Starting phenix.real_space_refine on Wed Aug 5 20:39:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9mvs_48668/08_2026/9mvs_48668.cif Found real_map, /net/cci-nas-00/data/ceres_data/9mvs_48668/08_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_48668/08_2026/9mvs_48668.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9mvs_48668/08_2026/9mvs_48668.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9mvs_48668/08_2026/9mvs_48668.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9mvs_48668/08_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-2.2rc3-6140/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: 2.29, per 1000 atoms: 0.20 Number of scatterers: 11346 At special positions: 0 Unit cell: (81.4233, 111.372, 120.731, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 73 15.00 O 2347 8.00 N 1922 7.00 C 6980 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.96 Conformation dependent library (CDL) restraints added in 495.8 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: 1.10 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: 2.51 Time building geometry restraints manager: 1.26 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=" P A C 28 " pdb=" O5' A C 28 " ideal model delta sigma weight residual 1.593 1.617 -0.024 1.00e-02 1.00e+04 5.85e+00 ... (remaining 11690 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 15597 1.58 - 3.17: 422 3.17 - 4.75: 25 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=" O5' U C 25 " pdb=" C5' U C 25 " pdb=" C4' U C 25 " ideal model delta sigma weight residual 109.40 113.05 -3.65 8.00e-01 1.56e+00 2.08e+01 angle pdb=" O5' C C 24 " pdb=" C5' C C 24 " pdb=" C4' C C 24 " ideal model delta sigma weight residual 109.40 112.91 -3.51 8.00e-01 1.56e+00 1.92e+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 ... (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: 1727 0.104 - 0.208: 81 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: 1.120 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: 0.030 Process input model: 12.240 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.740 ------------------------------------------------------------------------------- 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 : 0.003 0.035 11695 Z= 0.184 Angle : 0.575 7.918 16060 Z= 0.426 Chirality : 0.048 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 0.00251 / 0.18 (11695) covalent geometry : angle 0.57527 / 0.43 (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 : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7327 (mmt90) REVERT: A 68 PHE cc_start: 0.9073 (m-10) cc_final: 0.8798 (m-80) REVERT: A 163 ILE cc_start: 0.6116 (tp) cc_final: 0.5905 (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: 0.8386 (ptpp) REVERT: A 655 LEU cc_start: 0.9155 (mt) cc_final: 0.8820 (mt) 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: 0.8948 (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: 0.7331 (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: 0.8273 (mmm) outliers start: 26 outliers final: 9 residues processed: 327 average time/residue: 0.1115 time to fit residues: 50.3804 Evaluate side-chains 188 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 176 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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: 0.0770 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 30.0000 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 6.9990 overall best weight: 0.5158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 GLN A 139 ASN A 214 ASN A 235 ASN A 352 ASN A 659 GLN A 719 GLN ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 901 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.114816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.095138 restraints weight = 36796.170| |-----------------------------------------------------------------------------| r_work (start): 0.4031 rms_B_bonded: 4.14 r_work (final): 0.4031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7556 moved from start: 0.2168 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= 0.151 Angle : 0.622 13.491 16060 Z= 0.333 Chirality : 0.038 0.163 1813 Planarity : 0.003 0.041 1773 Dihedral : 15.841 129.178 2414 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 4.03 % Allowed : 15.24 % Favored : 80.73 % 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: 0.91 (0.24), residues: 1170 helix: 1.41 (0.18), residues: 785 sheet: -0.58 (0.61), residues: 69 loop : -1.10 (0.32), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 224 TYR 0.026 0.002 TYR B 57 PHE 0.024 0.002 PHE A 556 TRP 0.006 0.001 TRP A 971 HIS 0.014 0.002 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (11695) covalent geometry : angle 0.62248 / 0.33 (16060) hydrogen bonds : bond 0.06162 / 4.08 ( 655) hydrogen bonds : angle 4.68034 / 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 239 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.303 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: B 43 LEU cc_start: 0.7955 (tp) cc_final: 0.7414 (tp) REVERT: B 51 LEU cc_start: 0.9151 (OUTLIER) cc_final: 0.8944 (pp) REVERT: A 29 ARG cc_start: 0.7990 (mpt180) cc_final: 0.7626 (mmt90) REVERT: A 68 PHE cc_start: 0.9072 (m-10) cc_final: 0.8786 (m-80) REVERT: A 130 PHE cc_start: 0.7785 (m-80) cc_final: 0.7504 (m-80) REVERT: A 133 ASP cc_start: 0.8585 (m-30) cc_final: 0.8157 (p0) REVERT: A 194 GLU cc_start: 0.8318 (pp20) cc_final: 0.8083 (pp20) REVERT: A 210 LEU cc_start: 0.9214 (mt) cc_final: 0.8964 (pp) REVERT: A 254 MET cc_start: 0.5919 (tpt) cc_final: 0.5659 (tpt) REVERT: A 264 MET cc_start: 0.7693 (mpp) cc_final: 0.7430 (mpp) REVERT: A 274 TYR cc_start: 0.7639 (t80) cc_final: 0.7297 (t80) REVERT: A 442 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8335 (tttm) REVERT: A 529 LEU cc_start: 0.8547 (OUTLIER) cc_final: 0.8065 (tp) REVERT: A 542 ARG cc_start: 0.8447 (ttp-170) cc_final: 0.8215 (ptt-90) REVERT: A 548 LYS cc_start: 0.8888 (mtmm) cc_final: 0.8271 (ptpt) REVERT: A 549 ASN cc_start: 0.8650 (m-40) cc_final: 0.6771 (t0) REVERT: A 590 ASP cc_start: 0.8228 (m-30) cc_final: 0.7960 (m-30) REVERT: A 605 LEU cc_start: 0.9430 (OUTLIER) cc_final: 0.9190 (tt) REVERT: A 609 MET cc_start: 0.8338 (mmt) cc_final: 0.7938 (mmm) REVERT: A 762 PHE cc_start: 0.8244 (t80) cc_final: 0.7934 (t80) REVERT: A 766 LEU cc_start: 0.9218 (mt) cc_final: 0.8923 (mt) REVERT: A 768 LEU cc_start: 0.9204 (mt) cc_final: 0.8914 (mt) REVERT: A 801 ASN cc_start: 0.8499 (m-40) cc_final: 0.8204 (m-40) REVERT: A 837 GLU cc_start: 0.8522 (mp0) cc_final: 0.8288 (mp0) REVERT: A 1041 GLU cc_start: 0.9384 (mt-10) cc_final: 0.8916 (mp0) REVERT: A 1066 GLU cc_start: 0.8441 (mt-10) cc_final: 0.8226 (mt-10) REVERT: A 1086 MET cc_start: 0.8994 (mmm) cc_final: 0.8148 (mmm) outliers start: 42 outliers final: 22 residues processed: 219 average time/residue: 0.0891 time to fit residues: 27.7865 Evaluate side-chains 187 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 45 GLU Chi-restraints excluded: chain B residue 51 LEU 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 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 529 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 605 LEU Chi-restraints excluded: chain A residue 659 GLN 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: 4.9990 chunk 25 optimal weight: 0.9990 chunk 48 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 120 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 61 GLN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 352 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 414 ASN A 659 GLN ** A 719 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 A 908 HIS 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 = 0.107758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.087790 restraints weight = 37790.932| |-----------------------------------------------------------------------------| r_work (start): 0.3907 rms_B_bonded: 4.11 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 11695 Z= 0.288 Angle : 0.725 10.923 16060 Z= 0.392 Chirality : 0.044 0.191 1813 Planarity : 0.004 0.035 1773 Dihedral : 15.887 134.797 2407 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 24.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.93 % Allowed : 17.16 % Favored : 78.91 % 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: 0.51 (0.24), residues: 1170 helix: 1.06 (0.18), residues: 791 sheet: -0.45 (0.55), residues: 84 loop : -1.27 (0.34), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 377 TYR 0.022 0.002 TYR B 32 PHE 0.023 0.002 PHE A 556 TRP 0.006 0.002 TRP A 971 HIS 0.017 0.002 HIS A 908 Details of bonding type rmsd/Z covalent geometry : bond 0.00601 / 0.29 (11695) covalent geometry : angle 0.72506 / 0.39 (16060) hydrogen bonds : bond 0.07218 / 4.74 ( 655) hydrogen bonds : angle 4.88859 / 3.53 ( 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 216 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 175 time to evaluate : 0.421 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: 0.8615 (tp30) cc_final: 0.7962 (tp30) REVERT: B 20 GLU cc_start: 0.9323 (mm-30) cc_final: 0.8959 (mm-30) REVERT: A 29 ARG cc_start: 0.7918 (mpt180) cc_final: 0.7701 (mpt180) REVERT: A 68 PHE cc_start: 0.9146 (m-10) cc_final: 0.8853 (m-80) REVERT: A 130 PHE cc_start: 0.7792 (m-80) cc_final: 0.7572 (m-80) REVERT: A 133 ASP cc_start: 0.8587 (m-30) cc_final: 0.8164 (p0) REVERT: A 163 ILE cc_start: 0.5819 (tp) cc_final: 0.5573 (tp) REVERT: A 210 LEU cc_start: 0.9284 (mt) cc_final: 0.9035 (pp) REVERT: A 254 MET cc_start: 0.6052 (tpt) cc_final: 0.5632 (tpt) REVERT: A 264 MET cc_start: 0.7780 (mpp) cc_final: 0.7459 (mpp) REVERT: A 274 TYR cc_start: 0.8096 (t80) cc_final: 0.7858 (t80) REVERT: A 330 LYS cc_start: 0.9293 (pptt) cc_final: 0.9060 (pptt) REVERT: A 406 MET cc_start: 0.7139 (OUTLIER) cc_final: 0.6930 (mpp) REVERT: A 442 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8513 (tttm) REVERT: A 542 ARG cc_start: 0.8607 (ttp-170) cc_final: 0.8264 (ptt-90) REVERT: A 548 LYS cc_start: 0.8971 (mtmm) cc_final: 0.8459 (ptpt) REVERT: A 556 PHE cc_start: 0.8475 (t80) cc_final: 0.8164 (t80) REVERT: A 590 ASP cc_start: 0.8460 (m-30) cc_final: 0.8198 (m-30) REVERT: A 762 PHE cc_start: 0.8292 (t80) cc_final: 0.7991 (t80) REVERT: A 766 LEU cc_start: 0.9308 (mt) cc_final: 0.8972 (mt) REVERT: A 768 LEU cc_start: 0.9228 (mt) cc_final: 0.8895 (mt) REVERT: A 785 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8729 (mm-40) REVERT: A 801 ASN cc_start: 0.8633 (m-40) cc_final: 0.8354 (m-40) REVERT: A 837 GLU cc_start: 0.8622 (mp0) cc_final: 0.8411 (mp0) REVERT: A 897 ILE cc_start: 0.8013 (pt) cc_final: 0.7600 (mm) REVERT: A 1041 GLU cc_start: 0.9428 (mt-10) cc_final: 0.8975 (mp0) REVERT: A 1046 TYR cc_start: 0.8259 (m-80) cc_final: 0.8004 (m-80) REVERT: A 1086 MET cc_start: 0.9121 (mmm) cc_final: 0.8486 (mmm) outliers start: 41 outliers final: 23 residues processed: 203 average time/residue: 0.0936 time to fit residues: 27.4240 Evaluate side-chains 180 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 155 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 529 LEU Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 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 1131 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: 7.9990 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 9.9990 chunk 107 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 92 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 ASN ** A 139 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 214 ASN A 352 ASN A 414 ASN A 463 ASN A 614 ASN A 659 GLN ** A 719 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 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.108042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.087513 restraints weight = 39105.922| |-----------------------------------------------------------------------------| r_work (start): 0.3905 rms_B_bonded: 4.30 r_work (final): 0.3905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7736 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 11695 Z= 0.229 Angle : 0.665 10.782 16060 Z= 0.360 Chirality : 0.042 0.253 1813 Planarity : 0.004 0.060 1773 Dihedral : 15.915 132.858 2403 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.12 % Allowed : 18.79 % Favored : 77.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1170 helix: 1.04 (0.18), residues: 790 sheet: -0.58 (0.60), residues: 72 loop : -1.32 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 224 TYR 0.017 0.002 TYR A 537 PHE 0.037 0.002 PHE A 848 TRP 0.004 0.001 TRP A 971 HIS 0.009 0.002 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.23 (11695) covalent geometry : angle 0.66514 / 0.36 (16060) hydrogen bonds : bond 0.06986 / 4.55 ( 655) hydrogen bonds : angle 4.87855 / 3.50 ( 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 211 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 168 time to evaluate : 0.280 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: 0.8695 (tp30) cc_final: 0.8142 (tp30) REVERT: B 20 GLU cc_start: 0.9347 (mm-30) cc_final: 0.9030 (mm-30) REVERT: A 68 PHE cc_start: 0.9153 (m-10) cc_final: 0.8846 (m-80) REVERT: A 130 PHE cc_start: 0.7967 (m-80) cc_final: 0.7758 (m-80) REVERT: A 133 ASP cc_start: 0.8514 (m-30) cc_final: 0.8097 (p0) REVERT: A 210 LEU cc_start: 0.9287 (mt) cc_final: 0.9052 (pp) REVERT: A 274 TYR cc_start: 0.8098 (t80) cc_final: 0.7848 (t80) REVERT: A 332 LEU cc_start: 0.9310 (tp) cc_final: 0.9090 (tt) REVERT: A 406 MET cc_start: 0.7130 (OUTLIER) cc_final: 0.6844 (mpp) REVERT: A 442 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8500 (tttp) REVERT: A 542 ARG cc_start: 0.8717 (ttp-170) cc_final: 0.8366 (ptt-90) REVERT: A 548 LYS cc_start: 0.8857 (mtmm) cc_final: 0.8242 (ptpp) REVERT: A 556 PHE cc_start: 0.8387 (t80) cc_final: 0.8158 (t80) REVERT: A 590 ASP cc_start: 0.8452 (m-30) cc_final: 0.8178 (m-30) REVERT: A 716 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.7988 (tm-30) REVERT: A 762 PHE cc_start: 0.8322 (t80) cc_final: 0.8018 (t80) REVERT: A 766 LEU cc_start: 0.9312 (mt) cc_final: 0.8963 (mt) REVERT: A 768 LEU cc_start: 0.9213 (mt) cc_final: 0.8905 (mt) REVERT: A 785 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8688 (mm-40) REVERT: A 801 ASN cc_start: 0.8586 (m-40) cc_final: 0.8280 (m-40) REVERT: A 897 ILE cc_start: 0.7942 (pt) cc_final: 0.7583 (mm) REVERT: A 978 ARG cc_start: 0.8698 (OUTLIER) cc_final: 0.8208 (ttm110) REVERT: A 1041 GLU cc_start: 0.9409 (mt-10) cc_final: 0.8970 (mp0) REVERT: A 1086 MET cc_start: 0.9148 (mmm) cc_final: 0.8080 (mmm) outliers start: 43 outliers final: 23 residues processed: 201 average time/residue: 0.0954 time to fit residues: 27.7501 Evaluate side-chains 175 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LYS 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 216 THR Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 546 VAL Chi-restraints excluded: chain A residue 559 LEU Chi-restraints excluded: chain A residue 580 ASN Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain A residue 655 LEU Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 716 GLU Chi-restraints excluded: chain A residue 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 978 ARG Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1039 LYS Chi-restraints excluded: chain A residue 1057 ILE 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: 6.9990 chunk 25 optimal weight: 0.9980 chunk 118 optimal weight: 20.0000 chunk 57 optimal weight: 2.9990 chunk 47 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 107 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 598 ASN ** A 731 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 785 GLN ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.109942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.089970 restraints weight = 37448.174| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 4.12 r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.3420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11695 Z= 0.157 Angle : 0.615 11.149 16060 Z= 0.334 Chirality : 0.040 0.311 1813 Planarity : 0.003 0.047 1773 Dihedral : 15.820 130.764 2401 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 4.41 % Allowed : 18.79 % Favored : 76.80 % 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: 0.54 (0.24), residues: 1170 helix: 1.12 (0.18), residues: 793 sheet: -0.54 (0.62), residues: 72 loop : -1.31 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 405 TYR 0.026 0.002 TYR A 537 PHE 0.020 0.002 PHE A 680 TRP 0.005 0.001 TRP A 971 HIS 0.011 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (11695) covalent geometry : angle 0.61499 / 0.33 (16060) hydrogen bonds : bond 0.06371 / 4.15 ( 655) hydrogen bonds : angle 4.78741 / 3.43 ( 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: 46 poor density : 166 time to evaluate : 0.409 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: 0.8689 (tp30) cc_final: 0.8407 (tp30) REVERT: B 32 TYR cc_start: 0.7954 (OUTLIER) cc_final: 0.7627 (t80) REVERT: A 29 ARG cc_start: 0.8048 (mpt180) cc_final: 0.7768 (mpt180) REVERT: A 68 PHE cc_start: 0.9106 (m-10) cc_final: 0.8799 (m-80) REVERT: A 130 PHE cc_start: 0.7896 (m-80) cc_final: 0.7690 (m-80) REVERT: A 133 ASP cc_start: 0.8529 (m-30) cc_final: 0.8105 (p0) REVERT: A 171 LYS cc_start: 0.7382 (OUTLIER) cc_final: 0.7175 (mttm) REVERT: A 330 LYS cc_start: 0.9258 (pptt) cc_final: 0.8969 (pptt) REVERT: A 406 MET cc_start: 0.7060 (OUTLIER) cc_final: 0.6845 (mpp) REVERT: A 442 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8432 (tttm) REVERT: A 542 ARG cc_start: 0.8621 (ttp-170) cc_final: 0.8272 (ptt-90) REVERT: A 548 LYS cc_start: 0.8738 (mtmm) cc_final: 0.8050 (ptpp) REVERT: A 549 ASN cc_start: 0.8301 (m-40) cc_final: 0.6263 (t0) REVERT: A 556 PHE cc_start: 0.8277 (t80) cc_final: 0.7965 (t80) REVERT: A 590 ASP cc_start: 0.8323 (m-30) cc_final: 0.7998 (m-30) REVERT: A 662 TYR cc_start: 0.8481 (t80) cc_final: 0.8122 (t80) REVERT: A 716 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.7955 (tm-30) REVERT: A 762 PHE cc_start: 0.8218 (t80) cc_final: 0.7897 (t80) REVERT: A 766 LEU cc_start: 0.9277 (mt) cc_final: 0.8987 (mt) REVERT: A 768 LEU cc_start: 0.9179 (mt) cc_final: 0.8879 (mt) REVERT: A 785 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.8732 (mm-40) REVERT: A 801 ASN cc_start: 0.8546 (m-40) cc_final: 0.8261 (m-40) REVERT: A 949 GLU cc_start: 0.7814 (pm20) cc_final: 0.7601 (pm20) REVERT: A 978 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8224 (ttm110) REVERT: A 1086 MET cc_start: 0.9122 (mmm) cc_final: 0.8026 (mmm) outliers start: 46 outliers final: 29 residues processed: 200 average time/residue: 0.1035 time to fit residues: 29.7006 Evaluate side-chains 183 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 148 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 171 LYS 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 406 MET Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 456 GLU 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 765 ILE Chi-restraints excluded: chain A residue 785 GLN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 834 ASP 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 1039 LYS Chi-restraints excluded: chain A residue 1057 ILE Chi-restraints excluded: chain A residue 1073 LYS Chi-restraints excluded: chain A residue 1094 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 61 optimal weight: 10.0000 chunk 121 optimal weight: 20.0000 chunk 68 optimal weight: 9.9990 chunk 56 optimal weight: 10.0000 chunk 89 optimal weight: 7.9990 chunk 27 optimal weight: 20.0000 chunk 102 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 659 GLN ** A 719 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 908 HIS ** 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 = 0.4237 r_free = 0.4237 target = 0.104255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.083890 restraints weight = 38864.702| |-----------------------------------------------------------------------------| r_work (start): 0.3837 rms_B_bonded: 4.15 r_work (final): 0.3837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 11695 Z= 0.337 Angle : 0.788 12.633 16060 Z= 0.419 Chirality : 0.047 0.236 1813 Planarity : 0.005 0.043 1773 Dihedral : 15.942 135.790 2399 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 26.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 5.18 % Allowed : 20.23 % Favored : 74.59 % 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: 0.09 (0.23), residues: 1170 helix: 0.78 (0.18), residues: 790 sheet: -0.70 (0.59), residues: 73 loop : -1.50 (0.33), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1072 TYR 0.029 0.003 TYR A 784 PHE 0.024 0.003 PHE A 977 TRP 0.005 0.002 TRP A 971 HIS 0.009 0.002 HIS A 11 Details of bonding type rmsd/Z covalent geometry : bond 0.00698 / 0.34 (11695) covalent geometry : angle 0.78849 / 0.42 (16060) hydrogen bonds : bond 0.08124 / 5.28 ( 655) hydrogen bonds : angle 5.06802 / 3.62 ( 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 199 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 145 time to evaluate : 0.416 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: 0.8749 (tp30) cc_final: 0.8034 (tm-30) REVERT: B 20 GLU cc_start: 0.9368 (mm-30) cc_final: 0.8874 (mm-30) REVERT: B 32 TYR cc_start: 0.8130 (OUTLIER) cc_final: 0.7820 (t80) REVERT: A 68 PHE cc_start: 0.9163 (m-10) cc_final: 0.8814 (m-80) REVERT: A 133 ASP cc_start: 0.8524 (m-30) cc_final: 0.8103 (p0) REVERT: A 274 TYR cc_start: 0.8221 (t80) cc_final: 0.8010 (t80) REVERT: A 406 MET cc_start: 0.7235 (OUTLIER) cc_final: 0.6892 (mpp) REVERT: A 529 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8400 (tt) REVERT: A 548 LYS cc_start: 0.8786 (mtmm) cc_final: 0.8403 (mtmm) REVERT: A 556 PHE cc_start: 0.8386 (t80) cc_final: 0.7976 (t80) REVERT: A 716 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8418 (tm-30) REVERT: A 762 PHE cc_start: 0.8364 (t80) cc_final: 0.8051 (t80) REVERT: A 766 LEU cc_start: 0.9349 (mt) cc_final: 0.9023 (mt) REVERT: A 801 ASN cc_start: 0.8669 (m-40) cc_final: 0.8326 (m110) REVERT: A 897 ILE cc_start: 0.7861 (pt) cc_final: 0.7473 (mm) REVERT: A 978 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8254 (ttm110) REVERT: A 1041 GLU cc_start: 0.9451 (mt-10) cc_final: 0.9076 (mp0) REVERT: A 1046 TYR cc_start: 0.8637 (m-80) cc_final: 0.8141 (m-80) REVERT: A 1086 MET cc_start: 0.9159 (mmm) cc_final: 0.8146 (mmm) outliers start: 54 outliers final: 37 residues processed: 187 average time/residue: 0.0974 time to fit residues: 26.7890 Evaluate side-chains 178 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 136 time to evaluate : 0.343 ------------------------------------------------------------------------------- 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 B residue 61 GLN Chi-restraints excluded: chain A residue 9 ILE 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 208 LEU Chi-restraints excluded: chain A residue 214 ASN 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 406 MET Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 456 GLU 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 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 832 VAL Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 853 ILE 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 1131 LEU Chi-restraints excluded: chain A residue 1148 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 49 optimal weight: 2.9990 chunk 112 optimal weight: 3.9990 chunk 50 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 99 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 214 ASN A 235 ASN A 271 GLN A 659 GLN ** A 719 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 908 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.107759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.087361 restraints weight = 38825.265| |-----------------------------------------------------------------------------| r_work (start): 0.3902 rms_B_bonded: 4.24 r_work (final): 0.3902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 11695 Z= 0.169 Angle : 0.661 12.833 16060 Z= 0.351 Chirality : 0.041 0.324 1813 Planarity : 0.003 0.043 1773 Dihedral : 15.845 132.007 2397 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 4.31 % Allowed : 22.34 % 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: 0.32 (0.24), residues: 1170 helix: 0.97 (0.18), residues: 791 sheet: -0.45 (0.68), residues: 61 loop : -1.48 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 180 TYR 0.022 0.002 TYR A 537 PHE 0.020 0.002 PHE A 680 TRP 0.006 0.001 TRP A 971 HIS 0.011 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.17 (11695) covalent geometry : angle 0.66077 / 0.35 (16060) hydrogen bonds : bond 0.06963 / 4.49 ( 655) hydrogen bonds : angle 4.84997 / 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 194 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 149 time to evaluate : 0.420 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: 0.8740 (tp30) cc_final: 0.8030 (tm-30) REVERT: B 20 GLU cc_start: 0.9391 (mm-30) cc_final: 0.8897 (mm-30) REVERT: B 32 TYR cc_start: 0.8309 (OUTLIER) cc_final: 0.7995 (t80) REVERT: A 29 ARG cc_start: 0.8056 (mpt180) cc_final: 0.7780 (mpt180) REVERT: A 68 PHE cc_start: 0.9160 (m-10) cc_final: 0.8835 (m-80) REVERT: A 130 PHE cc_start: 0.7785 (m-80) cc_final: 0.7562 (m-80) REVERT: A 133 ASP cc_start: 0.8486 (m-30) cc_final: 0.8072 (p0) REVERT: A 274 TYR cc_start: 0.7969 (t80) cc_final: 0.7755 (t80) REVERT: A 330 LYS cc_start: 0.9244 (pptt) cc_final: 0.8939 (pptt) REVERT: A 442 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8436 (tttm) REVERT: A 529 LEU cc_start: 0.8598 (OUTLIER) cc_final: 0.8356 (tt) REVERT: A 548 LYS cc_start: 0.8653 (mtmm) cc_final: 0.8432 (mtmm) REVERT: A 556 PHE cc_start: 0.8262 (t80) cc_final: 0.7896 (t80) REVERT: A 590 ASP cc_start: 0.8304 (m-30) cc_final: 0.8024 (m-30) REVERT: A 716 GLU cc_start: 0.8818 (OUTLIER) cc_final: 0.8362 (tm-30) REVERT: A 762 PHE cc_start: 0.8272 (t80) cc_final: 0.7963 (t80) REVERT: A 766 LEU cc_start: 0.9254 (mt) cc_final: 0.8931 (mt) REVERT: A 801 ASN cc_start: 0.8552 (m-40) cc_final: 0.8228 (m-40) REVERT: A 978 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8216 (ttm110) REVERT: A 1041 GLU cc_start: 0.9423 (mt-10) cc_final: 0.9021 (mp0) REVERT: A 1086 MET cc_start: 0.9116 (mmm) cc_final: 0.7992 (mmm) outliers start: 45 outliers final: 30 residues processed: 180 average time/residue: 0.1036 time to fit residues: 27.2947 Evaluate side-chains 172 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 137 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 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 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 442 LYS 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 655 LEU Chi-restraints excluded: chain A residue 659 GLN 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 834 ASP Chi-restraints excluded: chain A residue 838 LEU Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 884 ILE 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 1073 LYS Chi-restraints excluded: chain A residue 1094 LYS Chi-restraints excluded: chain A residue 1131 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 102 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 12 optimal weight: 20.0000 chunk 104 optimal weight: 0.0670 chunk 118 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 75 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 1.0722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 659 GLN ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 788 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** 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 = 0.4318 r_free = 0.4318 target = 0.109390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.089122 restraints weight = 37939.037| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 4.31 r_work (final): 0.3940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.3970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11695 Z= 0.138 Angle : 0.640 12.200 16060 Z= 0.338 Chirality : 0.040 0.323 1813 Planarity : 0.003 0.040 1773 Dihedral : 15.677 130.021 2394 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 19.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 3.64 % Allowed : 23.78 % Favored : 72.58 % 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: 0.48 (0.24), residues: 1170 helix: 1.10 (0.18), residues: 791 sheet: -0.35 (0.70), residues: 61 loop : -1.47 (0.31), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 224 TYR 0.022 0.002 TYR A 537 PHE 0.016 0.002 PHE A 824 TRP 0.006 0.001 TRP A 971 HIS 0.012 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.14 (11695) covalent geometry : angle 0.64021 / 0.34 (16060) hydrogen bonds : bond 0.06188 / 4.00 ( 655) hydrogen bonds : angle 4.70832 / 3.35 ( 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 187 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.443 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: 0.8778 (tp30) cc_final: 0.7999 (tm-30) REVERT: B 20 GLU cc_start: 0.9404 (mm-30) cc_final: 0.8895 (mm-30) REVERT: B 32 TYR cc_start: 0.8375 (OUTLIER) cc_final: 0.8132 (t80) REVERT: B 48 PHE cc_start: 0.8798 (m-80) cc_final: 0.8540 (m-80) REVERT: A 29 ARG cc_start: 0.8138 (mpt180) cc_final: 0.7866 (mpt180) REVERT: A 68 PHE cc_start: 0.9122 (m-10) cc_final: 0.8799 (m-80) REVERT: A 274 TYR cc_start: 0.7966 (t80) cc_final: 0.7722 (t80) REVERT: A 330 LYS cc_start: 0.9237 (pptt) cc_final: 0.8966 (pptt) REVERT: A 442 LYS cc_start: 0.8803 (OUTLIER) cc_final: 0.8386 (tttm) REVERT: A 529 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8329 (tt) REVERT: A 548 LYS cc_start: 0.8706 (mtmm) cc_final: 0.8285 (mtmm) REVERT: A 549 ASN cc_start: 0.8245 (m-40) cc_final: 0.6465 (t0) REVERT: A 556 PHE cc_start: 0.8123 (t80) cc_final: 0.7784 (t80) REVERT: A 590 ASP cc_start: 0.8326 (m-30) cc_final: 0.8083 (m-30) REVERT: A 716 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: A 801 ASN cc_start: 0.8528 (m-40) cc_final: 0.8193 (m-40) REVERT: A 949 GLU cc_start: 0.7946 (pm20) cc_final: 0.7613 (pm20) REVERT: A 996 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7715 (tm-30) REVERT: A 1041 GLU cc_start: 0.9428 (mt-10) cc_final: 0.8998 (mp0) REVERT: A 1086 MET cc_start: 0.9126 (mmm) cc_final: 0.7915 (mmm) outliers start: 38 outliers final: 26 residues processed: 181 average time/residue: 0.1058 time to fit residues: 28.1162 Evaluate side-chains 170 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 139 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 TYR 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 208 LEU Chi-restraints excluded: chain A residue 216 THR 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 442 LYS 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 807 ASN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 996 GLU Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1039 LYS Chi-restraints excluded: chain A residue 1057 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 67 optimal weight: 3.9990 chunk 12 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 84 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 59 optimal weight: 10.0000 chunk 118 optimal weight: 20.0000 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 719 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 908 HIS ** 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 = 0.4265 r_free = 0.4265 target = 0.105993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.085653 restraints weight = 38401.744| |-----------------------------------------------------------------------------| r_work (start): 0.3863 rms_B_bonded: 4.21 r_work (final): 0.3863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.4213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.089 11695 Z= 0.244 Angle : 0.710 12.485 16060 Z= 0.376 Chirality : 0.043 0.288 1813 Planarity : 0.004 0.049 1773 Dihedral : 15.753 133.512 2394 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 23.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 4.03 % Allowed : 24.16 % Favored : 71.81 % 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: 1.00 (0.18), residues: 792 sheet: -0.65 (0.67), residues: 61 loop : -1.49 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 180 TYR 0.019 0.002 TYR A 245 PHE 0.015 0.002 PHE A 604 TRP 0.004 0.001 TRP A 971 HIS 0.009 0.002 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00520 / 0.24 (11695) covalent geometry : angle 0.70979 / 0.38 (16060) hydrogen bonds : bond 0.06979 / 4.54 ( 655) hydrogen bonds : angle 4.85452 / 3.45 ( 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 177 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 135 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 16 GLU cc_start: 0.8791 (tp30) cc_final: 0.8404 (tm-30) REVERT: B 32 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.8110 (t80) REVERT: A 29 ARG cc_start: 0.8085 (mpt180) cc_final: 0.7823 (mpt180) REVERT: A 68 PHE cc_start: 0.9141 (m-10) cc_final: 0.8794 (m-80) REVERT: A 274 TYR cc_start: 0.8095 (t80) cc_final: 0.7877 (t80) REVERT: A 330 LYS cc_start: 0.9236 (pptt) cc_final: 0.8991 (pptt) REVERT: A 442 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8426 (tttm) REVERT: A 529 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8346 (tt) REVERT: A 548 LYS cc_start: 0.8676 (mtmm) cc_final: 0.8115 (ptpt) REVERT: A 549 ASN cc_start: 0.8341 (m-40) cc_final: 0.6670 (t0) REVERT: A 556 PHE cc_start: 0.8249 (t80) cc_final: 0.7930 (t80) REVERT: A 716 GLU cc_start: 0.8792 (OUTLIER) cc_final: 0.8367 (tm-30) REVERT: A 801 ASN cc_start: 0.8589 (m-40) cc_final: 0.8267 (m-40) REVERT: A 1041 GLU cc_start: 0.9422 (mt-10) cc_final: 0.9035 (mp0) REVERT: A 1086 MET cc_start: 0.9119 (mmm) cc_final: 0.7970 (mmm) REVERT: A 1118 GLU cc_start: 0.8220 (tm-30) cc_final: 0.7881 (tm-30) outliers start: 42 outliers final: 27 residues processed: 169 average time/residue: 0.1014 time to fit residues: 25.6970 Evaluate side-chains 165 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 45 GLU 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 208 LEU Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 251 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 442 LYS Chi-restraints excluded: chain A residue 456 GLU 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 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 807 ASN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 834 ASP 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 992 ILE Chi-restraints excluded: chain A residue 1018 GLU Chi-restraints excluded: chain A residue 1057 ILE Chi-restraints excluded: chain A residue 1131 LEU Chi-restraints excluded: chain A residue 1148 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 97 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 115 optimal weight: 0.0060 chunk 30 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 12 optimal weight: 20.0000 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 414 ASN ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 751 ASN ** A 908 HIS ** 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 = 0.4325 r_free = 0.4325 target = 0.109723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.089569 restraints weight = 37796.360| |-----------------------------------------------------------------------------| r_work (start): 0.3938 rms_B_bonded: 4.23 r_work (final): 0.3938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.4199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 11695 Z= 0.140 Angle : 0.661 13.207 16060 Z= 0.347 Chirality : 0.040 0.348 1813 Planarity : 0.003 0.039 1773 Dihedral : 15.719 129.764 2394 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 19.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.07 % Allowed : 25.50 % Favored : 71.43 % 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: 0.40 (0.24), residues: 1170 helix: 1.07 (0.18), residues: 791 sheet: -0.65 (0.68), residues: 61 loop : -1.52 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 370 TYR 0.025 0.002 TYR A 387 PHE 0.028 0.002 PHE A 848 TRP 0.004 0.001 TRP A 971 HIS 0.013 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (11695) covalent geometry : angle 0.66104 / 0.35 (16060) hydrogen bonds : bond 0.05951 / 3.83 ( 655) hydrogen bonds : angle 4.72716 / 3.35 ( 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 180 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.431 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: 0.8800 (tp30) cc_final: 0.7997 (tm-30) REVERT: B 20 GLU cc_start: 0.9410 (mm-30) cc_final: 0.8864 (mm-30) REVERT: B 32 TYR cc_start: 0.8448 (OUTLIER) cc_final: 0.8223 (t80) REVERT: B 48 PHE cc_start: 0.8796 (m-80) cc_final: 0.8540 (m-10) REVERT: A 29 ARG cc_start: 0.8121 (mpt180) cc_final: 0.7877 (mpt180) REVERT: A 68 PHE cc_start: 0.9083 (m-10) cc_final: 0.8764 (m-80) REVERT: A 274 TYR cc_start: 0.7985 (t80) cc_final: 0.7754 (t80) REVERT: A 330 LYS cc_start: 0.9223 (pptt) cc_final: 0.8976 (pptt) REVERT: A 442 LYS cc_start: 0.8736 (OUTLIER) cc_final: 0.8310 (tttm) REVERT: A 548 LYS cc_start: 0.8740 (mtmm) cc_final: 0.8461 (mtmm) REVERT: A 556 PHE cc_start: 0.8077 (t80) cc_final: 0.7795 (t80) REVERT: A 716 GLU cc_start: 0.8764 (OUTLIER) cc_final: 0.8322 (tm-30) REVERT: A 801 ASN cc_start: 0.8509 (m-40) cc_final: 0.8208 (m-40) REVERT: A 1041 GLU cc_start: 0.9379 (mt-10) cc_final: 0.9009 (mp0) REVERT: A 1086 MET cc_start: 0.9047 (mmm) cc_final: 0.7801 (mmm) REVERT: A 1136 ASN cc_start: 0.7530 (m110) cc_final: 0.7120 (m110) outliers start: 32 outliers final: 22 residues processed: 174 average time/residue: 0.1070 time to fit residues: 27.3373 Evaluate side-chains 164 residues out of total 1102 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 32 TYR Chi-restraints excluded: chain B residue 45 GLU 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 208 LEU 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 442 LYS 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 807 ASN Chi-restraints excluded: chain A residue 832 VAL Chi-restraints excluded: chain A residue 834 ASP Chi-restraints excluded: chain A residue 871 LEU Chi-restraints excluded: chain A residue 884 ILE Chi-restraints excluded: chain A residue 935 ILE Chi-restraints excluded: chain A residue 961 LEU Chi-restraints excluded: chain A residue 1018 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 93 optimal weight: 9.9990 chunk 97 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 chunk 115 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 47 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 GLN ** A 719 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 751 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 908 HIS ** 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 = 0.4323 r_free = 0.4323 target = 0.109598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.089399 restraints weight = 38418.010| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 4.27 r_work (final): 0.3950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.4221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.140 11695 Z= 0.221 Angle : 0.928 59.166 16060 Z= 0.546 Chirality : 0.041 0.301 1813 Planarity : 0.004 0.045 1773 Dihedral : 15.713 129.752 2394 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 21.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.97 % Allowed : 25.79 % Favored : 71.24 % Cbeta Deviations : 0.09 % 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: 0.39 (0.24), residues: 1170 helix: 1.07 (0.18), residues: 791 sheet: -0.65 (0.68), residues: 61 loop : -1.53 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 180 TYR 0.045 0.002 TYR A 784 PHE 0.039 0.002 PHE A 848 TRP 0.004 0.001 TRP A 971 HIS 0.012 0.001 HIS A 962 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.22 (11695) covalent geometry : angle 0.92780 / 0.55 (16060) hydrogen bonds : bond 0.05953 / 3.83 ( 655) hydrogen bonds : angle 4.72485 / 3.35 ( 1867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2103.85 seconds wall clock time: 37 minutes 22.28 seconds (2242.28 seconds total)