Starting phenix.real_space_refine on Wed Mar 4 06:56:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mvs_48668/03_2026/9mvs_48668.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mvs_48668/03_2026/9mvs_48668.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.43 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9mvs_48668/03_2026/9mvs_48668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mvs_48668/03_2026/9mvs_48668.map" model { file = "/net/cci-nas-00/data/ceres_data/9mvs_48668/03_2026/9mvs_48668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mvs_48668/03_2026/9mvs_48668.cif" } resolution = 3.43 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.009 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 73 5.49 5 S 24 5.16 5 C 6980 2.51 5 N 1922 2.21 5 O 2347 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11346 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "A" Number of atoms: 9145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1111, 9145 Classifications: {'peptide': 1111} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 10, 'TRANS': 1100} Chain breaks: 6 Unresolved non-hydrogen bonds: 233 Unresolved non-hydrogen angles: 274 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASN:plan1': 7, 'GLU:plan': 11, 'GLN:plan1': 1, 'ASP:plan': 6, 'ARG:plan': 4, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 121 Chain: "C" Number of atoms: 1083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 1083 Classifications: {'RNA': 52} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 4, 'rna3p_pur': 14, 'rna3p_pyr': 28} Link IDs: {'rna2p': 10, 'rna3p': 41} Chain: "D" Number of atoms: 508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 508 Classifications: {'RNA': 23} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 21, 'rna3p_pyr': 1} Link IDs: {'rna3p': 22} Time building chain proxies: 2.39, per 1000 atoms: 0.21 Number of scatterers: 11346 At special positions: 0 Unit cell: (81.4233, 111.372, 120.731, 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 24 16.00 P 73 15.00 O 2347 8.00 N 1922 7.00 C 6980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 477.5 milliseconds 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2288 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 7 sheets defined 69.5% alpha, 5.0% beta 28 base pairs and 48 stacking pairs defined. Time for finding SS restraints: 1.36 Creating SS restraints... Processing helix chain 'B' and resid 14 through 33 Processing helix chain 'B' and resid 48 through 76 removed outlier: 3.742A pdb=" N VAL B 53 " --> pdb=" O PRO B 49 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ASP B 54 " --> pdb=" O TRP B 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 38 Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 54 through 69 Processing helix chain 'A' and resid 106 through 119 removed outlier: 4.568A pdb=" N VAL A 112 " --> pdb=" O LYS A 108 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS A 114 " --> pdb=" O PHE A 110 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N LYS A 115 " --> pdb=" O ALA A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 150 removed outlier: 4.144A pdb=" N VAL A 129 " --> pdb=" O GLU A 125 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N PHE A 130 " --> pdb=" O GLU A 126 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ASN A 132 " --> pdb=" O GLU A 128 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ASP A 133 " --> pdb=" O VAL A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 179 Processing helix chain 'A' and resid 184 through 200 Processing helix chain 'A' and resid 201 through 214 Processing helix chain 'A' and resid 219 through 232 removed outlier: 3.820A pdb=" N ILE A 223 " --> pdb=" O GLU A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 239 Processing helix chain 'A' and resid 240 through 251 Processing helix chain 'A' and resid 253 through 261 Processing helix chain 'A' and resid 265 through 277 Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 290 through 308 removed outlier: 4.031A pdb=" N HIS A 294 " --> pdb=" O TYR A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.824A pdb=" N ARG A 322 " --> pdb=" O ASP A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 355 Processing helix chain 'A' and resid 362 through 377 Processing helix chain 'A' and resid 379 through 394 removed outlier: 3.577A pdb=" N LEU A 394 " --> pdb=" O LEU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 432 removed outlier: 3.690A pdb=" N ILE A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N TYR A 429 " --> pdb=" O VAL A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 453 through 476 removed outlier: 3.537A pdb=" N ILE A 457 " --> pdb=" O ASN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 487 Processing helix chain 'A' and resid 496 through 507 Processing helix chain 'A' and resid 508 through 523 Processing helix chain 'A' and resid 530 through 541 removed outlier: 3.669A pdb=" N ARG A 540 " --> pdb=" O ASN A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 4.679A pdb=" N ASP A 564 " --> pdb=" O TYR A 560 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N ASP A 565 " --> pdb=" O SER A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 602 removed outlier: 3.886A pdb=" N GLY A 602 " --> pdb=" O ASN A 598 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 609 Processing helix chain 'A' and resid 614 through 629 Processing helix chain 'A' and resid 651 through 666 Processing helix chain 'A' and resid 676 through 697 Processing helix chain 'A' and resid 698 through 704 removed outlier: 3.583A pdb=" N LEU A 701 " --> pdb=" O ARG A 698 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE A 704 " --> pdb=" O LEU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 714 Processing helix chain 'A' and resid 716 through 732 removed outlier: 3.524A pdb=" N GLU A 720 " --> pdb=" O GLU A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 747 removed outlier: 4.379A pdb=" N PHE A 743 " --> pdb=" O GLU A 739 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLU A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 756 through 769 removed outlier: 3.677A pdb=" N LEU A 768 " --> pdb=" O LEU A 764 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 769 " --> pdb=" O ILE A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 788 removed outlier: 3.775A pdb=" N ASN A 788 " --> pdb=" O TYR A 784 " (cutoff:3.500A) Processing helix chain 'A' and resid 793 through 805 removed outlier: 3.961A pdb=" N LEU A 805 " --> pdb=" O ASN A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 823 removed outlier: 3.699A pdb=" N ILE A 821 " --> pdb=" O GLU A 817 " (cutoff:3.500A) Processing helix chain 'A' and resid 834 through 842 Processing helix chain 'A' and resid 856 through 866 Processing helix chain 'A' and resid 867 through 879 Processing helix chain 'A' and resid 883 through 913 removed outlier: 3.697A pdb=" N GLU A 896 " --> pdb=" O ASN A 892 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N GLU A 898 " --> pdb=" O LYS A 894 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LYS A 899 " --> pdb=" O ASN A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 921 through 947 Processing helix chain 'A' and resid 947 through 983 Processing helix chain 'A' and resid 987 through 994 removed outlier: 4.082A pdb=" N GLU A 991 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE A 993 " --> pdb=" O ILE A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 1007 through 1020 Processing helix chain 'A' and resid 1023 through 1030 removed outlier: 4.068A pdb=" N ILE A1027 " --> pdb=" O ASP A1023 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR A1030 " --> pdb=" O LYS A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1042 Processing helix chain 'A' and resid 1045 through 1053 removed outlier: 3.728A pdb=" N ASN A1049 " --> pdb=" O LEU A1045 " (cutoff:3.500A) Processing helix chain 'A' and resid 1063 through 1075 Processing helix chain 'A' and resid 1078 through 1083 Processing helix chain 'A' and resid 1084 through 1096 Processing helix chain 'A' and resid 1137 through 1150 Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 10 removed outlier: 5.924A pdb=" N ILE B 4 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N GLU B 39 " --> pdb=" O ILE B 4 " (cutoff:3.500A) removed outlier: 6.021A pdb=" N VAL B 6 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N TYR B 41 " --> pdb=" O VAL B 6 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N VAL B 8 " --> pdb=" O TYR B 41 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 9 through 13 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 155 through 158 Processing sheet with id=AA5, first strand: chain 'A' and resid 409 through 411 Processing sheet with id=AA6, first strand: chain 'A' and resid 1098 through 1103 removed outlier: 6.709A pdb=" N VAL A1099 " --> pdb=" O LEU A1115 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N LEU A1115 " --> pdb=" O VAL A1099 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N THR A1101 " --> pdb=" O GLN A1113 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1119 through 1122 removed outlier: 4.139A pdb=" N LEU A1131 " --> pdb=" O HIS A1122 " (cutoff:3.500A) 587 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 68 hydrogen bonds 136 hydrogen bond angles 0 basepair planarities 28 basepair parallelities 48 stacking parallelities Total time for adding SS restraints: 2.54 Time building geometry restraints manager: 1.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3143 1.34 - 1.45: 2213 1.45 - 1.57: 6148 1.57 - 1.69: 146 1.69 - 1.81: 45 Bond restraints: 11695 Sorted by residual: bond pdb=" CA GLY A 18 " pdb=" C GLY A 18 " ideal model delta sigma weight residual 1.519 1.540 -0.022 7.00e-03 2.04e+04 9.46e+00 bond pdb=" N HIS A1059 " pdb=" CA HIS A1059 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.16e-02 7.43e+03 9.28e+00 bond pdb=" N ILE A1057 " pdb=" CA ILE A1057 " ideal model delta sigma weight residual 1.461 1.496 -0.035 1.23e-02 6.61e+03 8.20e+00 bond pdb=" N TYR A1056 " pdb=" CA TYR A1056 " ideal model delta sigma weight residual 1.459 1.489 -0.031 1.24e-02 6.50e+03 6.06e+00 bond pdb=" O5' U C 31 " pdb=" C5' U C 31 " ideal model delta sigma weight residual 1.420 1.452 -0.032 1.50e-02 4.44e+03 4.46e+00 ... (remaining 11690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 15778 1.58 - 3.17: 243 3.17 - 4.75: 23 4.75 - 6.33: 14 6.33 - 7.92: 2 Bond angle restraints: 16060 Sorted by residual: angle pdb=" N PRO A1058 " pdb=" CD PRO A1058 " pdb=" CG PRO A1058 " ideal model delta sigma weight residual 103.20 98.63 4.57 1.50e+00 4.44e-01 9.28e+00 angle pdb=" N PRO A1058 " pdb=" CA PRO A1058 " pdb=" C PRO A1058 " ideal model delta sigma weight residual 112.47 118.22 -5.75 2.06e+00 2.36e-01 7.78e+00 angle pdb=" N ILE A1057 " pdb=" CA ILE A1057 " pdb=" C ILE A1057 " ideal model delta sigma weight residual 108.88 114.79 -5.91 2.16e+00 2.14e-01 7.50e+00 angle pdb=" C PRO A1058 " pdb=" N HIS A1059 " pdb=" CA HIS A1059 " ideal model delta sigma weight residual 122.67 118.52 4.15 1.59e+00 3.96e-01 6.81e+00 angle pdb=" O4' A C 28 " pdb=" C4' A C 28 " pdb=" C3' A C 28 " ideal model delta sigma weight residual 104.00 106.42 -2.42 1.00e+00 1.00e+00 5.83e+00 ... (remaining 16055 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.16: 6781 26.16 - 52.33: 316 52.33 - 78.49: 92 78.49 - 104.66: 1 104.66 - 130.82: 1 Dihedral angle restraints: 7191 sinusoidal: 3652 harmonic: 3539 Sorted by residual: dihedral pdb=" O4' C C 3 " pdb=" C1' C C 3 " pdb=" N1 C C 3 " pdb=" C2 C C 3 " ideal model delta sinusoidal sigma weight residual -160.00 -108.56 -51.44 1 1.50e+01 4.44e-03 1.61e+01 dihedral pdb=" O4' C C 4 " pdb=" C1' C C 4 " pdb=" N1 C C 4 " pdb=" C2 C C 4 " ideal model delta sinusoidal sigma weight residual -128.00 -176.10 48.10 1 1.70e+01 3.46e-03 1.10e+01 dihedral pdb=" CA ASN A 807 " pdb=" CB ASN A 807 " pdb=" CG ASN A 807 " pdb=" OD1 ASN A 807 " ideal model delta sinusoidal sigma weight residual -90.00 -162.73 72.73 2 2.00e+01 2.50e-03 1.09e+01 ... (remaining 7188 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.104: 1784 0.104 - 0.208: 24 0.208 - 0.312: 0 0.312 - 0.416: 2 0.416 - 0.520: 3 Chirality restraints: 1813 Sorted by residual: chirality pdb=" P A C 28 " pdb=" OP1 A C 28 " pdb=" OP2 A C 28 " pdb=" O5' A C 28 " both_signs ideal model delta sigma weight residual True 2.41 -2.93 -0.52 2.00e-01 2.50e+01 6.77e+00 chirality pdb=" P A C 29 " pdb=" OP1 A C 29 " pdb=" OP2 A C 29 " pdb=" O5' A C 29 " both_signs ideal model delta sigma weight residual True 2.41 -2.89 -0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" P U C 31 " pdb=" OP1 U C 31 " pdb=" OP2 U C 31 " pdb=" O5' U C 31 " both_signs ideal model delta sigma weight residual True 2.41 -2.87 -0.46 2.00e-01 2.50e+01 5.36e+00 ... (remaining 1810 not shown) Planarity restraints: 1773 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR A1056 " -0.007 2.00e-02 2.50e+03 1.49e-02 2.21e+00 pdb=" C TYR A1056 " 0.026 2.00e-02 2.50e+03 pdb=" O TYR A1056 " -0.009 2.00e-02 2.50e+03 pdb=" N ILE A1057 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C C 38 " -0.020 2.00e-02 2.50e+03 9.85e-03 2.18e+00 pdb=" N1 C C 38 " 0.016 2.00e-02 2.50e+03 pdb=" C2 C C 38 " -0.001 2.00e-02 2.50e+03 pdb=" O2 C C 38 " 0.007 2.00e-02 2.50e+03 pdb=" N3 C C 38 " -0.002 2.00e-02 2.50e+03 pdb=" C4 C C 38 " -0.005 2.00e-02 2.50e+03 pdb=" N4 C C 38 " -0.006 2.00e-02 2.50e+03 pdb=" C5 C C 38 " 0.003 2.00e-02 2.50e+03 pdb=" C6 C C 38 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 962 " 0.013 2.00e-02 2.50e+03 1.16e-02 2.01e+00 pdb=" CG HIS A 962 " -0.024 2.00e-02 2.50e+03 pdb=" ND1 HIS A 962 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS A 962 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 HIS A 962 " 0.005 2.00e-02 2.50e+03 pdb=" NE2 HIS A 962 " 0.002 2.00e-02 2.50e+03 ... (remaining 1770 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1032 2.74 - 3.28: 12442 3.28 - 3.82: 21483 3.82 - 4.36: 25003 4.36 - 4.90: 38765 Nonbonded interactions: 98725 Sorted by model distance: nonbonded pdb=" O GLU A 395 " pdb=" NZ LYS A 433 " model vdw 2.204 3.120 nonbonded pdb=" O LYS A 76 " pdb=" OG1 THR A 79 " model vdw 2.283 3.040 nonbonded pdb=" OP2 A C 13 " pdb=" O2' A C 14 " model vdw 2.295 3.040 nonbonded pdb=" O ALA A 187 " pdb=" OG SER A 190 " model vdw 2.324 3.040 nonbonded pdb=" OG SER A 786 " pdb=" OP1 A D 25 " model vdw 2.338 3.040 ... (remaining 98720 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: 1.080 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7466 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 : 0.002 0.035 11695 Z= 0.143 Angle : 0.514 7.918 16060 Z= 0.272 Chirality : 0.042 0.520 1813 Planarity : 0.002 0.026 1773 Dihedral : 15.313 130.821 4903 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.22 % Favored : 97.69 % Rotamer: Outliers : 2.49 % Allowed : 7.77 % Favored : 89.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.24), residues: 1170 helix: 1.66 (0.19), residues: 761 sheet: -0.17 (0.65), residues: 64 loop : -1.09 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.014 0.001 TYR A 860 PHE 0.010 0.001 PHE A 556 TRP 0.001 0.000 TRP A 971 HIS 0.010 0.001 HIS A 962 Details of bonding type rmsd covalent geometry : bond 0.00246 (11695) covalent geometry : angle 0.51390 (16060) hydrogen bonds : bond 0.13131 ( 655) hydrogen bonds : angle 5.34773 ( 1867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 310 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 TYR cc_start: 0.8287 (m-80) cc_final: 0.6540 (m-80) REVERT: B 57 TYR cc_start: 0.8639 (t80) cc_final: 0.8143 (t80) REVERT: A 29 ARG cc_start: 0.7928 (mpt180) cc_final: 0.7328 (mmt90) REVERT: A 68 PHE cc_start: 0.9073 (m-10) cc_final: 0.8797 (m-80) REVERT: A 163 ILE cc_start: 0.6116 (tp) cc_final: 0.5904 (tp) REVERT: A 264 MET cc_start: 0.7742 (mpp) cc_final: 0.7465 (mpp) REVERT: A 274 TYR cc_start: 0.7634 (t80) cc_final: 0.7298 (t80) REVERT: A 279 ASP cc_start: 0.8035 (p0) cc_final: 0.7752 (p0) REVERT: A 298 ILE cc_start: 0.8281 (OUTLIER) cc_final: 0.7936 (mt) REVERT: A 442 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8373 (tttm) REVERT: A 475 ILE cc_start: 0.7282 (mm) cc_final: 0.6941 (mm) REVERT: A 529 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8038 (tp) REVERT: A 532 TYR cc_start: 0.8837 (t80) cc_final: 0.8596 (t80) REVERT: A 548 LYS cc_start: 0.9003 (mtmm) cc_final: 0.8393 (ptpp) REVERT: A 655 LEU cc_start: 0.9155 (mt) cc_final: 0.8830 (mt) REVERT: A 723 LYS cc_start: 0.9431 (mmpt) cc_final: 0.9190 (mmmm) REVERT: A 762 PHE cc_start: 0.8275 (t80) cc_final: 0.7977 (t80) REVERT: A 766 LEU cc_start: 0.9265 (mt) cc_final: 0.8947 (mt) REVERT: A 768 LEU cc_start: 0.9227 (mt) cc_final: 0.8946 (mt) REVERT: A 805 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7357 (pt) REVERT: A 1041 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8862 (mp0) REVERT: A 1086 MET cc_start: 0.9018 (mmm) cc_final: 0.8274 (mmm) outliers start: 26 outliers final: 9 residues processed: 327 average time/residue: 0.1256 time to fit residues: 56.0625 Evaluate side-chains 185 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 173 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 GLU Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 805 LEU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 956 LEU Chi-restraints excluded: chain A residue 1057 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 0.4980 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 0.9990 chunk 113 optimal weight: 0.0060 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 61 GLN ** A 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 352 ASN A 414 ASN A 659 GLN ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 808 ASN A 901 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.114745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.095002 restraints weight = 36855.213| |-----------------------------------------------------------------------------| r_work (start): 0.4029 rms_B_bonded: 4.17 r_work (final): 0.4029 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11695 Z= 0.135 Angle : 0.617 11.826 16060 Z= 0.314 Chirality : 0.037 0.149 1813 Planarity : 0.003 0.044 1773 Dihedral : 15.813 133.103 2414 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 17.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 3.45 % Allowed : 15.44 % Favored : 81.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.24), residues: 1170 helix: 1.53 (0.18), residues: 789 sheet: -0.43 (0.62), residues: 69 loop : -1.16 (0.32), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 224 TYR 0.028 0.001 TYR B 57 PHE 0.022 0.001 PHE A 556 TRP 0.007 0.001 TRP A 971 HIS 0.010 0.001 HIS A 962 Details of bonding type rmsd covalent geometry : bond 0.00290 (11695) covalent geometry : angle 0.61720 (16060) hydrogen bonds : bond 0.04798 ( 655) hydrogen bonds : angle 4.43481 ( 1867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 202 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 4 ILE cc_start: 0.8117 (OUTLIER) cc_final: 0.7424 (pt) REVERT: B 43 LEU cc_start: 0.8024 (tp) cc_final: 0.7556 (tp) REVERT: B 57 TYR cc_start: 0.8511 (t80) cc_final: 0.8296 (t80) REVERT: A 29 ARG cc_start: 0.7981 (mpt180) cc_final: 0.7728 (mpt180) REVERT: A 68 PHE cc_start: 0.9071 (m-10) cc_final: 0.8766 (m-80) REVERT: A 133 ASP cc_start: 0.8562 (m-30) cc_final: 0.8136 (p0) REVERT: A 210 LEU cc_start: 0.9243 (mt) cc_final: 0.9015 (pp) REVERT: A 254 MET cc_start: 0.6002 (tpt) cc_final: 0.5798 (tpt) REVERT: A 264 MET cc_start: 0.7766 (mpp) cc_final: 0.7465 (mpp) REVERT: A 274 TYR cc_start: 0.7778 (t80) cc_final: 0.7398 (t80) REVERT: A 279 ASP cc_start: 0.8328 (p0) cc_final: 0.8060 (p0) REVERT: A 442 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8350 (tttm) REVERT: A 445 TYR cc_start: 0.7471 (m-10) cc_final: 0.7186 (m-10) REVERT: A 529 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8232 (tp) REVERT: A 532 TYR cc_start: 0.8893 (t80) cc_final: 0.8686 (t80) REVERT: A 548 LYS cc_start: 0.8869 (mtmm) cc_final: 0.8406 (ptpt) REVERT: A 590 ASP cc_start: 0.8240 (m-30) cc_final: 0.8019 (m-30) REVERT: A 605 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9228 (tt) REVERT: A 609 MET cc_start: 0.8259 (mmt) cc_final: 0.7744 (mmm) REVERT: A 622 ILE cc_start: 0.8921 (mt) cc_final: 0.8636 (mt) REVERT: A 762 PHE cc_start: 0.8098 (t80) cc_final: 0.7834 (t80) REVERT: A 766 LEU cc_start: 0.9221 (mt) cc_final: 0.8974 (mt) REVERT: A 801 ASN cc_start: 0.8587 (m-40) cc_final: 0.8256 (m-40) REVERT: A 837 GLU cc_start: 0.8599 (mp0) cc_final: 0.8303 (mp0) REVERT: A 1041 GLU cc_start: 0.9394 (mt-10) cc_final: 0.8918 (mp0) REVERT: A 1086 MET cc_start: 0.8987 (mmm) cc_final: 0.8213 (mmm) outliers start: 36 outliers final: 14 residues processed: 222 average time/residue: 0.1126 time to fit residues: 35.4262 Evaluate side-chains 180 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 163 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 4 ILE Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 1057 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 27 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 63 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 120 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 76 optimal weight: 0.2980 chunk 100 optimal weight: 2.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 235 ASN A 328 ASN A 463 ASN A 547 ASN A 614 ASN ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 GLN ** 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 = 0.4256 r_free = 0.4256 target = 0.105729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3892 r_free = 0.3892 target = 0.085573 restraints weight = 38518.869| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 4.21 r_work (final): 0.3869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 11695 Z= 0.292 Angle : 0.769 11.636 16060 Z= 0.387 Chirality : 0.042 0.207 1813 Planarity : 0.004 0.037 1773 Dihedral : 16.007 140.948 2402 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 23.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.74 % Allowed : 17.74 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.24), residues: 1170 helix: 1.20 (0.18), residues: 790 sheet: -0.75 (0.52), residues: 84 loop : -1.14 (0.33), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1072 TYR 0.018 0.002 TYR A1056 PHE 0.019 0.002 PHE A 841 TRP 0.007 0.001 TRP A 971 HIS 0.008 0.002 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00608 (11695) covalent geometry : angle 0.76932 (16060) hydrogen bonds : bond 0.06791 ( 655) hydrogen bonds : angle 4.82045 ( 1867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 169 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.8677 (tp30) cc_final: 0.8234 (tp30) REVERT: B 20 GLU cc_start: 0.9229 (mm-30) cc_final: 0.8946 (mm-30) REVERT: A 29 ARG cc_start: 0.7914 (mpt180) cc_final: 0.7704 (mpt180) REVERT: A 68 PHE cc_start: 0.9164 (m-10) cc_final: 0.8836 (m-80) REVERT: A 133 ASP cc_start: 0.8584 (m-30) cc_final: 0.8146 (p0) REVERT: A 210 LEU cc_start: 0.9294 (mt) cc_final: 0.9078 (pp) REVERT: A 254 MET cc_start: 0.6004 (tpt) cc_final: 0.5734 (tpt) REVERT: A 277 TYR cc_start: 0.8043 (m-80) cc_final: 0.7744 (m-80) REVERT: A 406 MET cc_start: 0.7279 (OUTLIER) cc_final: 0.6936 (mpp) REVERT: A 442 LYS cc_start: 0.8774 (mmtt) cc_final: 0.8526 (tttm) REVERT: A 529 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8450 (tp) REVERT: A 556 PHE cc_start: 0.8260 (t80) cc_final: 0.8025 (t80) REVERT: A 716 GLU cc_start: 0.8861 (OUTLIER) cc_final: 0.8029 (tm-30) REVERT: A 762 PHE cc_start: 0.8318 (t80) cc_final: 0.8008 (t80) REVERT: A 766 LEU cc_start: 0.9331 (mt) cc_final: 0.8957 (mt) REVERT: A 801 ASN cc_start: 0.8643 (m-40) cc_final: 0.8245 (m110) REVERT: A 837 GLU cc_start: 0.8831 (mp0) cc_final: 0.8545 (mp0) REVERT: A 978 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.8218 (ttm110) REVERT: A 1036 LYS cc_start: 0.9373 (tttt) cc_final: 0.9117 (ptpp) REVERT: A 1143 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7853 (tt) outliers start: 39 outliers final: 24 residues processed: 197 average time/residue: 0.1133 time to fit residues: 31.8605 Evaluate side-chains 172 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 143 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 978 ARG Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1057 ILE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1143 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 16 optimal weight: 50.0000 chunk 84 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 71 optimal weight: 0.9980 chunk 59 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 41 optimal weight: 9.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN A 598 ASN A 659 GLN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.111038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.090961 restraints weight = 38224.350| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 4.32 r_work (final): 0.3957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11695 Z= 0.135 Angle : 0.615 12.753 16060 Z= 0.311 Chirality : 0.037 0.162 1813 Planarity : 0.003 0.051 1773 Dihedral : 15.704 133.287 2399 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.07 % Allowed : 19.85 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.24), residues: 1170 helix: 1.43 (0.18), residues: 794 sheet: -0.82 (0.61), residues: 67 loop : -1.25 (0.31), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.025 0.002 TYR A 274 PHE 0.021 0.001 PHE A 848 TRP 0.003 0.001 TRP A 574 HIS 0.011 0.002 HIS A 962 Details of bonding type rmsd covalent geometry : bond 0.00290 (11695) covalent geometry : angle 0.61536 (16060) hydrogen bonds : bond 0.05037 ( 655) hydrogen bonds : angle 4.51507 ( 1867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ASP cc_start: 0.8020 (m-30) cc_final: 0.7770 (m-30) REVERT: B 16 GLU cc_start: 0.8767 (tp30) cc_final: 0.8492 (tm-30) REVERT: B 57 TYR cc_start: 0.8508 (t80) cc_final: 0.8295 (t80) REVERT: A 29 ARG cc_start: 0.8136 (mpt180) cc_final: 0.7710 (mmt90) REVERT: A 68 PHE cc_start: 0.9095 (m-10) cc_final: 0.8777 (m-80) REVERT: A 133 ASP cc_start: 0.8527 (m-30) cc_final: 0.8118 (p0) REVERT: A 210 LEU cc_start: 0.9299 (mt) cc_final: 0.9094 (pp) REVERT: A 254 MET cc_start: 0.5800 (tpt) cc_final: 0.5423 (tpt) REVERT: A 277 TYR cc_start: 0.7693 (m-80) cc_final: 0.7428 (m-80) REVERT: A 406 MET cc_start: 0.7129 (OUTLIER) cc_final: 0.6850 (mpp) REVERT: A 442 LYS cc_start: 0.8637 (mmtt) cc_final: 0.8342 (tttm) REVERT: A 529 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8333 (tp) REVERT: A 548 LYS cc_start: 0.8565 (mtmm) cc_final: 0.8005 (ptpt) REVERT: A 769 LEU cc_start: 0.9009 (mt) cc_final: 0.8794 (mt) REVERT: A 801 ASN cc_start: 0.8604 (m-40) cc_final: 0.8236 (m-40) REVERT: A 1041 GLU cc_start: 0.9371 (mt-10) cc_final: 0.9026 (mp0) REVERT: A 1046 TYR cc_start: 0.8449 (m-80) cc_final: 0.8119 (m-80) REVERT: A 1143 LEU cc_start: 0.8162 (mm) cc_final: 0.7864 (tt) outliers start: 32 outliers final: 17 residues processed: 192 average time/residue: 0.1111 time to fit residues: 30.4719 Evaluate side-chains 171 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TYR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1018 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 35 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 105 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 57 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 117 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 51 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 271 GLN ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 954 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.110623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.090502 restraints weight = 38268.228| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 4.26 r_work (final): 0.3960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11695 Z= 0.146 Angle : 0.631 12.822 16060 Z= 0.315 Chirality : 0.037 0.214 1813 Planarity : 0.003 0.037 1773 Dihedral : 15.573 135.672 2397 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.16 % Allowed : 21.19 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.24), residues: 1170 helix: 1.52 (0.18), residues: 792 sheet: -0.43 (0.62), residues: 72 loop : -1.27 (0.32), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 346 TYR 0.024 0.002 TYR A 537 PHE 0.013 0.001 PHE A 604 TRP 0.009 0.001 TRP A 971 HIS 0.011 0.002 HIS A 962 Details of bonding type rmsd covalent geometry : bond 0.00315 (11695) covalent geometry : angle 0.63114 (16060) hydrogen bonds : bond 0.04992 ( 655) hydrogen bonds : angle 4.43036 ( 1867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ASP cc_start: 0.8101 (m-30) cc_final: 0.7821 (m-30) REVERT: B 16 GLU cc_start: 0.8807 (tp30) cc_final: 0.8493 (tm-30) REVERT: B 57 TYR cc_start: 0.8462 (t80) cc_final: 0.8251 (t80) REVERT: A 29 ARG cc_start: 0.8140 (mpt180) cc_final: 0.7936 (mpt180) REVERT: A 68 PHE cc_start: 0.9087 (m-10) cc_final: 0.8753 (m-80) REVERT: A 133 ASP cc_start: 0.8551 (m-30) cc_final: 0.8155 (p0) REVERT: A 171 LYS cc_start: 0.7258 (OUTLIER) cc_final: 0.7000 (mttm) REVERT: A 210 LEU cc_start: 0.9317 (mt) cc_final: 0.9110 (pp) REVERT: A 254 MET cc_start: 0.5783 (tpt) cc_final: 0.5434 (tpt) REVERT: A 330 LYS cc_start: 0.9233 (pptt) cc_final: 0.9011 (pptt) REVERT: A 406 MET cc_start: 0.7177 (OUTLIER) cc_final: 0.6905 (mpp) REVERT: A 442 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8279 (tttm) REVERT: A 556 PHE cc_start: 0.8214 (t80) cc_final: 0.7654 (t80) REVERT: A 716 GLU cc_start: 0.8801 (OUTLIER) cc_final: 0.8198 (tm-30) REVERT: A 1046 TYR cc_start: 0.8391 (m-80) cc_final: 0.8078 (m-80) REVERT: A 1086 MET cc_start: 0.9036 (mmm) cc_final: 0.7800 (mmm) REVERT: A 1143 LEU cc_start: 0.8071 (mm) cc_final: 0.7758 (tt) outliers start: 33 outliers final: 15 residues processed: 188 average time/residue: 0.1083 time to fit residues: 29.3598 Evaluate side-chains 171 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1039 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 10.0000 chunk 61 optimal weight: 8.9990 chunk 121 optimal weight: 9.9990 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 chunk 27 optimal weight: 7.9990 chunk 102 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN A 731 ASN A 751 ASN A1028 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.107095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.086780 restraints weight = 39095.655| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 4.27 r_work (final): 0.3893 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 11695 Z= 0.216 Angle : 0.704 13.839 16060 Z= 0.353 Chirality : 0.040 0.224 1813 Planarity : 0.003 0.032 1773 Dihedral : 15.720 138.893 2393 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.84 % Allowed : 21.86 % Favored : 74.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.24), residues: 1170 helix: 1.34 (0.18), residues: 795 sheet: -0.63 (0.62), residues: 72 loop : -1.31 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 180 TYR 0.024 0.002 TYR A 880 PHE 0.015 0.002 PHE A 604 TRP 0.007 0.001 TRP A 971 HIS 0.012 0.002 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00457 (11695) covalent geometry : angle 0.70373 (16060) hydrogen bonds : bond 0.05844 ( 655) hydrogen bonds : angle 4.62517 ( 1867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 152 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 7 ASP cc_start: 0.8160 (m-30) cc_final: 0.7852 (m-30) REVERT: B 16 GLU cc_start: 0.8868 (tp30) cc_final: 0.8564 (tm-30) REVERT: A 68 PHE cc_start: 0.9134 (m-10) cc_final: 0.8774 (m-80) REVERT: A 177 ASP cc_start: 0.8519 (OUTLIER) cc_final: 0.8267 (t0) REVERT: A 254 MET cc_start: 0.6057 (tpt) cc_final: 0.5833 (tpt) REVERT: A 406 MET cc_start: 0.7297 (OUTLIER) cc_final: 0.7012 (mpp) REVERT: A 442 LYS cc_start: 0.8682 (mmtt) cc_final: 0.8416 (tttm) REVERT: A 556 PHE cc_start: 0.8327 (t80) cc_final: 0.7773 (t80) REVERT: A 716 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8457 (tm-30) REVERT: A 978 ARG cc_start: 0.8646 (OUTLIER) cc_final: 0.8106 (ttm110) REVERT: A 1046 TYR cc_start: 0.8436 (m-80) cc_final: 0.8050 (m-80) REVERT: A 1086 MET cc_start: 0.9009 (mmm) cc_final: 0.7892 (mmm) REVERT: A 1143 LEU cc_start: 0.8204 (mm) cc_final: 0.7955 (tt) outliers start: 40 outliers final: 24 residues processed: 182 average time/residue: 0.1078 time to fit residues: 28.4293 Evaluate side-chains 172 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 435 ASN Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 880 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 978 ARG Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1039 LYS Chi-restraints excluded: chain A residue 1131 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 49 optimal weight: 3.9990 chunk 112 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.6980 chunk 120 optimal weight: 6.9990 chunk 105 optimal weight: 0.4980 chunk 52 optimal weight: 0.9980 chunk 45 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 93 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.111843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.091728 restraints weight = 38264.742| |-----------------------------------------------------------------------------| r_work (start): 0.3987 rms_B_bonded: 4.28 r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11695 Z= 0.130 Angle : 0.652 15.182 16060 Z= 0.323 Chirality : 0.038 0.284 1813 Planarity : 0.003 0.039 1773 Dihedral : 15.555 133.236 2393 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.88 % Allowed : 22.91 % Favored : 74.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.24), residues: 1170 helix: 1.36 (0.18), residues: 795 sheet: -0.69 (0.62), residues: 72 loop : -1.30 (0.32), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 29 TYR 0.029 0.002 TYR B 57 PHE 0.017 0.001 PHE A 824 TRP 0.005 0.001 TRP A 971 HIS 0.012 0.002 HIS A 962 Details of bonding type rmsd covalent geometry : bond 0.00276 (11695) covalent geometry : angle 0.65154 (16060) hydrogen bonds : bond 0.04820 ( 655) hydrogen bonds : angle 4.41645 ( 1867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.8856 (tp30) cc_final: 0.8166 (tm-30) REVERT: B 20 GLU cc_start: 0.9316 (mm-30) cc_final: 0.8808 (mm-30) REVERT: B 61 GLN cc_start: 0.9027 (pt0) cc_final: 0.8593 (tp-100) REVERT: A 68 PHE cc_start: 0.9093 (m-10) cc_final: 0.8756 (m-80) REVERT: A 140 LYS cc_start: 0.7853 (tttt) cc_final: 0.7578 (mttt) REVERT: A 171 LYS cc_start: 0.7175 (OUTLIER) cc_final: 0.6926 (mttm) REVERT: A 177 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8255 (t0) REVERT: A 254 MET cc_start: 0.6013 (tpt) cc_final: 0.5770 (tpt) REVERT: A 406 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6968 (mpp) REVERT: A 442 LYS cc_start: 0.8606 (mmtt) cc_final: 0.8304 (tttm) REVERT: A 549 ASN cc_start: 0.8383 (m-40) cc_final: 0.6443 (t0) REVERT: A 556 PHE cc_start: 0.8263 (t80) cc_final: 0.7720 (t80) REVERT: A 601 TYR cc_start: 0.7763 (m-80) cc_final: 0.7371 (m-80) REVERT: A 716 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.7816 (tm-30) REVERT: A 903 MET cc_start: 0.9125 (ttp) cc_final: 0.8826 (ptm) REVERT: A 1024 GLU cc_start: 0.9271 (pm20) cc_final: 0.9012 (pm20) REVERT: A 1143 LEU cc_start: 0.8089 (mm) cc_final: 0.7823 (tt) outliers start: 30 outliers final: 14 residues processed: 181 average time/residue: 0.1037 time to fit residues: 27.4239 Evaluate side-chains 167 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 171 LYS Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1039 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 102 optimal weight: 0.6980 chunk 7 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 12 optimal weight: 20.0000 chunk 104 optimal weight: 0.8980 chunk 118 optimal weight: 10.0000 chunk 55 optimal weight: 6.9990 chunk 33 optimal weight: 2.9990 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.110210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.090195 restraints weight = 37801.966| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 4.23 r_work (final): 0.3949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 11695 Z= 0.156 Angle : 0.661 13.456 16060 Z= 0.329 Chirality : 0.039 0.303 1813 Planarity : 0.003 0.037 1773 Dihedral : 15.592 136.211 2392 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.97 % Allowed : 23.20 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.24), residues: 1170 helix: 1.31 (0.18), residues: 793 sheet: -0.85 (0.60), residues: 74 loop : -1.23 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 29 TYR 0.022 0.002 TYR A 880 PHE 0.015 0.001 PHE A 824 TRP 0.007 0.001 TRP A 971 HIS 0.012 0.002 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00338 (11695) covalent geometry : angle 0.66065 (16060) hydrogen bonds : bond 0.05018 ( 655) hydrogen bonds : angle 4.45138 ( 1867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 155 time to evaluate : 0.425 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.8883 (tp30) cc_final: 0.8195 (tm-30) REVERT: B 20 GLU cc_start: 0.9325 (mm-30) cc_final: 0.8832 (mm-30) REVERT: B 61 GLN cc_start: 0.9027 (pt0) cc_final: 0.8540 (tp-100) REVERT: A 68 PHE cc_start: 0.9092 (m-10) cc_final: 0.8735 (m-80) REVERT: A 140 LYS cc_start: 0.7934 (tttt) cc_final: 0.7562 (mmtt) REVERT: A 177 ASP cc_start: 0.8523 (OUTLIER) cc_final: 0.8285 (t0) REVERT: A 254 MET cc_start: 0.6011 (tpt) cc_final: 0.5771 (tpt) REVERT: A 406 MET cc_start: 0.7088 (OUTLIER) cc_final: 0.6879 (mpp) REVERT: A 442 LYS cc_start: 0.8623 (mmtt) cc_final: 0.8346 (tttt) REVERT: A 549 ASN cc_start: 0.8428 (m-40) cc_final: 0.8223 (m-40) REVERT: A 556 PHE cc_start: 0.8308 (t80) cc_final: 0.7774 (t80) REVERT: A 601 TYR cc_start: 0.7819 (m-80) cc_final: 0.7443 (m-80) REVERT: A 716 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.7814 (tm-30) REVERT: A 903 MET cc_start: 0.9099 (ttp) cc_final: 0.8812 (ptm) REVERT: A 978 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.8047 (ttm110) REVERT: A 1086 MET cc_start: 0.8874 (mmm) cc_final: 0.8297 (mtp) outliers start: 31 outliers final: 17 residues processed: 177 average time/residue: 0.1066 time to fit residues: 27.1808 Evaluate side-chains 171 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 978 ARG Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1131 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 67 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 80 optimal weight: 7.9990 chunk 104 optimal weight: 0.0270 chunk 84 optimal weight: 9.9990 chunk 49 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 overall best weight: 2.5242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 954 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 = 0.4296 r_free = 0.4296 target = 0.108010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.087929 restraints weight = 37824.972| |-----------------------------------------------------------------------------| r_work (start): 0.3908 rms_B_bonded: 4.21 r_work (final): 0.3908 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11695 Z= 0.197 Angle : 0.708 14.065 16060 Z= 0.354 Chirality : 0.041 0.315 1813 Planarity : 0.003 0.037 1773 Dihedral : 15.736 138.361 2392 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.16 % Allowed : 23.49 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1170 helix: 1.17 (0.18), residues: 791 sheet: -0.95 (0.60), residues: 74 loop : -1.24 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 29 TYR 0.021 0.002 TYR A 880 PHE 0.020 0.002 PHE A 365 TRP 0.010 0.001 TRP A 971 HIS 0.011 0.002 HIS A 908 Details of bonding type rmsd covalent geometry : bond 0.00424 (11695) covalent geometry : angle 0.70752 (16060) hydrogen bonds : bond 0.05622 ( 655) hydrogen bonds : angle 4.61005 ( 1867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 154 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.8852 (tp30) cc_final: 0.8288 (tm-30) REVERT: B 20 GLU cc_start: 0.9317 (mm-30) cc_final: 0.8869 (mm-30) REVERT: B 61 GLN cc_start: 0.9087 (pt0) cc_final: 0.8522 (tp-100) REVERT: A 68 PHE cc_start: 0.9103 (m-10) cc_final: 0.8729 (m-80) REVERT: A 140 LYS cc_start: 0.7973 (tttt) cc_final: 0.7739 (ttmt) REVERT: A 177 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.8210 (t0) REVERT: A 254 MET cc_start: 0.5922 (tpt) cc_final: 0.5685 (tpt) REVERT: A 406 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6823 (mpp) REVERT: A 442 LYS cc_start: 0.8663 (mmtt) cc_final: 0.8386 (tttm) REVERT: A 556 PHE cc_start: 0.8227 (t80) cc_final: 0.7663 (t80) REVERT: A 716 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8519 (tm-30) REVERT: A 903 MET cc_start: 0.9105 (ttp) cc_final: 0.8806 (ptm) REVERT: A 978 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.8063 (ttm110) outliers start: 33 outliers final: 21 residues processed: 178 average time/residue: 0.1001 time to fit residues: 25.6993 Evaluate side-chains 173 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 174 ILE Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 596 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 880 TYR Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 978 ARG Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1131 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 97 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 118 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 115 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 ASN ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 801 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.112141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.091921 restraints weight = 38026.968| |-----------------------------------------------------------------------------| r_work (start): 0.3963 rms_B_bonded: 4.43 r_work (final): 0.3963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.4806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11695 Z= 0.137 Angle : 0.678 15.006 16060 Z= 0.337 Chirality : 0.040 0.354 1813 Planarity : 0.003 0.034 1773 Dihedral : 15.648 134.183 2392 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.40 % Allowed : 24.35 % Favored : 73.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.24), residues: 1170 helix: 1.20 (0.18), residues: 790 sheet: -1.09 (0.61), residues: 69 loop : -1.29 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 405 TYR 0.025 0.002 TYR A 387 PHE 0.021 0.001 PHE A 365 TRP 0.005 0.001 TRP A 971 HIS 0.012 0.002 HIS A 962 Details of bonding type rmsd covalent geometry : bond 0.00295 (11695) covalent geometry : angle 0.67798 (16060) hydrogen bonds : bond 0.04906 ( 655) hydrogen bonds : angle 4.51480 ( 1867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2340 Ramachandran restraints generated. 1170 Oldfield, 0 Emsley, 1170 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 152 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.8855 (tp30) cc_final: 0.8289 (tm-30) REVERT: B 20 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8881 (mm-30) REVERT: B 61 GLN cc_start: 0.9062 (pt0) cc_final: 0.8630 (tp-100) REVERT: A 68 PHE cc_start: 0.9126 (m-10) cc_final: 0.8756 (m-80) REVERT: A 140 LYS cc_start: 0.7845 (tttt) cc_final: 0.7533 (mmtt) REVERT: A 177 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8248 (t0) REVERT: A 254 MET cc_start: 0.5967 (tpt) cc_final: 0.5704 (tpt) REVERT: A 406 MET cc_start: 0.7233 (OUTLIER) cc_final: 0.7012 (mpp) REVERT: A 442 LYS cc_start: 0.8607 (mmtt) cc_final: 0.8320 (tttm) REVERT: A 556 PHE cc_start: 0.8384 (t80) cc_final: 0.7853 (t80) REVERT: A 601 TYR cc_start: 0.7690 (m-80) cc_final: 0.7211 (m-80) REVERT: A 716 GLU cc_start: 0.8868 (OUTLIER) cc_final: 0.8541 (tm-30) REVERT: A 903 MET cc_start: 0.9202 (ttp) cc_final: 0.8874 (ptm) REVERT: A 978 ARG cc_start: 0.8654 (OUTLIER) cc_final: 0.8155 (ttm-80) REVERT: A 1086 MET cc_start: 0.9027 (mmm) cc_final: 0.8043 (mtp) outliers start: 25 outliers final: 19 residues processed: 171 average time/residue: 0.1069 time to fit residues: 26.2798 Evaluate side-chains 170 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 271 GLN Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 609 MET Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 751 ASN Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 801 ASN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 978 ARG Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1131 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 93 optimal weight: 10.0000 chunk 97 optimal weight: 0.8980 chunk 109 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 115 optimal weight: 7.9990 chunk 116 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 107 optimal weight: 5.9990 chunk 31 optimal weight: 8.9990 chunk 91 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN A 801 ASN ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.111161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.090852 restraints weight = 38168.864| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 4.39 r_work (final): 0.3954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7690 moved from start: 0.4903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11695 Z= 0.146 Angle : 0.683 17.008 16060 Z= 0.338 Chirality : 0.039 0.343 1813 Planarity : 0.003 0.064 1773 Dihedral : 15.662 135.126 2392 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.49 % Allowed : 24.74 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.24), residues: 1170 helix: 1.23 (0.18), residues: 791 sheet: -0.99 (0.61), residues: 69 loop : -1.24 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 405 TYR 0.031 0.002 TYR A 351 PHE 0.020 0.001 PHE A 365 TRP 0.005 0.001 TRP A 971 HIS 0.011 0.002 HIS A 962 Details of bonding type rmsd covalent geometry : bond 0.00317 (11695) covalent geometry : angle 0.68338 (16060) hydrogen bonds : bond 0.04920 ( 655) hydrogen bonds : angle 4.54920 ( 1867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2253.74 seconds wall clock time: 40 minutes 1.68 seconds (2401.68 seconds total)