Starting phenix.real_space_refine on Fri Jul 3 04:19:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nl2_49515/07_2026/9nl2_49515.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nl2_49515/07_2026/9nl2_49515.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nl2_49515/07_2026/9nl2_49515.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nl2_49515/07_2026/9nl2_49515.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nl2_49515/07_2026/9nl2_49515.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nl2_49515/07_2026/9nl2_49515.map" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 121 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Zn 4 6.06 5 P 159 5.49 5 Mg 1 5.21 5 S 50 5.16 5 C 7134 2.51 5 N 2172 2.21 5 O 2618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12138 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 8854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1107, 8854 Classifications: {'peptide': 1107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 56, 'TRANS': 1049} Chain breaks: 1 Chain: "B" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 791 Classifications: {'DNA': 39} Link IDs: {'rna3p': 38} Chain: "P" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "R" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 1140 Classifications: {'RNA': 53} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 3, 'rna3p_pur': 24, 'rna3p_pyr': 18} Link IDs: {'rna2p': 11, 'rna3p': 41} Chain breaks: 2 Chain: "T" Number of atoms: 1052 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 1052 Classifications: {'DNA': 51} Link IDs: {'rna3p': 50} Chain: "A" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 34 Unusual residues: {' MG': 1, ' ZN': 4, 'TTP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 107 SG CYS A 14 79.077 95.346 69.639 1.00 95.68 S ATOM 131 SG CYS A 17 82.012 97.787 70.031 1.00101.52 S ATOM 340 SG CYS A 44 60.507 92.311 61.054 1.00 92.73 S ATOM 360 SG CYS A 47 57.484 89.668 62.141 1.00101.78 S ATOM 489 SG CYS A 64 57.087 92.335 59.338 1.00 99.79 S ATOM 594 SG CYS A 78 47.731 69.980 70.976 1.00 86.36 S ATOM 616 SG CYS A 81 50.695 72.437 70.309 1.00 87.31 S ATOM 7380 SG CYS A 941 93.349 100.820 36.648 1.00 91.42 S ATOM 7405 SG CYS A 944 95.312 102.733 33.786 1.00 83.84 S ATOM 7509 SG CYS A 958 96.971 100.002 35.868 1.00 91.83 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" C1' TTP A1206 " occ=0.65 ... (27 atoms not shown) pdb=" PG TTP A1206 " occ=0.65 Time building chain proxies: 2.86, per 1000 atoms: 0.24 Number of scatterers: 12138 At special positions: 0 Unit cell: (133.096, 119.472, 100.608, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 4 29.99 S 50 16.00 P 159 15.00 Mg 1 11.99 O 2618 8.00 N 2172 7.00 C 7134 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: 1.12 Conformation dependent library (CDL) restraints added in 417.6 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1202 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 35 " pdb="ZN ZN A1202 " - pdb=" NE2 HIS A 30 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 17 " pdb="ZN ZN A1202 " - pdb=" SG CYS A 14 " pdb=" ZN A1203 " pdb="ZN ZN A1203 " - pdb=" NE2 HIS A 60 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 64 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 44 " pdb="ZN ZN A1203 " - pdb=" SG CYS A 47 " pdb=" ZN A1204 " pdb="ZN ZN A1204 " - pdb=" NE2 HIS A 99 " pdb="ZN ZN A1204 " - pdb=" NE2 HIS A 94 " pdb="ZN ZN A1204 " - pdb=" SG CYS A 81 " pdb="ZN ZN A1204 " - pdb=" SG CYS A 78 " pdb=" ZN A1205 " pdb="ZN ZN A1205 " - pdb=" NE2 HIS A 953 " pdb="ZN ZN A1205 " - pdb=" SG CYS A 958 " pdb="ZN ZN A1205 " - pdb=" SG CYS A 941 " pdb="ZN ZN A1205 " - pdb=" SG CYS A 944 " Number of angles added : 10 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2100 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 10 sheets defined 55.0% alpha, 5.7% beta 55 base pairs and 100 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 53 through 64 removed outlier: 3.737A pdb=" N ILE A 57 " --> pdb=" O LYS A 53 " (cutoff:3.500A) Proline residue: A 62 - end of helix Processing helix chain 'A' and resid 87 through 99 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 127 through 141 Processing helix chain 'A' and resid 149 through 155 removed outlier: 4.226A pdb=" N ASP A 153 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ILE A 155 " --> pdb=" O ILE A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 170 Processing helix chain 'A' and resid 203 through 220 removed outlier: 3.628A pdb=" N THR A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 239 through 256 Processing helix chain 'A' and resid 284 through 301 Processing helix chain 'A' and resid 303 through 313 Processing helix chain 'A' and resid 322 through 335 Processing helix chain 'A' and resid 353 through 358 removed outlier: 3.563A pdb=" N ALA A 356 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 372 Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 396 through 410 Processing helix chain 'A' and resid 413 through 417 Processing helix chain 'A' and resid 429 through 435 removed outlier: 4.211A pdb=" N GLU A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 464 Processing helix chain 'A' and resid 477 through 497 removed outlier: 3.736A pdb=" N GLU A 481 " --> pdb=" O PRO A 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 524 Processing helix chain 'A' and resid 529 through 540 Processing helix chain 'A' and resid 568 through 588 removed outlier: 4.600A pdb=" N LEU A 572 " --> pdb=" O PRO A 568 " (cutoff:3.500A) Proline residue: A 580 - end of helix Processing helix chain 'A' and resid 614 through 633 Processing helix chain 'A' and resid 662 through 666 Processing helix chain 'A' and resid 694 through 708 Processing helix chain 'A' and resid 712 through 724 Processing helix chain 'A' and resid 724 through 735 removed outlier: 3.737A pdb=" N ILE A 728 " --> pdb=" O THR A 724 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LEU A 731 " --> pdb=" O ARG A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 758 Processing helix chain 'A' and resid 764 through 770 removed outlier: 3.575A pdb=" N ILE A 768 " --> pdb=" O CYS A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 775 Processing helix chain 'A' and resid 781 through 799 Proline residue: A 787 - end of helix Processing helix chain 'A' and resid 802 through 812 removed outlier: 3.618A pdb=" N ASN A 812 " --> pdb=" O ILE A 808 " (cutoff:3.500A) Processing helix chain 'A' and resid 813 through 825 removed outlier: 3.751A pdb=" N GLU A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 846 through 853 removed outlier: 3.581A pdb=" N LEU A 853 " --> pdb=" O ILE A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 882 removed outlier: 3.617A pdb=" N LEU A 882 " --> pdb=" O HIS A 878 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 904 removed outlier: 4.074A pdb=" N GLN A 903 " --> pdb=" O ASN A 899 " (cutoff:3.500A) Processing helix chain 'A' and resid 909 through 922 Processing helix chain 'A' and resid 926 through 931 Processing helix chain 'A' and resid 950 through 957 Processing helix chain 'A' and resid 958 through 960 No H-bonds generated for 'chain 'A' and resid 958 through 960' Processing helix chain 'A' and resid 961 through 983 Processing helix chain 'A' and resid 1026 through 1038 removed outlier: 4.546A pdb=" N GLU A1030 " --> pdb=" O GLU A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1040 through 1042 No H-bonds generated for 'chain 'A' and resid 1040 through 1042' Processing helix chain 'A' and resid 1043 through 1052 Processing helix chain 'A' and resid 1070 through 1081 removed outlier: 3.940A pdb=" N GLU A1074 " --> pdb=" O PRO A1070 " (cutoff:3.500A) Processing helix chain 'A' and resid 1083 through 1120 removed outlier: 4.984A pdb=" N GLY A1113 " --> pdb=" O PHE A1109 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N LYS A1114 " --> pdb=" O GLU A1110 " (cutoff:3.500A) removed outlier: 5.568A pdb=" N ASN A1116 " --> pdb=" O ILE A1112 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'A' and resid 76 through 77 Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 425 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 604 removed outlier: 3.519A pdb=" N GLY A 643 " --> pdb=" O ASN A 669 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 507 through 508 removed outlier: 4.479A pdb=" N LYS A 635 " --> pdb=" O ALA A 508 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 548 through 549 Processing sheet with id=AA7, first strand: chain 'A' and resid 684 through 685 Processing sheet with id=AA8, first strand: chain 'A' and resid 841 through 842 Processing sheet with id=AA9, first strand: chain 'A' and resid 986 through 989 Processing sheet with id=AB1, first strand: chain 'A' and resid 1018 through 1021 removed outlier: 6.450A pdb=" N THR A1019 " --> pdb=" O LEU A1063 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 438 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 139 hydrogen bonds 270 hydrogen bond angles 0 basepair planarities 55 basepair parallelities 100 stacking parallelities Total time for adding SS restraints: 2.61 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2628 1.33 - 1.45: 3408 1.45 - 1.57: 6290 1.57 - 1.70: 311 1.70 - 1.82: 73 Bond restraints: 12710 Sorted by residual: bond pdb=" O3B TTP A1206 " pdb=" PG TTP A1206 " ideal model delta sigma weight residual 1.748 1.606 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" C1' DC B 24 " pdb=" N1 DC B 24 " ideal model delta sigma weight residual 1.468 1.536 -0.068 1.40e-02 5.10e+03 2.35e+01 bond pdb=" C1' DC T 11 " pdb=" N1 DC T 11 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" C1' DT B 55 " pdb=" N1 DT B 55 " ideal model delta sigma weight residual 1.468 1.530 -0.062 1.40e-02 5.10e+03 1.95e+01 bond pdb=" C1' DC T 9 " pdb=" N1 DC T 9 " ideal model delta sigma weight residual 1.468 1.528 -0.060 1.40e-02 5.10e+03 1.85e+01 ... (remaining 12705 not shown) Histogram of bond angle deviations from ideal: 0.00 - 8.30: 17875 8.30 - 16.61: 5 16.61 - 24.91: 2 24.91 - 33.22: 4 33.22 - 41.52: 1 Bond angle restraints: 17887 Sorted by residual: angle pdb=" OP1 DC B 57 " pdb=" P DC B 57 " pdb=" OP2 DC B 57 " ideal model delta sigma weight residual 120.00 78.48 41.52 3.00e+00 1.11e-01 1.92e+02 angle pdb=" O3' DA B 56 " pdb=" P DC B 57 " pdb=" OP1 DC B 57 " ideal model delta sigma weight residual 108.00 76.01 31.99 3.00e+00 1.11e-01 1.14e+02 angle pdb=" OP2 DC B 57 " pdb=" P DC B 57 " pdb=" O5' DC B 57 " ideal model delta sigma weight residual 108.00 76.63 31.37 3.00e+00 1.11e-01 1.09e+02 angle pdb=" O3' DA B 56 " pdb=" P DC B 57 " pdb=" OP2 DC B 57 " ideal model delta sigma weight residual 108.00 139.35 -31.35 3.00e+00 1.11e-01 1.09e+02 angle pdb=" O3' DA B 28 " pdb=" P DA B 29 " pdb=" OP1 DA B 29 " ideal model delta sigma weight residual 108.00 80.96 27.04 3.00e+00 1.11e-01 8.13e+01 ... (remaining 17882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.71: 6684 33.71 - 67.41: 789 67.41 - 101.12: 40 101.12 - 134.83: 3 134.83 - 168.54: 5 Dihedral angle restraints: 7521 sinusoidal: 4293 harmonic: 3228 Sorted by residual: dihedral pdb=" O4' U R 248 " pdb=" C1' U R 248 " pdb=" N1 U R 248 " pdb=" C2 U R 248 " ideal model delta sinusoidal sigma weight residual 200.00 76.20 123.80 1 1.50e+01 4.44e-03 6.64e+01 dihedral pdb=" CA PRO A 477 " pdb=" C PRO A 477 " pdb=" N GLY A 478 " pdb=" CA GLY A 478 " ideal model delta harmonic sigma weight residual 180.00 156.23 23.77 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA GLN A 524 " pdb=" C GLN A 524 " pdb=" N GLU A 525 " pdb=" CA GLU A 525 " ideal model delta harmonic sigma weight residual -180.00 -156.83 -23.17 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 7518 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.398: 2041 0.398 - 0.796: 0 0.796 - 1.193: 0 1.193 - 1.591: 0 1.591 - 1.989: 1 Chirality restraints: 2042 Sorted by residual: chirality pdb=" P DA B 29 " pdb=" OP1 DA B 29 " pdb=" OP2 DA B 29 " pdb=" O5' DA B 29 " both_signs ideal model delta sigma weight residual True 2.34 0.35 1.99 2.00e-01 2.50e+01 9.89e+01 chirality pdb=" C3' DT B 35 " pdb=" C4' DT B 35 " pdb=" O3' DT B 35 " pdb=" C2' DT B 35 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.72e-01 chirality pdb=" C3' DC T 31 " pdb=" C4' DC T 31 " pdb=" O3' DC T 31 " pdb=" C2' DC T 31 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 2039 not shown) Planarity restraints: 1718 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 138 " 0.013 2.00e-02 2.50e+03 2.67e-02 7.11e+00 pdb=" CG ASN A 138 " -0.046 2.00e-02 2.50e+03 pdb=" OD1 ASN A 138 " 0.017 2.00e-02 2.50e+03 pdb=" ND2 ASN A 138 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC B 61 " -0.026 2.00e-02 2.50e+03 1.65e-02 6.15e+00 pdb=" N1 DC B 61 " 0.025 2.00e-02 2.50e+03 pdb=" C2 DC B 61 " 0.029 2.00e-02 2.50e+03 pdb=" O2 DC B 61 " -0.006 2.00e-02 2.50e+03 pdb=" N3 DC B 61 " -0.014 2.00e-02 2.50e+03 pdb=" C4 DC B 61 " 0.001 2.00e-02 2.50e+03 pdb=" N4 DC B 61 " -0.009 2.00e-02 2.50e+03 pdb=" C5 DC B 61 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC B 61 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET A 282 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.94e+00 pdb=" C MET A 282 " -0.042 2.00e-02 2.50e+03 pdb=" O MET A 282 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU A 283 " 0.014 2.00e-02 2.50e+03 ... (remaining 1715 not shown) Histogram of nonbonded interaction distances: 1.83 - 2.44: 84 2.44 - 3.06: 8236 3.06 - 3.67: 20676 3.67 - 4.29: 30295 4.29 - 4.90: 46744 Nonbonded interactions: 106035 Sorted by model distance: nonbonded pdb="MG MG A1201 " pdb=" O1B TTP A1206 " model vdw 1.829 2.170 nonbonded pdb=" OG1 THR A 740 " pdb=" OP2 DA T 33 " model vdw 1.901 3.040 nonbonded pdb=" OG SER A 593 " pdb=" OD2 ASP A 613 " model vdw 1.907 3.040 nonbonded pdb=" O ILE A 251 " pdb=" OG1 THR A 254 " model vdw 1.934 3.040 nonbonded pdb=" N2 DG B 60 " pdb=" O2 DC T 11 " model vdw 1.984 3.120 ... (remaining 106030 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=0.65 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.860 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.142 12726 Z= 0.386 Angle : 0.960 41.522 17897 Z= 0.571 Chirality : 0.066 1.989 2042 Planarity : 0.004 0.044 1718 Dihedral : 23.620 168.536 5421 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.54 % Allowed : 7.43 % Favored : 92.02 % Rotamer: Outliers : 0.30 % Allowed : 20.41 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.18 (0.26), residues: 1103 helix: 1.52 (0.23), residues: 530 sheet: -0.92 (0.60), residues: 63 loop : -1.28 (0.28), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 934 TYR 0.010 0.001 TYR A 330 PHE 0.018 0.001 PHE A1059 TRP 0.005 0.001 TRP A 615 HIS 0.005 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00503 / 0.39 (12710) covalent geometry : angle 0.95473 / 0.57 (17887) hydrogen bonds : bond 0.11330 / 7.87 ( 577) hydrogen bonds : angle 6.36050 / 4.81 ( 1533) metal coordination : bond 0.01366 / 0.72 ( 16) metal coordination : angle 4.46498 / 2.83 ( 10) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 97 time to evaluate : 0.388 Fit side-chains revert: symmetry clash REVERT: A 400 GLU cc_start: 0.8251 (tt0) cc_final: 0.8045 (tt0) outliers start: 3 outliers final: 3 residues processed: 100 average time/residue: 0.1119 time to fit residues: 15.6600 Evaluate side-chains 92 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 944 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 20.0000 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 154 HIS A 589 ASN A 894 ASN A 962 GLN A 969 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.153411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.114152 restraints weight = 18976.990| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 1.84 r_work: 0.3251 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3117 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3117 r_free = 0.3117 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.65 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3114 r_free = 0.3114 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (10 function evaluations) r_final: 0.3114 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.0883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 12726 Z= 0.210 Angle : 0.914 40.292 17897 Z= 0.437 Chirality : 0.065 2.044 2042 Planarity : 0.005 0.046 1718 Dihedral : 25.738 177.239 3151 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.89 % Favored : 92.66 % Rotamer: Outliers : 2.54 % Allowed : 19.49 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.33 (0.26), residues: 1103 helix: 1.60 (0.23), residues: 541 sheet: -0.76 (0.59), residues: 63 loop : -1.24 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 546 TYR 0.013 0.002 TYR A 330 PHE 0.014 0.002 PHE A 908 TRP 0.008 0.001 TRP A 661 HIS 0.008 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.21 (12710) covalent geometry : angle 0.91144 / 0.44 (17887) hydrogen bonds : bond 0.05941 / 3.89 ( 577) hydrogen bonds : angle 5.03915 / 3.70 ( 1533) metal coordination : bond 0.00874 / 0.45 ( 16) metal coordination : angle 2.93938 / 1.92 ( 10) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 99 time to evaluate : 0.399 Fit side-chains REVERT: A 33 ARG cc_start: 0.7597 (tpp80) cc_final: 0.6786 (mmm-85) REVERT: A 281 TRP cc_start: 0.6689 (m100) cc_final: 0.6308 (t-100) REVERT: A 400 GLU cc_start: 0.8489 (tt0) cc_final: 0.8264 (tt0) REVERT: A 607 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7663 (m-30) REVERT: A 834 ARG cc_start: 0.8568 (mtp85) cc_final: 0.7957 (mtm-85) REVERT: A 1038 ARG cc_start: 0.7539 (mtm-85) cc_final: 0.7287 (mtm-85) REVERT: A 1049 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6430 (mt-10) outliers start: 25 outliers final: 16 residues processed: 113 average time/residue: 0.1162 time to fit residues: 18.8584 Evaluate side-chains 108 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 359 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 607 ASP Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 61 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 74 optimal weight: 0.3980 chunk 41 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 110 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 13 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.153148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114126 restraints weight = 19053.001| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.68 r_work: 0.3236 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.88 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3244 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 12726 Z= 0.181 Angle : 0.885 40.522 17897 Z= 0.417 Chirality : 0.062 1.979 2042 Planarity : 0.005 0.037 1718 Dihedral : 25.704 176.103 3148 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.98 % Favored : 93.56 % Rotamer: Outliers : 2.64 % Allowed : 19.39 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.36 (0.26), residues: 1103 helix: 1.65 (0.23), residues: 541 sheet: -0.83 (0.55), residues: 69 loop : -1.25 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 294 TYR 0.011 0.002 TYR A 723 PHE 0.014 0.001 PHE A 908 TRP 0.007 0.001 TRP A 233 HIS 0.007 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.18 (12710) covalent geometry : angle 0.88325 / 0.42 (17887) hydrogen bonds : bond 0.05396 / 3.46 ( 577) hydrogen bonds : angle 4.83889 / 3.56 ( 1533) metal coordination : bond 0.00799 / 0.42 ( 16) metal coordination : angle 2.49207 / 1.71 ( 10) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.429 Fit side-chains REVERT: A 33 ARG cc_start: 0.7487 (tpp80) cc_final: 0.6644 (mmm-85) REVERT: A 96 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.7539 (ttp-170) REVERT: A 281 TRP cc_start: 0.6595 (m100) cc_final: 0.6221 (t-100) REVERT: A 400 GLU cc_start: 0.8206 (tt0) cc_final: 0.7973 (tt0) REVERT: A 697 GLU cc_start: 0.8411 (mp0) cc_final: 0.8189 (mp0) REVERT: A 834 ARG cc_start: 0.8401 (mtp85) cc_final: 0.7868 (mtm-85) REVERT: A 1038 ARG cc_start: 0.7286 (mtm-85) cc_final: 0.6975 (mtm-85) REVERT: A 1049 GLU cc_start: 0.6878 (mm-30) cc_final: 0.6393 (mt-10) outliers start: 26 outliers final: 19 residues processed: 115 average time/residue: 0.1239 time to fit residues: 20.3156 Evaluate side-chains 112 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 33 optimal weight: 0.0980 chunk 78 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 116 optimal weight: 10.0000 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 957 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.152225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.110814 restraints weight = 18895.023| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.90 r_work: 0.3218 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3082 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3086 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.94 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3086 r_free = 0.3086 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3086 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12726 Z= 0.176 Angle : 0.876 40.189 17897 Z= 0.409 Chirality : 0.062 1.967 2042 Planarity : 0.004 0.034 1718 Dihedral : 25.680 175.200 3148 Min Nonbonded Distance : 1.957 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.17 % Favored : 93.38 % Rotamer: Outliers : 3.25 % Allowed : 20.00 % Favored : 76.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.26), residues: 1103 helix: 1.67 (0.23), residues: 541 sheet: -0.75 (0.55), residues: 69 loop : -1.21 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1038 TYR 0.011 0.002 TYR A 723 PHE 0.014 0.001 PHE A 908 TRP 0.007 0.001 TRP A 985 HIS 0.006 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.18 (12710) covalent geometry : angle 0.87448 / 0.41 (17887) hydrogen bonds : bond 0.05159 / 3.28 ( 577) hydrogen bonds : angle 4.72956 / 3.47 ( 1533) metal coordination : bond 0.00781 / 0.40 ( 16) metal coordination : angle 2.34625 / 1.62 ( 10) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 100 time to evaluate : 0.390 Fit side-chains REVERT: A 33 ARG cc_start: 0.7606 (tpp80) cc_final: 0.6821 (mmm-85) REVERT: A 96 ARG cc_start: 0.7844 (OUTLIER) cc_final: 0.7589 (ttp-170) REVERT: A 281 TRP cc_start: 0.6543 (m100) cc_final: 0.6133 (t-100) REVERT: A 373 MET cc_start: 0.8780 (mtp) cc_final: 0.8476 (mtp) REVERT: A 400 GLU cc_start: 0.8451 (tt0) cc_final: 0.8158 (tt0) REVERT: A 697 GLU cc_start: 0.8700 (mp0) cc_final: 0.8471 (mp0) REVERT: A 834 ARG cc_start: 0.8600 (mtp85) cc_final: 0.7905 (mtm-85) REVERT: A 1049 GLU cc_start: 0.6864 (mm-30) cc_final: 0.6527 (mt-10) REVERT: A 1059 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7765 (p90) outliers start: 32 outliers final: 21 residues processed: 123 average time/residue: 0.1199 time to fit residues: 21.2357 Evaluate side-chains 119 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 106 optimal weight: 0.9990 chunk 12 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 112 optimal weight: 9.9990 chunk 61 optimal weight: 2.9990 chunk 7 optimal weight: 0.3980 chunk 50 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 589 ASN A 878 HIS A 903 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.153036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.112074 restraints weight = 19010.283| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 1.83 r_work: 0.3236 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3097 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3096 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3096 r_free = 0.3096 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3096 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12726 Z= 0.155 Angle : 0.863 40.060 17897 Z= 0.402 Chirality : 0.061 1.960 2042 Planarity : 0.004 0.037 1718 Dihedral : 25.617 174.901 3148 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.71 % Favored : 93.83 % Rotamer: Outliers : 2.94 % Allowed : 20.61 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.26), residues: 1103 helix: 1.74 (0.23), residues: 543 sheet: -0.72 (0.55), residues: 69 loop : -1.16 (0.28), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1038 TYR 0.014 0.002 TYR A 330 PHE 0.013 0.001 PHE A 908 TRP 0.008 0.001 TRP A 233 HIS 0.006 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (12710) covalent geometry : angle 0.86124 / 0.40 (17887) hydrogen bonds : bond 0.04909 / 3.09 ( 577) hydrogen bonds : angle 4.61030 / 3.36 ( 1533) metal coordination : bond 0.00713 / 0.35 ( 16) metal coordination : angle 2.20025 / 1.53 ( 10) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 108 time to evaluate : 0.392 Fit side-chains REVERT: A 33 ARG cc_start: 0.7594 (tpp80) cc_final: 0.6881 (mmm-85) REVERT: A 281 TRP cc_start: 0.6541 (m100) cc_final: 0.6130 (t-100) REVERT: A 358 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.7822 (mp0) REVERT: A 373 MET cc_start: 0.8779 (mtp) cc_final: 0.8405 (mtp) REVERT: A 400 GLU cc_start: 0.8449 (tt0) cc_final: 0.8145 (tt0) REVERT: A 697 GLU cc_start: 0.8695 (mp0) cc_final: 0.8449 (mp0) REVERT: A 834 ARG cc_start: 0.8562 (mtp85) cc_final: 0.7845 (mtm-85) REVERT: A 1038 ARG cc_start: 0.7385 (mtp-110) cc_final: 0.7003 (mtm-85) REVERT: A 1049 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6442 (mt-10) REVERT: A 1059 PHE cc_start: 0.8337 (OUTLIER) cc_final: 0.7689 (p90) outliers start: 29 outliers final: 22 residues processed: 128 average time/residue: 0.1251 time to fit residues: 22.7895 Evaluate side-chains 123 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 99 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 358 GLU Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 45 optimal weight: 0.7980 chunk 58 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 chunk 2 optimal weight: 2.9990 chunk 119 optimal weight: 40.0000 chunk 114 optimal weight: 10.0000 chunk 105 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 116 optimal weight: 10.0000 chunk 26 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 345 GLN A 894 ASN A 903 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.149386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.108490 restraints weight = 18994.928| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.03 r_work: 0.3170 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3026 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3026 r_free = 0.3026 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3026 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 12726 Z= 0.277 Angle : 0.926 39.949 17897 Z= 0.436 Chirality : 0.064 1.937 2042 Planarity : 0.005 0.045 1718 Dihedral : 25.716 173.547 3148 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.45 % Allowed : 6.26 % Favored : 93.29 % Rotamer: Outliers : 4.37 % Allowed : 19.80 % Favored : 75.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.18 (0.25), residues: 1103 helix: 1.47 (0.22), residues: 543 sheet: -0.87 (0.47), residues: 84 loop : -1.31 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 471 TYR 0.016 0.002 TYR A1040 PHE 0.019 0.002 PHE A 644 TRP 0.008 0.002 TRP A 856 HIS 0.007 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00615 / 0.28 (12710) covalent geometry : angle 0.92375 / 0.44 (17887) hydrogen bonds : bond 0.05562 / 3.62 ( 577) hydrogen bonds : angle 4.76328 / 3.49 ( 1533) metal coordination : bond 0.01115 / 0.68 ( 16) metal coordination : angle 2.70112 / 1.75 ( 10) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 100 time to evaluate : 0.393 Fit side-chains REVERT: A 33 ARG cc_start: 0.7721 (tpp80) cc_final: 0.7037 (mmm-85) REVERT: A 112 GLN cc_start: 0.8447 (mt0) cc_final: 0.8162 (mt0) REVERT: A 206 LYS cc_start: 0.7022 (mtpp) cc_final: 0.6648 (ttpt) REVERT: A 281 TRP cc_start: 0.6542 (m100) cc_final: 0.6050 (t-100) REVERT: A 373 MET cc_start: 0.8822 (mtp) cc_final: 0.8436 (mtp) REVERT: A 400 GLU cc_start: 0.8481 (tt0) cc_final: 0.8188 (tt0) REVERT: A 697 GLU cc_start: 0.8778 (mp0) cc_final: 0.8215 (mp0) REVERT: A 834 ARG cc_start: 0.8615 (mtp85) cc_final: 0.7883 (mtm-85) REVERT: A 1059 PHE cc_start: 0.8586 (OUTLIER) cc_final: 0.7937 (p90) outliers start: 43 outliers final: 28 residues processed: 132 average time/residue: 0.1252 time to fit residues: 23.4911 Evaluate side-chains 123 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 94 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 728 ILE Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 794 LEU Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 57 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 95 optimal weight: 0.9980 chunk 88 optimal weight: 0.4980 chunk 98 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.151926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.111407 restraints weight = 18949.094| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 1.78 r_work: 0.3207 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3210 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3210 r_free = 0.3210 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3210 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12726 Z= 0.160 Angle : 0.876 39.908 17897 Z= 0.405 Chirality : 0.061 1.959 2042 Planarity : 0.005 0.052 1718 Dihedral : 25.658 172.846 3148 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.80 % Favored : 93.83 % Rotamer: Outliers : 3.35 % Allowed : 21.32 % Favored : 75.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.38 (0.26), residues: 1103 helix: 1.62 (0.22), residues: 545 sheet: -0.76 (0.47), residues: 84 loop : -1.22 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A1038 TYR 0.012 0.002 TYR A 330 PHE 0.013 0.001 PHE A 908 TRP 0.009 0.001 TRP A 233 HIS 0.005 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.16 (12710) covalent geometry : angle 0.87436 / 0.40 (17887) hydrogen bonds : bond 0.04937 / 3.11 ( 577) hydrogen bonds : angle 4.60461 / 3.36 ( 1533) metal coordination : bond 0.00932 / 0.46 ( 16) metal coordination : angle 2.35328 / 1.63 ( 10) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 101 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7414 (tpp80) cc_final: 0.6732 (mmm-85) REVERT: A 112 GLN cc_start: 0.8257 (mt0) cc_final: 0.7965 (mt0) REVERT: A 281 TRP cc_start: 0.6359 (m100) cc_final: 0.5940 (t-100) REVERT: A 373 MET cc_start: 0.8722 (mtp) cc_final: 0.8299 (mtp) REVERT: A 400 GLU cc_start: 0.8279 (tt0) cc_final: 0.7983 (tt0) REVERT: A 697 GLU cc_start: 0.8544 (mp0) cc_final: 0.7940 (mp0) REVERT: A 834 ARG cc_start: 0.8464 (mtp85) cc_final: 0.7795 (mtm-85) REVERT: A 981 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7814 (mmmm) REVERT: A 1001 ARG cc_start: 0.6846 (mmt180) cc_final: 0.6370 (mmt90) REVERT: A 1009 LYS cc_start: 0.8075 (OUTLIER) cc_final: 0.7702 (ttpp) REVERT: A 1040 TYR cc_start: 0.7575 (m-80) cc_final: 0.7191 (m-80) REVERT: A 1059 PHE cc_start: 0.8397 (OUTLIER) cc_final: 0.7512 (p90) outliers start: 33 outliers final: 24 residues processed: 122 average time/residue: 0.1323 time to fit residues: 22.5490 Evaluate side-chains 123 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 96 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 535 ILE Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 103 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 101 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 903 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.152605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.112619 restraints weight = 18906.930| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.85 r_work: 0.3213 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3213 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12726 Z= 0.150 Angle : 0.860 39.905 17897 Z= 0.395 Chirality : 0.060 1.947 2042 Planarity : 0.004 0.042 1718 Dihedral : 25.564 172.452 3148 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.35 % Favored : 94.29 % Rotamer: Outliers : 2.94 % Allowed : 22.44 % Favored : 74.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.46 (0.26), residues: 1103 helix: 1.70 (0.22), residues: 545 sheet: -0.80 (0.47), residues: 84 loop : -1.17 (0.29), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 294 TYR 0.011 0.002 TYR A 330 PHE 0.013 0.001 PHE A 908 TRP 0.009 0.001 TRP A 233 HIS 0.004 0.001 HIS A 734 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.15 (12710) covalent geometry : angle 0.85900 / 0.40 (17887) hydrogen bonds : bond 0.04791 / 2.98 ( 577) hydrogen bonds : angle 4.51863 / 3.29 ( 1533) metal coordination : bond 0.00677 / 0.33 ( 16) metal coordination : angle 2.21452 / 1.51 ( 10) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 106 time to evaluate : 0.334 Fit side-chains REVERT: A 33 ARG cc_start: 0.7373 (tpp80) cc_final: 0.6764 (mmm-85) REVERT: A 373 MET cc_start: 0.8745 (mtp) cc_final: 0.8306 (mtp) REVERT: A 400 GLU cc_start: 0.8256 (tt0) cc_final: 0.7974 (tt0) REVERT: A 697 GLU cc_start: 0.8528 (mp0) cc_final: 0.8261 (mp0) REVERT: A 834 ARG cc_start: 0.8475 (mtp85) cc_final: 0.7765 (mtm-85) REVERT: A 957 GLN cc_start: 0.8357 (mm110) cc_final: 0.8111 (mm110) REVERT: A 1009 LYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7675 (ttpp) REVERT: A 1038 ARG cc_start: 0.7610 (ptt180) cc_final: 0.7368 (mtp-110) REVERT: A 1059 PHE cc_start: 0.8439 (OUTLIER) cc_final: 0.7577 (p90) outliers start: 29 outliers final: 23 residues processed: 126 average time/residue: 0.1239 time to fit residues: 22.1580 Evaluate side-chains 121 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 96 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 843 TYR Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1078 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 64 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 101 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 75 optimal weight: 0.6980 chunk 16 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.150496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.110286 restraints weight = 18958.487| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.88 r_work: 0.3174 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.2116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12726 Z= 0.220 Angle : 0.908 39.874 17897 Z= 0.417 Chirality : 0.062 1.926 2042 Planarity : 0.005 0.041 1718 Dihedral : 25.606 171.001 3148 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.53 % Favored : 94.11 % Rotamer: Outliers : 3.25 % Allowed : 21.93 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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 (0.26), residues: 1103 helix: 1.59 (0.22), residues: 547 sheet: -0.87 (0.46), residues: 84 loop : -1.22 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 33 TYR 0.012 0.002 TYR A 594 PHE 0.016 0.002 PHE A 644 TRP 0.008 0.001 TRP A 856 HIS 0.007 0.001 HIS A 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (12710) covalent geometry : angle 0.90636 / 0.42 (17887) hydrogen bonds : bond 0.05170 / 3.27 ( 577) hydrogen bonds : angle 4.59809 / 3.35 ( 1533) metal coordination : bond 0.00850 / 0.51 ( 16) metal coordination : angle 2.40270 / 1.58 ( 10) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 99 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7463 (tpp80) cc_final: 0.6838 (mmm-85) REVERT: A 373 MET cc_start: 0.8745 (mtp) cc_final: 0.8297 (mtp) REVERT: A 400 GLU cc_start: 0.8255 (tt0) cc_final: 0.7956 (tt0) REVERT: A 697 GLU cc_start: 0.8587 (mp0) cc_final: 0.8013 (mp0) REVERT: A 834 ARG cc_start: 0.8475 (mtp85) cc_final: 0.7813 (mtm-85) REVERT: A 981 LYS cc_start: 0.8158 (OUTLIER) cc_final: 0.7793 (mmmm) REVERT: A 1001 ARG cc_start: 0.6853 (mmt180) cc_final: 0.6390 (mmt90) REVERT: A 1009 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7779 (ttpp) REVERT: A 1059 PHE cc_start: 0.8546 (OUTLIER) cc_final: 0.7635 (p90) outliers start: 32 outliers final: 27 residues processed: 121 average time/residue: 0.1232 time to fit residues: 21.3187 Evaluate side-chains 124 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 852 LEU Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain A residue 1009 LYS Chi-restraints excluded: chain A residue 1051 THR Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1078 THR Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 22 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 95 optimal weight: 0.5980 chunk 69 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 87 optimal weight: 0.4980 chunk 12 optimal weight: 8.9990 chunk 109 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 812 ASN A 903 GLN A 957 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.152892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.112936 restraints weight = 19169.929| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.86 r_work: 0.3217 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3212 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3212 r_free = 0.3212 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3212 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12726 Z= 0.146 Angle : 0.875 39.830 17897 Z= 0.398 Chirality : 0.060 1.937 2042 Planarity : 0.004 0.043 1718 Dihedral : 25.545 170.651 3148 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.53 % Favored : 94.11 % Rotamer: Outliers : 2.54 % Allowed : 22.54 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.53 (0.26), residues: 1103 helix: 1.75 (0.23), residues: 546 sheet: -0.69 (0.48), residues: 84 loop : -1.14 (0.29), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1038 TYR 0.010 0.002 TYR A 330 PHE 0.013 0.001 PHE A 908 TRP 0.007 0.001 TRP A 871 HIS 0.003 0.001 HIS A1039 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.15 (12710) covalent geometry : angle 0.87406 / 0.40 (17887) hydrogen bonds : bond 0.04762 / 2.93 ( 577) hydrogen bonds : angle 4.51096 / 3.29 ( 1533) metal coordination : bond 0.00784 / 0.39 ( 16) metal coordination : angle 2.20119 / 1.55 ( 10) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.403 Fit side-chains revert: symmetry clash REVERT: A 33 ARG cc_start: 0.7347 (tpp80) cc_final: 0.6741 (mmm-85) REVERT: A 239 ASN cc_start: 0.8033 (p0) cc_final: 0.7699 (t0) REVERT: A 373 MET cc_start: 0.8738 (mtp) cc_final: 0.8287 (mtp) REVERT: A 400 GLU cc_start: 0.8255 (tt0) cc_final: 0.7987 (tt0) REVERT: A 697 GLU cc_start: 0.8527 (mp0) cc_final: 0.8002 (mp0) REVERT: A 834 ARG cc_start: 0.8469 (mtp85) cc_final: 0.7781 (mtm-85) REVERT: A 1001 ARG cc_start: 0.6806 (mmt180) cc_final: 0.6349 (mmt90) REVERT: A 1059 PHE cc_start: 0.8466 (OUTLIER) cc_final: 0.7590 (p90) outliers start: 25 outliers final: 24 residues processed: 118 average time/residue: 0.1249 time to fit residues: 21.0224 Evaluate side-chains 122 residues out of total 985 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 97 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 87 THR Chi-restraints excluded: chain A residue 89 SER Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 178 VAL Chi-restraints excluded: chain A residue 190 CYS Chi-restraints excluded: chain A residue 201 THR Chi-restraints excluded: chain A residue 228 GLU Chi-restraints excluded: chain A residue 304 CYS Chi-restraints excluded: chain A residue 376 ASN Chi-restraints excluded: chain A residue 538 ASP Chi-restraints excluded: chain A residue 547 MET Chi-restraints excluded: chain A residue 589 ASN Chi-restraints excluded: chain A residue 609 VAL Chi-restraints excluded: chain A residue 691 SER Chi-restraints excluded: chain A residue 764 CYS Chi-restraints excluded: chain A residue 780 THR Chi-restraints excluded: chain A residue 784 SER Chi-restraints excluded: chain A residue 835 ILE Chi-restraints excluded: chain A residue 939 VAL Chi-restraints excluded: chain A residue 1059 PHE Chi-restraints excluded: chain A residue 1120 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 95 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 119 optimal weight: 40.0000 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 chunk 29 optimal weight: 0.7980 chunk 58 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.152888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.113021 restraints weight = 18973.772| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.84 r_work: 0.3222 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.96 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12726 Z= 0.150 Angle : 0.873 39.817 17897 Z= 0.397 Chirality : 0.060 1.923 2042 Planarity : 0.004 0.042 1718 Dihedral : 25.490 170.636 3148 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.36 % Allowed : 4.99 % Favored : 94.65 % Rotamer: Outliers : 2.84 % Allowed : 22.44 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.75 % 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: 0.57 (0.26), residues: 1103 helix: 1.74 (0.22), residues: 549 sheet: -0.68 (0.48), residues: 84 loop : -1.07 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1038 TYR 0.011 0.002 TYR A 330 PHE 0.013 0.001 PHE A 908 TRP 0.007 0.001 TRP A 871 HIS 0.004 0.001 HIS A 878 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.15 (12710) covalent geometry : angle 0.87171 / 0.40 (17887) hydrogen bonds : bond 0.04739 / 2.91 ( 577) hydrogen bonds : angle 4.46986 / 3.25 ( 1533) metal coordination : bond 0.00661 / 0.33 ( 16) metal coordination : angle 2.16703 / 1.47 ( 10) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3307.50 seconds wall clock time: 57 minutes 33.19 seconds (3453.19 seconds total)