Starting phenix.real_space_refine on Fri Jul 3 02:42:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mvs_48668/07_2026/9mvs_48668.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mvs_48668/07_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 { model { file = "/net/cci-nas-00/data/ceres_data/9mvs_48668/07_2026/9mvs_48668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mvs_48668/07_2026/9mvs_48668.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mvs_48668/07_2026/9mvs_48668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mvs_48668/07_2026/9mvs_48668.map" } 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-6108/lib/python3.11/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: 2.54, per 1000 atoms: 0.22 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: 0.91 Conformation dependent library (CDL) restraints added in 477.0 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: 1.53 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: 2.29 Time building geometry restraints manager: 1.21 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=" C1' C C 38 " pdb=" N1 C C 38 " pdb=" C2 C C 38 " ideal model delta sigma weight residual 118.80 124.27 -5.47 1.10e+00 8.26e-01 2.48e+01 angle pdb=" N1 C C 38 " pdb=" C6 C C 38 " pdb=" C5 C C 38 " ideal model delta sigma weight residual 121.00 123.43 -2.43 5.00e-01 4.00e+00 2.36e+01 angle pdb=" O4 U C 32 " pdb=" C4 U C 32 " pdb=" C5 U C 32 " ideal model delta sigma weight residual 125.90 123.57 2.33 6.00e-01 2.78e+00 1.50e+01 angle pdb=" N1 C C 38 " pdb=" C2 C C 38 " pdb=" O2 C C 38 " ideal model delta sigma weight residual 118.90 121.23 -2.33 6.00e-01 2.78e+00 1.50e+01 angle pdb=" C2 C C 38 " pdb=" N1 C C 38 " pdb=" C6 C C 38 " ideal model delta sigma weight residual 120.30 118.78 1.52 4.00e-01 6.25e+00 1.45e+01 ... (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: 1.110 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.790 Find NCS groups from input model: 0.050 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 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= 0.174 Angle : 0.514 7.918 16060 Z= 0.371 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/Z covalent geometry : bond 0.00246 / 0.17 (11695) covalent geometry : angle 0.51396 / 0.37 (16060) hydrogen bonds : bond 0.13131 / 8.62 ( 655) hydrogen bonds : angle 5.34773 / 3.85 ( 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 : 0.392 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: 0.1200 time to fit residues: 53.5096 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 : 0.394 ------------------------------------------------------------------------------- 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: 20.0000 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 GLN A 214 ASN A 352 ASN A 614 ASN ** 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 901 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.114682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.094976 restraints weight = 36754.996| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 4.14 r_work (final): 0.4028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 11695 Z= 0.152 Angle : 0.635 13.523 16060 Z= 0.338 Chirality : 0.039 0.193 1813 Planarity : 0.003 0.041 1773 Dihedral : 15.954 132.531 2414 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 18.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.03 % Allowed : 14.86 % 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: 0.76 (0.24), residues: 1170 helix: 1.28 (0.18), residues: 786 sheet: -0.59 (0.61), residues: 69 loop : -1.13 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 224 TYR 0.026 0.002 TYR B 57 PHE 0.024 0.002 PHE A 556 TRP 0.006 0.002 TRP A 971 HIS 0.010 0.002 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (11695) covalent geometry : angle 0.63490 / 0.34 (16060) hydrogen bonds : bond 0.05966 / 3.96 ( 655) hydrogen bonds : angle 4.67489 / 3.38 ( 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 240 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 198 time to evaluate : 0.392 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 43 LEU cc_start: 0.7997 (tp) cc_final: 0.7472 (tp) REVERT: A 29 ARG cc_start: 0.8025 (mpt180) cc_final: 0.7634 (mmt90) REVERT: A 68 PHE cc_start: 0.9077 (m-10) cc_final: 0.8790 (m-80) REVERT: A 130 PHE cc_start: 0.7811 (m-80) cc_final: 0.7546 (m-80) REVERT: A 133 ASP cc_start: 0.8576 (m-30) cc_final: 0.8159 (p0) REVERT: A 194 GLU cc_start: 0.8349 (pp20) cc_final: 0.8117 (pp20) REVERT: A 210 LEU cc_start: 0.9173 (mt) cc_final: 0.8933 (pp) REVERT: A 254 MET cc_start: 0.5959 (tpt) cc_final: 0.5715 (tpt) REVERT: A 264 MET cc_start: 0.7697 (mpp) cc_final: 0.7436 (mpp) REVERT: A 274 TYR cc_start: 0.7645 (t80) cc_final: 0.7303 (t80) REVERT: A 442 LYS cc_start: 0.8670 (mmtt) cc_final: 0.8360 (tttm) REVERT: A 542 ARG cc_start: 0.8434 (ttp-170) cc_final: 0.8172 (ptt-90) REVERT: A 548 LYS cc_start: 0.8845 (mtmm) cc_final: 0.8217 (ptpp) REVERT: A 590 ASP cc_start: 0.8234 (m-30) cc_final: 0.7968 (m-30) REVERT: A 609 MET cc_start: 0.8332 (mmt) cc_final: 0.7938 (mmm) REVERT: A 762 PHE cc_start: 0.8244 (t80) cc_final: 0.7928 (t80) REVERT: A 766 LEU cc_start: 0.9219 (mt) cc_final: 0.8919 (mt) REVERT: A 768 LEU cc_start: 0.9195 (mt) cc_final: 0.8899 (mt) REVERT: A 801 ASN cc_start: 0.8547 (m-40) cc_final: 0.8238 (m-40) REVERT: A 837 GLU cc_start: 0.8550 (mp0) cc_final: 0.8198 (mp0) REVERT: A 999 LYS cc_start: 0.9001 (mttt) cc_final: 0.8798 (mmtm) REVERT: A 1041 GLU cc_start: 0.9392 (mt-10) cc_final: 0.8923 (mp0) REVERT: A 1064 LEU cc_start: 0.7695 (mt) cc_final: 0.7480 (mp) REVERT: A 1086 MET cc_start: 0.9002 (mmm) cc_final: 0.8152 (mmm) outliers start: 42 outliers final: 23 residues processed: 221 average time/residue: 0.1075 time to fit residues: 33.5818 Evaluate side-chains 184 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 61 GLN Chi-restraints excluded: chain B residue 62 GLU 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 214 ASN 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 463 ASN Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 595 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 964 LEU Chi-restraints excluded: chain A residue 1057 ILE Chi-restraints excluded: chain A residue 1118 GLU 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: 6.9990 chunk 25 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 63 optimal weight: 8.9990 chunk 41 optimal weight: 10.0000 chunk 32 optimal weight: 7.9990 chunk 120 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 352 ASN A 414 ASN A 659 GLN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.108235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.088286 restraints weight = 38008.540| |-----------------------------------------------------------------------------| r_work (start): 0.3915 rms_B_bonded: 4.15 r_work (final): 0.3915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 11695 Z= 0.283 Angle : 0.708 14.468 16060 Z= 0.384 Chirality : 0.042 0.190 1813 Planarity : 0.004 0.033 1773 Dihedral : 15.923 138.550 2407 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 23.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.22 % Allowed : 16.68 % Favored : 79.10 % 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: 0.55 (0.24), residues: 1170 helix: 1.10 (0.18), residues: 791 sheet: -0.59 (0.59), residues: 74 loop : -1.21 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 377 TYR 0.018 0.002 TYR A1003 PHE 0.022 0.002 PHE A 556 TRP 0.004 0.001 TRP A 971 HIS 0.009 0.002 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00594 / 0.28 (11695) covalent geometry : angle 0.70819 / 0.38 (16060) hydrogen bonds : bond 0.06881 / 4.52 ( 655) hydrogen bonds : angle 4.84085 / 3.50 ( 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 218 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 174 time to evaluate : 0.350 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: B 16 GLU cc_start: 0.8585 (tp30) cc_final: 0.7945 (tp30) REVERT: B 20 GLU cc_start: 0.9179 (mm-30) cc_final: 0.8774 (mm-30) REVERT: A 29 ARG cc_start: 0.7980 (mpt180) cc_final: 0.7718 (mpt180) REVERT: A 68 PHE cc_start: 0.9141 (m-10) cc_final: 0.8845 (m-80) REVERT: A 130 PHE cc_start: 0.7864 (m-80) cc_final: 0.7622 (m-80) REVERT: A 133 ASP cc_start: 0.8610 (m-30) cc_final: 0.8179 (p0) REVERT: A 163 ILE cc_start: 0.5821 (tp) cc_final: 0.5603 (tp) REVERT: A 210 LEU cc_start: 0.9277 (mt) cc_final: 0.9046 (pp) REVERT: A 254 MET cc_start: 0.5987 (tpt) cc_final: 0.5584 (tpt) REVERT: A 264 MET cc_start: 0.7760 (mpp) cc_final: 0.7447 (mpp) REVERT: A 274 TYR cc_start: 0.8008 (t80) cc_final: 0.7723 (t80) REVERT: A 330 LYS cc_start: 0.9297 (pptt) cc_final: 0.9047 (pptt) REVERT: A 442 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8503 (tttm) REVERT: A 542 ARG cc_start: 0.8590 (ttp-170) cc_final: 0.8241 (ptt-90) REVERT: A 548 LYS cc_start: 0.8942 (mtmm) cc_final: 0.8454 (ptpt) REVERT: A 556 PHE cc_start: 0.8457 (t80) cc_final: 0.8089 (t80) REVERT: A 590 ASP cc_start: 0.8442 (m-30) cc_final: 0.8179 (m-30) REVERT: A 659 GLN cc_start: 0.9314 (OUTLIER) cc_final: 0.9068 (pp30) REVERT: A 716 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8164 (tm-30) REVERT: A 723 LYS cc_start: 0.9410 (mmpt) cc_final: 0.9151 (mmmm) REVERT: A 762 PHE cc_start: 0.8342 (t80) cc_final: 0.8131 (t80) REVERT: A 766 LEU cc_start: 0.9322 (mt) cc_final: 0.9076 (mt) REVERT: A 768 LEU cc_start: 0.9248 (mt) cc_final: 0.8933 (mt) REVERT: A 785 GLN cc_start: 0.8993 (OUTLIER) cc_final: 0.8722 (mm-40) REVERT: A 801 ASN cc_start: 0.8606 (m-40) cc_final: 0.8297 (m-40) REVERT: A 897 ILE cc_start: 0.8070 (pt) cc_final: 0.7665 (mm) REVERT: A 1041 GLU cc_start: 0.9450 (mt-10) cc_final: 0.9086 (mp0) REVERT: A 1086 MET cc_start: 0.9092 (mmm) cc_final: 0.8419 (mmm) REVERT: A 1143 LEU cc_start: 0.8198 (OUTLIER) cc_final: 0.7994 (tp) outliers start: 44 outliers final: 24 residues processed: 204 average time/residue: 0.1005 time to fit residues: 29.5484 Evaluate side-chains 182 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.398 ------------------------------------------------------------------------------- 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 166 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 394 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 659 GLN Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 752 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1057 ILE Chi-restraints excluded: chain A residue 1062 ILE 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: 40.0000 chunk 84 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 71 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 111 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 41 optimal weight: 9.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN A 214 ASN A 414 ASN A 463 ASN A 659 GLN ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.107527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.087322 restraints weight = 38834.618| |-----------------------------------------------------------------------------| r_work (start): 0.3899 rms_B_bonded: 4.22 r_work (final): 0.3899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.3273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11695 Z= 0.257 Angle : 0.689 13.308 16060 Z= 0.371 Chirality : 0.042 0.241 1813 Planarity : 0.004 0.060 1773 Dihedral : 15.945 138.628 2403 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 22.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.79 % Allowed : 17.74 % Favored : 77.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.35 (0.24), residues: 1170 helix: 0.95 (0.18), residues: 791 sheet: -0.55 (0.60), residues: 72 loop : -1.30 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 527 TYR 0.017 0.002 TYR A 537 PHE 0.035 0.002 PHE A 848 TRP 0.005 0.001 TRP A 971 HIS 0.009 0.002 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00539 / 0.26 (11695) covalent geometry : angle 0.68863 / 0.37 (16060) hydrogen bonds : bond 0.07149 / 4.68 ( 655) hydrogen bonds : angle 4.93179 / 3.54 ( 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 215 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 165 time to evaluate : 0.391 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: B 16 GLU cc_start: 0.8672 (tp30) cc_final: 0.8102 (tp30) REVERT: B 20 GLU cc_start: 0.9225 (mm-30) cc_final: 0.8857 (mm-30) REVERT: B 32 TYR cc_start: 0.8105 (OUTLIER) cc_final: 0.7815 (t80) REVERT: A 29 ARG cc_start: 0.7966 (mpt180) cc_final: 0.7764 (mpt180) REVERT: A 68 PHE cc_start: 0.9147 (m-10) cc_final: 0.8830 (m-80) REVERT: A 130 PHE cc_start: 0.7913 (m-80) cc_final: 0.7711 (m-80) REVERT: A 133 ASP cc_start: 0.8564 (m-30) cc_final: 0.8151 (p0) REVERT: A 210 LEU cc_start: 0.9284 (mt) cc_final: 0.9042 (pp) REVERT: A 264 MET cc_start: 0.7800 (mpp) cc_final: 0.7488 (mpp) REVERT: A 274 TYR cc_start: 0.8103 (t80) cc_final: 0.7881 (t80) REVERT: A 332 LEU cc_start: 0.9303 (tp) cc_final: 0.9084 (tt) REVERT: A 442 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8525 (tttp) REVERT: A 542 ARG cc_start: 0.8672 (ttp-170) cc_final: 0.8292 (ptt-90) REVERT: A 548 LYS cc_start: 0.8859 (mtmm) cc_final: 0.8641 (ptpp) REVERT: A 556 PHE cc_start: 0.8403 (t80) cc_final: 0.8079 (t80) REVERT: A 590 ASP cc_start: 0.8463 (m-30) cc_final: 0.8193 (m-30) REVERT: A 716 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8336 (tm-30) REVERT: A 762 PHE cc_start: 0.8310 (t80) cc_final: 0.8017 (t80) REVERT: A 766 LEU cc_start: 0.9318 (mt) cc_final: 0.8975 (mt) REVERT: A 768 LEU cc_start: 0.9218 (mt) cc_final: 0.8910 (mt) REVERT: A 785 GLN cc_start: 0.8990 (OUTLIER) cc_final: 0.8694 (mm-40) REVERT: A 801 ASN cc_start: 0.8601 (m-40) cc_final: 0.8305 (m-40) REVERT: A 897 ILE cc_start: 0.8032 (pt) cc_final: 0.7625 (mm) REVERT: A 978 ARG cc_start: 0.8693 (OUTLIER) cc_final: 0.8208 (ttm110) REVERT: A 999 LYS cc_start: 0.8990 (mmtm) cc_final: 0.8736 (mmtm) REVERT: A 1041 GLU cc_start: 0.9397 (mt-10) cc_final: 0.9114 (mp0) REVERT: A 1086 MET cc_start: 0.9155 (mmm) cc_final: 0.8100 (mmm) outliers start: 50 outliers final: 30 residues processed: 203 average time/residue: 0.1010 time to fit residues: 29.5460 Evaluate side-chains 180 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 146 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain A residue 94 TYR 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 214 ASN Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 546 VAL 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 752 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 839 LYS Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 871 LEU 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 1057 ILE Chi-restraints excluded: chain A residue 1101 THR Chi-restraints excluded: chain A residue 1131 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 35 optimal weight: 4.9990 chunk 1 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 105 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 118 optimal weight: 10.0000 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 598 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.110450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.090420 restraints weight = 37667.380| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 4.17 r_work (final): 0.3959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11695 Z= 0.143 Angle : 0.622 13.749 16060 Z= 0.334 Chirality : 0.039 0.329 1813 Planarity : 0.003 0.047 1773 Dihedral : 15.847 135.561 2401 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 19.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 4.03 % Allowed : 19.08 % Favored : 76.89 % 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: 0.50 (0.24), residues: 1170 helix: 1.07 (0.18), residues: 788 sheet: -0.52 (0.61), residues: 72 loop : -1.25 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 224 TYR 0.025 0.002 TYR A 537 PHE 0.021 0.002 PHE A 680 TRP 0.005 0.001 TRP A 971 HIS 0.011 0.002 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (11695) covalent geometry : angle 0.62233 / 0.33 (16060) hydrogen bonds : bond 0.06238 / 4.05 ( 655) hydrogen bonds : angle 4.76786 / 3.42 ( 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 212 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 170 time to evaluate : 0.319 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: 0.8664 (tp30) cc_final: 0.8377 (tp30) REVERT: B 32 TYR cc_start: 0.8282 (OUTLIER) cc_final: 0.8061 (t80) REVERT: A 29 ARG cc_start: 0.8050 (mpt180) cc_final: 0.7773 (mpt180) REVERT: A 68 PHE cc_start: 0.9096 (m-10) cc_final: 0.8789 (m-80) REVERT: A 130 PHE cc_start: 0.7894 (m-80) cc_final: 0.7681 (m-80) REVERT: A 133 ASP cc_start: 0.8533 (m-30) cc_final: 0.8111 (p0) REVERT: A 171 LYS cc_start: 0.7345 (OUTLIER) cc_final: 0.7127 (mttm) REVERT: A 210 LEU cc_start: 0.9290 (mt) cc_final: 0.9048 (pp) REVERT: A 274 TYR cc_start: 0.7960 (t80) cc_final: 0.7717 (t80) REVERT: A 330 LYS cc_start: 0.9244 (pptt) cc_final: 0.8962 (pptt) REVERT: A 406 MET cc_start: 0.6684 (mpp) cc_final: 0.6478 (mpp) REVERT: A 442 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8416 (tttm) REVERT: A 542 ARG cc_start: 0.8653 (ttp-170) cc_final: 0.8392 (ptt-90) REVERT: A 548 LYS cc_start: 0.8801 (mtmm) cc_final: 0.8548 (ptpp) REVERT: A 556 PHE cc_start: 0.8244 (t80) cc_final: 0.7995 (t80) REVERT: A 590 ASP cc_start: 0.8268 (m-30) cc_final: 0.7920 (m-30) REVERT: A 716 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8033 (tm-30) REVERT: A 762 PHE cc_start: 0.8232 (t80) cc_final: 0.7935 (t80) REVERT: A 766 LEU cc_start: 0.9257 (mt) cc_final: 0.8953 (mt) REVERT: A 768 LEU cc_start: 0.9179 (mt) cc_final: 0.8889 (mt) REVERT: A 785 GLN cc_start: 0.8957 (OUTLIER) cc_final: 0.8690 (mm-40) REVERT: A 801 ASN cc_start: 0.8523 (m-40) cc_final: 0.8226 (m-40) REVERT: A 978 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7988 (ttm110) REVERT: A 1041 GLU cc_start: 0.9378 (mt-10) cc_final: 0.9087 (mp0) REVERT: A 1086 MET cc_start: 0.9103 (mmm) cc_final: 0.7966 (mmm) REVERT: A 1143 LEU cc_start: 0.8518 (tp) cc_final: 0.8087 (tt) outliers start: 42 outliers final: 28 residues processed: 199 average time/residue: 0.1018 time to fit residues: 29.0597 Evaluate side-chains 186 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 45 GLU 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 298 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 546 VAL 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 752 ILE Chi-restraints excluded: chain A residue 765 ILE Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 964 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 1057 ILE Chi-restraints excluded: chain A residue 1148 PHE 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: 9.9990 chunk 121 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 56 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 102 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 730 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 954 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.103315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.083178 restraints weight = 38871.196| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 4.19 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.078 11695 Z= 0.380 Angle : 0.827 13.175 16060 Z= 0.442 Chirality : 0.047 0.222 1813 Planarity : 0.005 0.045 1773 Dihedral : 16.046 142.615 2399 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 27.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 5.08 % Allowed : 20.42 % Favored : 74.50 % 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: -0.01 (0.23), residues: 1170 helix: 0.68 (0.18), residues: 788 sheet: -0.74 (0.58), residues: 73 loop : -1.42 (0.33), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1072 TYR 0.023 0.003 TYR A 738 PHE 0.026 0.003 PHE A 721 TRP 0.006 0.002 TRP A 574 HIS 0.010 0.002 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00780 / 0.38 (11695) covalent geometry : angle 0.82729 / 0.44 (16060) hydrogen bonds : bond 0.08493 / 5.53 ( 655) hydrogen bonds : angle 5.16649 / 3.71 ( 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 197 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 144 time to evaluate : 0.405 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: 0.8741 (tp30) cc_final: 0.7996 (tp30) REVERT: B 20 GLU cc_start: 0.9234 (mm-30) cc_final: 0.8785 (mm-30) REVERT: A 68 PHE cc_start: 0.9152 (m-10) cc_final: 0.8819 (m-80) REVERT: A 133 ASP cc_start: 0.8615 (m-30) cc_final: 0.8211 (p0) REVERT: A 210 LEU cc_start: 0.9300 (mt) cc_final: 0.9082 (pp) REVERT: A 332 LEU cc_start: 0.9327 (tp) cc_final: 0.9100 (tt) REVERT: A 390 LEU cc_start: 0.8718 (OUTLIER) cc_final: 0.8403 (tt) REVERT: A 406 MET cc_start: 0.6955 (mpp) cc_final: 0.6551 (mpp) REVERT: A 529 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8395 (tt) REVERT: A 548 LYS cc_start: 0.8865 (mtmm) cc_final: 0.8474 (mtmm) REVERT: A 556 PHE cc_start: 0.8389 (t80) cc_final: 0.8028 (t80) REVERT: A 716 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: A 766 LEU cc_start: 0.9341 (mt) cc_final: 0.9098 (mt) REVERT: A 785 GLN cc_start: 0.9058 (OUTLIER) cc_final: 0.8737 (mm-40) REVERT: A 801 ASN cc_start: 0.8719 (m-40) cc_final: 0.8446 (m-40) REVERT: A 978 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8247 (ttm110) REVERT: A 1041 GLU cc_start: 0.9436 (mt-10) cc_final: 0.9197 (mp0) REVERT: A 1086 MET cc_start: 0.9150 (mmm) cc_final: 0.8140 (mmm) outliers start: 53 outliers final: 32 residues processed: 186 average time/residue: 0.0978 time to fit residues: 26.6445 Evaluate side-chains 171 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 61 GLN 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 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 342 ASP Chi-restraints excluded: chain A residue 380 ILE Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 580 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 752 ILE Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 880 TYR Chi-restraints excluded: chain A residue 945 VAL 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 1057 ILE Chi-restraints excluded: chain A residue 1090 VAL Chi-restraints excluded: chain A residue 1101 THR 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: 0.8980 chunk 66 optimal weight: 5.9990 chunk 99 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 52 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 chunk 93 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 659 GLN ** 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 807 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.109434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.089416 restraints weight = 37617.999| |-----------------------------------------------------------------------------| r_work (start): 0.3928 rms_B_bonded: 4.15 r_work (final): 0.3928 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.3881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11695 Z= 0.146 Angle : 0.665 14.108 16060 Z= 0.353 Chirality : 0.041 0.334 1813 Planarity : 0.003 0.040 1773 Dihedral : 15.886 135.097 2396 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 18.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.45 % Allowed : 22.34 % 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: 0.31 (0.24), residues: 1170 helix: 0.95 (0.18), residues: 786 sheet: -0.39 (0.68), residues: 61 loop : -1.42 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A1048 TYR 0.037 0.002 TYR A 274 PHE 0.020 0.002 PHE A 824 TRP 0.006 0.001 TRP A 971 HIS 0.012 0.002 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (11695) covalent geometry : angle 0.66452 / 0.35 (16060) hydrogen bonds : bond 0.06556 / 4.19 ( 655) hydrogen bonds : angle 4.83684 / 3.46 ( 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 192 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 156 time to evaluate : 0.397 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: 0.8703 (tp30) cc_final: 0.7870 (tm-30) REVERT: B 20 GLU cc_start: 0.9306 (mm-30) cc_final: 0.8761 (mm-30) REVERT: A 29 ARG cc_start: 0.8134 (mpt180) cc_final: 0.7868 (mpt180) REVERT: A 68 PHE cc_start: 0.9094 (m-10) cc_final: 0.8767 (m-80) REVERT: A 140 LYS cc_start: 0.7885 (tttt) cc_final: 0.7522 (mmtt) REVERT: A 210 LEU cc_start: 0.9298 (mt) cc_final: 0.9080 (pp) REVERT: A 330 LYS cc_start: 0.9236 (pptt) cc_final: 0.8935 (pptt) REVERT: A 406 MET cc_start: 0.6854 (mpp) cc_final: 0.6558 (mpp) REVERT: A 548 LYS cc_start: 0.8708 (mtmm) cc_final: 0.8340 (mtmt) REVERT: A 549 ASN cc_start: 0.8555 (m-40) cc_final: 0.6881 (t0) REVERT: A 556 PHE cc_start: 0.8066 (t80) cc_final: 0.7800 (t80) REVERT: A 590 ASP cc_start: 0.8201 (m-30) cc_final: 0.7845 (m-30) REVERT: A 716 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.7865 (tm-30) REVERT: A 762 PHE cc_start: 0.8259 (t80) cc_final: 0.8007 (t80) REVERT: A 766 LEU cc_start: 0.9253 (mt) cc_final: 0.8961 (mt) REVERT: A 785 GLN cc_start: 0.8954 (OUTLIER) cc_final: 0.8669 (mm-40) REVERT: A 801 ASN cc_start: 0.8524 (m-40) cc_final: 0.8208 (m-40) REVERT: A 978 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.8186 (ttm110) REVERT: A 1086 MET cc_start: 0.9044 (mmm) cc_final: 0.7760 (mmm) REVERT: A 1143 LEU cc_start: 0.8534 (tp) cc_final: 0.8297 (tt) outliers start: 36 outliers final: 23 residues processed: 183 average time/residue: 0.0962 time to fit residues: 25.6756 Evaluate side-chains 167 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 61 GLN 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 170 SER 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 298 ILE Chi-restraints excluded: chain A residue 394 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 704 ILE Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 964 LEU Chi-restraints excluded: chain A residue 978 ARG Chi-restraints excluded: chain A residue 1018 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 102 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 12 optimal weight: 20.0000 chunk 104 optimal weight: 1.9990 chunk 118 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 41 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 39 optimal weight: 0.7980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 659 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.108847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.088907 restraints weight = 37819.530| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 4.13 r_work (final): 0.3932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7716 moved from start: 0.3973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 11695 Z= 0.156 Angle : 0.641 13.714 16060 Z= 0.342 Chirality : 0.040 0.308 1813 Planarity : 0.003 0.037 1773 Dihedral : 15.740 135.666 2394 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.36 % Allowed : 23.78 % Favored : 72.87 % 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: 0.43 (0.24), residues: 1170 helix: 1.05 (0.18), residues: 792 sheet: -0.52 (0.67), residues: 61 loop : -1.41 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 405 TYR 0.030 0.002 TYR A 274 PHE 0.020 0.002 PHE A 680 TRP 0.005 0.001 TRP A 971 HIS 0.011 0.002 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.16 (11695) covalent geometry : angle 0.64125 / 0.34 (16060) hydrogen bonds : bond 0.06271 / 4.07 ( 655) hydrogen bonds : angle 4.73262 / 3.37 ( 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 177 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 142 time to evaluate : 0.399 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: B 16 GLU cc_start: 0.8724 (tp30) cc_final: 0.7896 (tm-30) REVERT: B 20 GLU cc_start: 0.9319 (mm-30) cc_final: 0.8740 (mm-30) REVERT: A 29 ARG cc_start: 0.8151 (mpt180) cc_final: 0.7893 (mpt180) REVERT: A 68 PHE cc_start: 0.9121 (m-10) cc_final: 0.8796 (m-80) REVERT: A 140 LYS cc_start: 0.7889 (tttt) cc_final: 0.7446 (mmtt) REVERT: A 210 LEU cc_start: 0.9296 (mt) cc_final: 0.9080 (pp) REVERT: A 330 LYS cc_start: 0.9240 (pptt) cc_final: 0.8979 (pptt) REVERT: A 406 MET cc_start: 0.6885 (mpp) cc_final: 0.6678 (mpp) REVERT: A 529 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8306 (tt) REVERT: A 556 PHE cc_start: 0.8110 (t80) cc_final: 0.7834 (t80) REVERT: A 716 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.7823 (tm-30) REVERT: A 766 LEU cc_start: 0.9208 (mt) cc_final: 0.8993 (mt) REVERT: A 785 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8689 (mm-40) REVERT: A 1143 LEU cc_start: 0.8519 (tp) cc_final: 0.8277 (tt) outliers start: 35 outliers final: 23 residues processed: 168 average time/residue: 0.0868 time to fit residues: 21.4321 Evaluate side-chains 161 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 61 GLN 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 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 437 VAL Chi-restraints excluded: chain A residue 529 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 785 GLN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 871 LEU 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 1094 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 67 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 80 optimal weight: 7.9990 chunk 104 optimal weight: 0.0970 chunk 84 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 29 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 59 optimal weight: 9.9990 chunk 118 optimal weight: 10.0000 overall best weight: 3.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.106500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.086364 restraints weight = 38577.340| |-----------------------------------------------------------------------------| r_work (start): 0.3883 rms_B_bonded: 4.18 r_work (final): 0.3883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.4182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11695 Z= 0.232 Angle : 0.681 13.728 16060 Z= 0.368 Chirality : 0.042 0.292 1813 Planarity : 0.004 0.039 1773 Dihedral : 15.790 138.185 2394 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 3.45 % Allowed : 23.59 % Favored : 72.96 % 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: 0.29 (0.24), residues: 1170 helix: 0.93 (0.18), residues: 791 sheet: -0.73 (0.66), residues: 63 loop : -1.39 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 405 TYR 0.025 0.002 TYR A 274 PHE 0.016 0.002 PHE A 824 TRP 0.002 0.001 TRP A 971 HIS 0.010 0.002 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00491 / 0.23 (11695) covalent geometry : angle 0.68133 / 0.37 (16060) hydrogen bonds : bond 0.06856 / 4.45 ( 655) hydrogen bonds : angle 4.87117 / 3.47 ( 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 173 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.284 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: B 16 GLU cc_start: 0.8760 (tp30) cc_final: 0.8089 (tm-30) REVERT: B 20 GLU cc_start: 0.9331 (mm-30) cc_final: 0.8816 (mm-30) REVERT: A 29 ARG cc_start: 0.8078 (mpt180) cc_final: 0.7839 (mpt180) REVERT: A 68 PHE cc_start: 0.9152 (m-10) cc_final: 0.8804 (m-80) REVERT: A 330 LYS cc_start: 0.9255 (pptt) cc_final: 0.9021 (pptt) REVERT: A 406 MET cc_start: 0.6848 (mpp) cc_final: 0.6638 (mpp) REVERT: A 529 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8312 (tt) REVERT: A 556 PHE cc_start: 0.8191 (t80) cc_final: 0.7920 (t80) REVERT: A 716 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8498 (tm-30) REVERT: A 762 PHE cc_start: 0.8246 (t80) cc_final: 0.7967 (t80) REVERT: A 766 LEU cc_start: 0.9266 (mt) cc_final: 0.9050 (mt) REVERT: A 1143 LEU cc_start: 0.8586 (tp) cc_final: 0.8190 (tt) outliers start: 36 outliers final: 22 residues processed: 166 average time/residue: 0.0905 time to fit residues: 22.4135 Evaluate side-chains 159 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 166 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 394 LEU Chi-restraints excluded: chain A residue 507 ILE Chi-restraints excluded: chain A residue 529 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 838 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 880 TYR Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 992 ILE 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: 0.8980 chunk 39 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 414 ASN ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** 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 = 0.4310 r_free = 0.4310 target = 0.109120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.089000 restraints weight = 38137.215| |-----------------------------------------------------------------------------| r_work (start): 0.3922 rms_B_bonded: 4.21 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.4172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 11695 Z= 0.149 Angle : 0.664 17.010 16060 Z= 0.348 Chirality : 0.041 0.407 1813 Planarity : 0.003 0.041 1773 Dihedral : 15.740 135.499 2394 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.59 % Allowed : 24.07 % 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: 0.34 (0.24), residues: 1170 helix: 0.98 (0.18), residues: 793 sheet: -0.63 (0.68), residues: 63 loop : -1.43 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 405 TYR 0.028 0.002 TYR A 274 PHE 0.020 0.002 PHE A 680 TRP 0.004 0.001 TRP A 971 HIS 0.012 0.002 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (11695) covalent geometry : angle 0.66388 / 0.35 (16060) hydrogen bonds : bond 0.06116 / 3.94 ( 655) hydrogen bonds : angle 4.74217 / 3.36 ( 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 171 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 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: B 16 GLU cc_start: 0.8762 (tp30) cc_final: 0.8473 (tm-30) REVERT: A 29 ARG cc_start: 0.8127 (mpt180) cc_final: 0.7882 (mpt180) REVERT: A 68 PHE cc_start: 0.9105 (m-10) cc_final: 0.8779 (m-80) REVERT: A 330 LYS cc_start: 0.9236 (pptt) cc_final: 0.8993 (pptt) REVERT: A 529 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8309 (tt) REVERT: A 556 PHE cc_start: 0.8061 (t80) cc_final: 0.7834 (t80) REVERT: A 716 GLU cc_start: 0.8799 (OUTLIER) cc_final: 0.7774 (tm-30) REVERT: A 1024 GLU cc_start: 0.9163 (pm20) cc_final: 0.8683 (pm20) REVERT: A 1086 MET cc_start: 0.8874 (mmm) cc_final: 0.7650 (mtp) REVERT: A 1143 LEU cc_start: 0.8526 (tp) cc_final: 0.8310 (tt) outliers start: 27 outliers final: 20 residues processed: 167 average time/residue: 0.0863 time to fit residues: 21.3728 Evaluate side-chains 160 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 166 VAL Chi-restraints excluded: chain A residue 170 SER Chi-restraints excluded: chain A residue 214 ASN Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 414 ASN Chi-restraints excluded: chain A residue 529 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 704 ILE Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1094 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 93 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 109 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 115 optimal weight: 0.9990 chunk 116 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN ** A 659 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** 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 = 0.4306 r_free = 0.4306 target = 0.108923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.088871 restraints weight = 38501.716| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 4.21 r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.4215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.259 11695 Z= 0.265 Angle : 1.113 59.120 16060 Z= 0.669 Chirality : 0.046 0.825 1813 Planarity : 0.004 0.058 1773 Dihedral : 15.749 135.485 2394 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.82 % Favored : 97.09 % Rotamer: Outliers : 2.40 % Allowed : 25.12 % Favored : 72.48 % Cbeta Deviations : 0.17 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.34 (0.24), residues: 1170 helix: 0.98 (0.18), residues: 793 sheet: -0.60 (0.68), residues: 63 loop : -1.44 (0.32), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 542 TYR 0.038 0.002 TYR A 784 PHE 0.020 0.002 PHE A 680 TRP 0.003 0.001 TRP A 971 HIS 0.011 0.002 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00529 / 0.26 (11695) covalent geometry : angle 1.11257 / 0.67 (16060) hydrogen bonds : bond 0.06108 / 3.93 ( 655) hydrogen bonds : angle 4.73734 / 3.36 ( 1867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1964.76 seconds wall clock time: 35 minutes 5.07 seconds (2105.07 seconds total)