG cc_start: 0.7502 (mmp-170) cc_final: 0.7231 (mmp80) REVERT: A 1011 GLU cc_start: 0.7478 (mp0) cc_final: 0.7140 (mp0) REVERT: B 87 ARG cc_start: 0.8231 (tpp80) cc_final: 0.7911 (tpp80) REVERT: C 105 LEU cc_start: 0.9130 (mt) cc_final: 0.8875 (pp) REVERT: C 106 GLU cc_start: 0.8443 (mt-10) cc_final: 0.8026 (mt-10) outliers start: 35 outliers final: 21 residues processed: 125 average time/residue: 0.2408 time to fit residues: 41.7913 Evaluate side-chains 115 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 92 time to evaluate : 1.008 ------------------------------------------------------------------------------- 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 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 575 MET 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 837 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 993 GLU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 92 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 17 optimal weight: 0.0770 chunk 72 optimal weight: 20.0000 chunk 107 optimal weight: 0.5980 chunk 49 optimal weight: 0.0770 chunk 0 optimal weight: 4.9990 chunk 3 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 96 optimal weight: 4.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- 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 = 0.4528 r_free = 0.4528 target = 0.209773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137613 restraints weight = 12908.461| |-----------------------------------------------------------------------------| r_work (start): 0.3754 rms_B_bonded: 3.78 r_work: 0.3415 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9851 Z= 0.172 Angle : 0.597 9.895 13419 Z= 0.282 Chirality : 0.040 0.244 1496 Planarity : 0.004 0.057 1762 Dihedral : 4.688 45.099 1332 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.35 % Favored : 95.48 % Rotamer: Outliers : 2.61 % Allowed : 16.14 % Favored : 81.26 % 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: 1.53 (0.24), residues: 468 sheet: -0.37 (0.36), residues: 191 loop : -0.44 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 666 HIS 0.003 0.000 HIS A 610 PHE 0.009 0.001 PHE C 63 TYR 0.017 0.001 TYR A 596 ARG 0.006 0.000 ARG A 204 *********************** 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 129 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8369 (mmm) cc_final: 0.7808 (mmm) REVERT: A 217 MET cc_start: 0.4293 (mpp) cc_final: 0.3620 (mmt) REVERT: A 256 VAL cc_start: 0.8960 (t) cc_final: 0.8693 (m) REVERT: A 258 ARG cc_start: 0.7489 (ptp-110) cc_final: 0.7066 (mtt-85) REVERT: A 363 MET cc_start: 0.7229 (tpt) cc_final: 0.6819 (tpt) REVERT: A 480 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8021 (mp10) REVERT: A 503 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.7939 (tt) REVERT: A 565 SER cc_start: 0.8278 (t) cc_final: 0.7865 (p) REVERT: A 738 MET cc_start: -0.1062 (mtp) cc_final: -0.1533 (mpp) REVERT: A 807 MET cc_start: 0.2642 (tpt) cc_final: 0.2359 (tpt) REVERT: A 988 ARG cc_start: 0.7488 (mmp-170) cc_final: 0.7232 (mmp80) REVERT: A 1011 GLU cc_start: 0.7438 (mp0) cc_final: 0.7109 (mp0) REVERT: B 87 ARG cc_start: 0.8192 (tpp80) cc_final: 0.7849 (tpp80) REVERT: C 105 LEU cc_start: 0.9143 (mt) cc_final: 0.8862 (pp) REVERT: C 106 GLU cc_start: 0.8425 (mt-10) cc_final: 0.8013 (mt-10) outliers start: 27 outliers final: 20 residues processed: 123 average time/residue: 0.2299 time to fit residues: 40.4269 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 : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 575 MET 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 837 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 993 GLU 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: 10.0000 chunk 110 optimal weight: 0.0870 chunk 118 optimal weight: 6.9990 chunk 112 optimal weight: 0.7980 chunk 108 optimal weight: 8.9990 chunk 20 optimal weight: 0.7980 chunk 24 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 ** B 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 151 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.207155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.129442 restraints weight = 12868.209| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 3.49 r_work: 0.3394 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 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 : 0.004 0.040 9851 Z= 0.276 Angle : 0.626 9.382 13419 Z= 0.298 Chirality : 0.042 0.221 1496 Planarity : 0.004 0.055 1762 Dihedral : 4.843 46.419 1332 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.77 % Favored : 95.07 % Rotamer: Outliers : 2.42 % Allowed : 16.23 % Favored : 81.35 % 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: 0.30 (0.24), residues: 1217 helix: 1.34 (0.24), residues: 468 sheet: -0.45 (0.36), residues: 191 loop : -0.47 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 666 HIS 0.005 0.001 HIS C 76 PHE 0.012 0.001 PHE A 146 TYR 0.012 0.001 TYR A 388 ARG 0.006 0.000 ARG A 204 *********************** 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 123 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 98 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8418 (mmm) cc_final: 0.7816 (mmm) REVERT: A 256 VAL cc_start: 0.8959 (t) cc_final: 0.8687 (m) REVERT: A 258 ARG cc_start: 0.7602 (ptp-110) cc_final: 0.7195 (mtt-85) REVERT: A 503 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.7988 (tt) REVERT: A 565 SER cc_start: 0.8360 (t) cc_final: 0.7979 (p) REVERT: A 738 MET cc_start: -0.1143 (mtp) cc_final: -0.1609 (mpp) REVERT: A 807 MET cc_start: 0.2628 (tpt) cc_final: 0.2342 (tpt) REVERT: A 988 ARG cc_start: 0.7549 (mmp-170) cc_final: 0.7277 (mmp80) REVERT: A 1011 GLU cc_start: 0.7459 (mp0) cc_final: 0.7076 (mp0) REVERT: B 87 ARG cc_start: 0.8261 (tpp80) cc_final: 0.7928 (tpp80) REVERT: B 134 GLN cc_start: 0.8602 (tp-100) cc_final: 0.8310 (tp-100) REVERT: C 89 ILE cc_start: 0.8208 (mm) cc_final: 0.7976 (mp) REVERT: C 105 LEU cc_start: 0.9098 (mt) cc_final: 0.8852 (pp) REVERT: C 106 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8017 (mt-10) outliers start: 25 outliers final: 22 residues processed: 117 average time/residue: 0.2402 time to fit residues: 39.3613 Evaluate side-chains 118 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 575 MET 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 837 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 A residue 993 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 90 optimal weight: 0.5980 chunk 53 optimal weight: 0.2980 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 17 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 chunk 9 optimal weight: 0.4980 chunk 117 optimal weight: 0.2980 chunk 31 optimal weight: 0.1980 chunk 95 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 overall best weight: 0.3780 ------------------------------------------------------------------------------- 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** B 134 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.209723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.131800 restraints weight = 12771.854| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 3.40 r_work: 0.3441 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9851 Z= 0.172 Angle : 0.603 9.966 13419 Z= 0.283 Chirality : 0.040 0.232 1496 Planarity : 0.004 0.055 1762 Dihedral : 4.661 45.802 1332 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.03 % Favored : 95.81 % Rotamer: Outliers : 2.13 % Allowed : 16.52 % Favored : 81.35 % 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: 1.52 (0.24), residues: 468 sheet: -0.42 (0.36), residues: 191 loop : -0.42 (0.28), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 666 HIS 0.004 0.001 HIS C 47 PHE 0.008 0.001 PHE C 63 TYR 0.010 0.001 TYR A1010 ARG 0.011 0.000 ARG A 942 ********************** 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 119 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 MET cc_start: 0.8391 (mmm) cc_final: 0.7832 (mmm) REVERT: A 217 MET cc_start: 0.4299 (mpp) cc_final: 0.3629 (mmt) REVERT: A 256 VAL cc_start: 0.8930 (t) cc_final: 0.8678 (m) REVERT: A 258 ARG cc_start: 0.7485 (ptp-110) cc_final: 0.7074 (mtt-85) REVERT: A 363 MET cc_start: 0.7275 (tpt) cc_final: 0.6869 (tpt) REVERT: A 480 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.7983 (mp10) REVERT: A 503 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7926 (tt) REVERT: A 565 SER cc_start: 0.8272 (t) cc_final: 0.7859 (p) REVERT: A 738 MET cc_start: -0.1059 (mtp) cc_final: -0.1534 (mpp) REVERT: A 807 MET cc_start: 0.2611 (tpt) cc_final: 0.2362 (tpt) REVERT: A 988 ARG cc_start: 0.7484 (mmp-170) cc_final: 0.7236 (mmp80) REVERT: A 1011 GLU cc_start: 0.7407 (mp0) cc_final: 0.7046 (mp0) REVERT: B 87 ARG cc_start: 0.8181 (tpp80) cc_final: 0.7808 (tpp80) REVERT: C 89 ILE cc_start: 0.8276 (mm) cc_final: 0.8037 (mp) REVERT: C 105 LEU cc_start: 0.9096 (mt) cc_final: 0.8862 (pp) REVERT: C 106 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8036 (mt-10) outliers start: 22 outliers final: 19 residues processed: 114 average time/residue: 0.2342 time to fit residues: 37.9021 Evaluate side-chains 118 residues out of total 1035 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 97 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 480 GLN Chi-restraints excluded: chain A residue 503 LEU Chi-restraints excluded: chain A residue 575 MET 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 837 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 993 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 5 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 107 optimal weight: 0.0470 chunk 79 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 13 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 94 optimal weight: 0.9980 chunk 91 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.4532 r_free = 0.4532 target = 0.210926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.134831 restraints weight = 12753.382| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 3.68 r_work: 0.3419 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9851 Z= 0.194 Angle : 0.607 9.737 13419 Z= 0.284 Chirality : 0.040 0.232 1496 Planarity : 0.004 0.054 1762 Dihedral : 4.629 46.706 1332 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.86 % Favored : 95.97 % Rotamer: Outliers : 2.22 % Allowed : 16.43 % Favored : 81.35 % 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: 1.54 (0.24), residues: 469 sheet: -0.41 (0.36), residues: 191 loop : -0.42 (0.28), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 666 HIS 0.004 0.001 HIS C 47 PHE 0.010 0.001 PHE C 63 TYR 0.024 0.001 TYR C 21 ARG 0.010 0.000 ARG A 942 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5685.14 seconds wall clock time: 101 minutes 25.09 seconds (6085.09 seconds total)