Starting phenix.real_space_refine on Fri Jul 3 20:35:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8han_34597/07_2026/8han_34597.cif Found real_map, /net/cci-nas-00/data/ceres_data/8han_34597/07_2026/8han_34597.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8han_34597/07_2026/8han_34597.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8han_34597/07_2026/8han_34597.map" model { file = "/net/cci-nas-00/data/ceres_data/8han_34597/07_2026/8han_34597.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8han_34597/07_2026/8han_34597.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8han_34597/07_2026/8han_34597.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8han_34597/07_2026/8han_34597.cif" } resolution = 4.2 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= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 294 5.49 5 S 45 5.16 5 C 9330 2.51 5 N 2940 2.21 5 O 3571 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 108 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: 16180 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 819 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 687 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain breaks: 1 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ALY:plan-2': 2, 'ALY:plan-1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 745 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "F" Number of atoms: 673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 673 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "G" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 810 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 730 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 4134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 4134 Classifications: {'peptide': 500} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 3, 'PTRANS': 28, 'TRANS': 468} Chain breaks: 4 Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 22 Chain: "I" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3016 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3011 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 Time building chain proxies: 3.22, per 1000 atoms: 0.20 Number of scatterers: 16180 At special positions: 0 Unit cell: (102.9, 127.89, 158.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 45 16.00 P 294 15.00 O 3571 8.00 N 2940 7.00 C 9330 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: 1.13 Conformation dependent library (CDL) restraints added in 425.4 milliseconds 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 14 sheets defined 61.5% alpha, 7.5% beta 118 base pairs and 226 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.555A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.516A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.659A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.393A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 46 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.583A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.724A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.419A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 1089 through 1103 Proline residue: K1096 - end of helix Processing helix chain 'K' and resid 1108 through 1112 Processing helix chain 'K' and resid 1116 through 1121 Processing helix chain 'K' and resid 1124 through 1129 removed outlier: 3.512A pdb=" N ILE K1128 " --> pdb=" O ASP K1124 " (cutoff:3.500A) Processing helix chain 'K' and resid 1134 through 1145 Processing helix chain 'K' and resid 1149 through 1168 removed outlier: 4.121A pdb=" N TYR K1153 " --> pdb=" O GLU K1149 " (cutoff:3.500A) Processing helix chain 'K' and resid 1172 through 1197 removed outlier: 4.042A pdb=" N ASP K1190 " --> pdb=" O GLU K1186 " (cutoff:3.500A) Proline residue: K1191 - end of helix Processing helix chain 'K' and resid 1237 through 1242 removed outlier: 3.502A pdb=" N PHE K1241 " --> pdb=" O CYS K1237 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N THR K1242 " --> pdb=" O GLU K1238 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 1237 through 1242' Processing helix chain 'K' and resid 1292 through 1296 Processing helix chain 'K' and resid 1308 through 1314 Processing helix chain 'K' and resid 1332 through 1350 Processing helix chain 'K' and resid 1445 through 1465 Processing helix chain 'K' and resid 1495 through 1513 Processing helix chain 'K' and resid 1522 through 1530 Processing helix chain 'K' and resid 1533 through 1537 Processing helix chain 'K' and resid 1543 through 1555 removed outlier: 3.752A pdb=" N ASN K1547 " --> pdb=" O ASP K1543 " (cutoff:3.500A) Processing helix chain 'K' and resid 1621 through 1628 Processing helix chain 'K' and resid 1663 through 1674 removed outlier: 3.940A pdb=" N PHE K1667 " --> pdb=" O GLY K1663 " (cutoff:3.500A) Processing helix chain 'K' and resid 1680 through 1698 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.604A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.397A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.985A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.005A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.635A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.202A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 1211 through 1212 removed outlier: 3.833A pdb=" N LEU K1211 " --> pdb=" O ILE K1221 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 1234 through 1236 Processing sheet with id=AB4, first strand: chain 'K' and resid 1280 through 1282 Processing sheet with id=AB5, first strand: chain 'K' and resid 1357 through 1370 removed outlier: 6.879A pdb=" N ALA K1395 " --> pdb=" O VAL K1362 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER K1364 " --> pdb=" O THR K1393 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR K1393 " --> pdb=" O SER K1364 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N ASP K1366 " --> pdb=" O TYR K1391 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N TYR K1391 " --> pdb=" O ASP K1366 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR K1368 " --> pdb=" O PHE K1389 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N PHE K1389 " --> pdb=" O THR K1368 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N LEU K1396 " --> pdb=" O MET K1412 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N MET K1412 " --> pdb=" O LEU K1396 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N PHE K1410 " --> pdb=" O ALA K1398 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU K1400 " --> pdb=" O CYS K1408 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N CYS K1408 " --> pdb=" O GLU K1400 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE K1402 " --> pdb=" O ASP K1406 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N ASP K1406 " --> pdb=" O ILE K1402 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TYR K1433 " --> pdb=" O HIS K1413 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLN K1415 " --> pdb=" O ILE K1431 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ILE K1431 " --> pdb=" O GLN K1415 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N TYR K1417 " --> pdb=" O VAL K1429 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N VAL K1429 " --> pdb=" O TYR K1417 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N TRP K1472 " --> pdb=" O ILE K1431 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N TYR K1433 " --> pdb=" O TRP K1472 " (cutoff:3.500A) 586 hydrogen bonds defined for protein. 1731 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 281 hydrogen bonds 558 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 226 stacking parallelities Total time for adding SS restraints: 3.56 Time building geometry restraints manager: 1.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4005 1.34 - 1.46: 4727 1.46 - 1.58: 7722 1.58 - 1.70: 586 1.70 - 1.82: 66 Bond restraints: 17106 Sorted by residual: bond pdb=" C3' DT J 135 " pdb=" C2' DT J 135 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.14e+01 bond pdb=" C3' DT I 91 " pdb=" C2' DT I 91 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DA J 116 " pdb=" C2' DA J 116 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.83e+00 bond pdb=" C3' DA J 59 " pdb=" C2' DA J 59 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.77e+00 bond pdb=" C3' DC J 39 " pdb=" C2' DC J 39 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.74e+00 ... (remaining 17101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 23276 1.66 - 3.31: 1037 3.31 - 4.97: 43 4.97 - 6.63: 4 6.63 - 8.28: 3 Bond angle restraints: 24363 Sorted by residual: angle pdb=" O4' DC I 105 " pdb=" C4' DC I 105 " pdb=" C3' DC I 105 " ideal model delta sigma weight residual 106.00 102.72 3.28 6.00e-01 2.78e+00 2.98e+01 angle pdb=" CA ALY B 16 " pdb=" C ALY B 16 " pdb=" O ALY B 16 " ideal model delta sigma weight residual 120.80 129.08 -8.28 1.70e+00 3.46e-01 2.37e+01 angle pdb=" N3 DT I 65 " pdb=" C4 DT I 65 " pdb=" O4 DT I 65 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT J 109 " pdb=" C4 DT J 109 " pdb=" O4 DT J 109 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.96e+01 angle pdb=" N3 DT J 135 " pdb=" C4 DT J 135 " pdb=" O4 DT J 135 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 24358 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.00: 8167 34.00 - 67.99: 1416 67.99 - 101.99: 28 101.99 - 135.98: 1 135.98 - 169.98: 2 Dihedral angle restraints: 9614 sinusoidal: 5937 harmonic: 3677 Sorted by residual: dihedral pdb=" C4' DT I 136 " pdb=" C3' DT I 136 " pdb=" O3' DT I 136 " pdb=" P DT I 137 " ideal model delta sinusoidal sigma weight residual 220.00 50.02 169.98 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA J 59 " pdb=" C3' DA J 59 " pdb=" O3' DA J 59 " pdb=" P DA J 60 " ideal model delta sinusoidal sigma weight residual 220.00 62.06 157.94 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" CG ARG H 33 " pdb=" CD ARG H 33 " pdb=" NE ARG H 33 " pdb=" CZ ARG H 33 " ideal model delta sinusoidal sigma weight residual -180.00 -135.34 -44.66 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 9611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1604 0.032 - 0.064: 770 0.064 - 0.096: 263 0.096 - 0.128: 70 0.128 - 0.160: 7 Chirality restraints: 2714 Sorted by residual: chirality pdb=" C3' DT I 136 " pdb=" C4' DT I 136 " pdb=" O3' DT I 136 " pdb=" C2' DT I 136 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.41e-01 chirality pdb=" P DA J 60 " pdb=" OP1 DA J 60 " pdb=" OP2 DA J 60 " pdb=" O5' DA J 60 " both_signs ideal model delta sigma weight residual True 2.34 -2.49 -0.15 2.00e-01 2.50e+01 5.69e-01 chirality pdb=" CA MET K1095 " pdb=" N MET K1095 " pdb=" C MET K1095 " pdb=" CB MET K1095 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.55e-01 ... (remaining 2711 not shown) Planarity restraints: 2077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 105 " -0.021 2.00e-02 2.50e+03 1.09e-02 2.67e+00 pdb=" N1 DC I 105 " 0.017 2.00e-02 2.50e+03 pdb=" C2 DC I 105 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DC I 105 " 0.012 2.00e-02 2.50e+03 pdb=" N3 DC I 105 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC I 105 " -0.003 2.00e-02 2.50e+03 pdb=" N4 DC I 105 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DC I 105 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DC I 105 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU D 102 " 0.023 5.00e-02 4.00e+02 3.48e-02 1.93e+00 pdb=" N PRO D 103 " -0.060 5.00e-02 4.00e+02 pdb=" CA PRO D 103 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO D 103 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 151 " 0.012 2.00e-02 2.50e+03 7.46e-03 1.67e+00 pdb=" N9 DG I 151 " -0.014 2.00e-02 2.50e+03 pdb=" C8 DG I 151 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 151 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DG I 151 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 151 " 0.015 2.00e-02 2.50e+03 pdb=" O6 DG I 151 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DG I 151 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 151 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG I 151 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 151 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 151 " -0.001 2.00e-02 2.50e+03 ... (remaining 2074 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1818 2.76 - 3.29: 15194 3.29 - 3.83: 31831 3.83 - 4.36: 35551 4.36 - 4.90: 52884 Nonbonded interactions: 137278 Sorted by model distance: nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.219 3.040 nonbonded pdb=" OD1 ASP A 123 " pdb=" NE2 HIS E 113 " model vdw 2.236 3.120 nonbonded pdb=" NH1 ARG C 17 " pdb=" OP2 DG J 48 " model vdw 2.244 3.120 nonbonded pdb=" NE2 HIS A 113 " pdb=" OD1 ASP E 123 " model vdw 2.274 3.120 nonbonded pdb=" N2 DG I 35 " pdb=" O2 DT J 147 " model vdw 2.277 3.120 ... (remaining 137273 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 45 through 134) selection = (chain 'E' and resid 45 through 134) } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and resid 21 through 102) } ncs_group { reference = (chain 'C' and resid 14 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and ((resid 31 and (name N or name CA or name C or name O or name CB \ )) or resid 32 through 124)) selection = chain 'H' } ncs_group { reference = (chain 'I' and resid 19 through 162) selection = (chain 'J' and resid 19 through 162) } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.350 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7177 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 0.042 17106 Z= 0.440 Angle : 0.684 8.284 24363 Z= 0.601 Chirality : 0.042 0.160 2714 Planarity : 0.003 0.035 2077 Dihedral : 24.993 169.976 7240 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.88 (0.24), residues: 1230 helix: 2.68 (0.18), residues: 756 sheet: 0.28 (0.63), residues: 66 loop : 0.81 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 29 TYR 0.019 0.001 TYR K1102 PHE 0.007 0.001 PHE K1484 TRP 0.009 0.001 TRP K1502 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.44 (17106) covalent geometry : angle 0.68411 / 0.60 (24363) hydrogen bonds : bond 0.11059 / 7.41 ( 867) hydrogen bonds : angle 3.83435 / 2.72 ( 2289) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 62 MET cc_start: 0.8444 (mmp) cc_final: 0.8209 (mmp) REVERT: H 62 MET cc_start: 0.8783 (mmp) cc_final: 0.8516 (mmt) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1027 time to fit residues: 5.2667 Evaluate side-chains 24 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 20.0000 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 40.0000 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 50.0000 chunk 91 optimal weight: 0.2980 chunk 149 optimal weight: 40.0000 overall best weight: 4.8590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 63 ASN H 95 GLN ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1628 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.047860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.034416 restraints weight = 238285.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.035056 restraints weight = 134365.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.035530 restraints weight = 90813.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.035702 restraints weight = 70183.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.035960 restraints weight = 61461.646| |-----------------------------------------------------------------------------| r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 17106 Z= 0.233 Angle : 0.739 10.674 24363 Z= 0.404 Chirality : 0.044 0.344 2714 Planarity : 0.006 0.044 2077 Dihedral : 29.312 173.813 4705 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.50 (0.23), residues: 1230 helix: 2.24 (0.18), residues: 767 sheet: 0.26 (0.63), residues: 67 loop : 0.89 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 29 TYR 0.024 0.002 TYR K1503 PHE 0.016 0.002 PHE A 67 TRP 0.019 0.002 TRP K1502 HIS 0.010 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.23 (17106) covalent geometry : angle 0.73856 / 0.40 (24363) hydrogen bonds : bond 0.08565 / 5.87 ( 867) hydrogen bonds : angle 3.57892 / 2.53 ( 2289) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.516 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: K 1691 MET cc_start: 0.7521 (ptp) cc_final: 0.6576 (tmm) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0929 time to fit residues: 4.9012 Evaluate side-chains 25 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 71 optimal weight: 2.9990 chunk 137 optimal weight: 30.0000 chunk 83 optimal weight: 30.0000 chunk 64 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 8 optimal weight: 4.9990 chunk 117 optimal weight: 20.0000 chunk 84 optimal weight: 0.0060 chunk 107 optimal weight: 30.0000 chunk 118 optimal weight: 6.9990 overall best weight: 1.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.048220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.034567 restraints weight = 239663.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.035204 restraints weight = 131727.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.035769 restraints weight = 88331.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.036068 restraints weight = 67044.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.036213 restraints weight = 56729.168| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 17106 Z= 0.139 Angle : 0.544 6.060 24363 Z= 0.323 Chirality : 0.038 0.318 2714 Planarity : 0.004 0.032 2077 Dihedral : 29.306 178.703 4705 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.83 (0.24), residues: 1230 helix: 2.59 (0.18), residues: 767 sheet: 0.08 (0.63), residues: 69 loop : 0.88 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K1498 TYR 0.012 0.001 TYR K1539 PHE 0.019 0.001 PHE E 104 TRP 0.007 0.001 TRP K1502 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.14 (17106) covalent geometry : angle 0.54415 / 0.32 (24363) hydrogen bonds : bond 0.05276 / 3.58 ( 867) hydrogen bonds : angle 3.21492 / 2.28 ( 2289) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.405 Fit side-chains REVERT: K 1160 MET cc_start: 0.7322 (tmm) cc_final: 0.7031 (ptt) REVERT: K 1691 MET cc_start: 0.7544 (ptp) cc_final: 0.6727 (tmm) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.0911 time to fit residues: 4.5612 Evaluate side-chains 25 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 95 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 72 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 50 optimal weight: 9.9990 chunk 146 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 68 optimal weight: 10.0000 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.048433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.034684 restraints weight = 233962.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.035382 restraints weight = 127627.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.035827 restraints weight = 85520.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.036230 restraints weight = 66483.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.036341 restraints weight = 55189.814| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17106 Z= 0.120 Angle : 0.523 6.238 24363 Z= 0.311 Chirality : 0.038 0.326 2714 Planarity : 0.003 0.040 2077 Dihedral : 29.256 178.057 4705 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.09 % Allowed : 1.20 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 3.02 (0.24), residues: 1230 helix: 2.76 (0.18), residues: 767 sheet: 0.12 (0.63), residues: 69 loop : 0.91 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K1202 TYR 0.022 0.001 TYR B 88 PHE 0.018 0.001 PHE E 104 TRP 0.007 0.001 TRP K1545 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.12 (17106) covalent geometry : angle 0.52275 / 0.31 (24363) hydrogen bonds : bond 0.04450 / 3.00 ( 867) hydrogen bonds : angle 3.00327 / 2.13 ( 2289) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 59 MET cc_start: 0.8402 (tmm) cc_final: 0.8184 (tpp) REVERT: K 1160 MET cc_start: 0.7415 (tmm) cc_final: 0.7087 (ptm) REVERT: K 1691 MET cc_start: 0.7512 (ptp) cc_final: 0.6671 (tmm) outliers start: 1 outliers final: 1 residues processed: 30 average time/residue: 0.0826 time to fit residues: 4.4210 Evaluate side-chains 26 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 25 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 122 optimal weight: 50.0000 chunk 11 optimal weight: 10.0000 chunk 147 optimal weight: 20.0000 chunk 98 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 139 optimal weight: 30.0000 chunk 106 optimal weight: 30.0000 chunk 90 optimal weight: 2.9990 chunk 117 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN K1146 GLN ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1343 ASN ** K1487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.045157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 88)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.031417 restraints weight = 210507.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.031955 restraints weight = 121342.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 63)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.032179 restraints weight = 85044.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.032256 restraints weight = 69917.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.032427 restraints weight = 64534.687| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 17106 Z= 0.240 Angle : 0.729 10.533 24363 Z= 0.402 Chirality : 0.043 0.327 2714 Planarity : 0.006 0.051 2077 Dihedral : 29.841 174.844 4705 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.21 (0.23), residues: 1230 helix: 2.08 (0.18), residues: 765 sheet: 0.28 (0.64), residues: 66 loop : 0.59 (0.30), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 35 TYR 0.020 0.003 TYR G 50 PHE 0.016 0.002 PHE H 65 TRP 0.012 0.002 TRP K1302 HIS 0.009 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.24 (17106) covalent geometry : angle 0.72935 / 0.40 (24363) hydrogen bonds : bond 0.09402 / 6.46 ( 867) hydrogen bonds : angle 3.61198 / 2.58 ( 2289) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.439 Fit side-chains revert: symmetry clash REVERT: E 120 MET cc_start: 0.8274 (mmp) cc_final: 0.7658 (mmm) REVERT: K 1691 MET cc_start: 0.7276 (ptp) cc_final: 0.6133 (tmm) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.1207 time to fit residues: 5.7312 Evaluate side-chains 24 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 145 optimal weight: 20.0000 chunk 12 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 100 optimal weight: 20.0000 chunk 101 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.045900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.032207 restraints weight = 206889.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.032714 restraints weight = 117171.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 59)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.033020 restraints weight = 82602.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 62)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.033183 restraints weight = 68063.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.033226 restraints weight = 61573.935| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.3342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 17106 Z= 0.133 Angle : 0.577 9.004 24363 Z= 0.334 Chirality : 0.040 0.318 2714 Planarity : 0.004 0.033 2077 Dihedral : 29.829 172.482 4705 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.58 (0.24), residues: 1230 helix: 2.41 (0.18), residues: 765 sheet: -0.02 (0.64), residues: 69 loop : 0.75 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K1498 TYR 0.012 0.001 TYR C 50 PHE 0.021 0.001 PHE K1397 TRP 0.027 0.002 TRP K1502 HIS 0.008 0.001 HIS K1291 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.13 (17106) covalent geometry : angle 0.57677 / 0.33 (24363) hydrogen bonds : bond 0.05064 / 3.46 ( 867) hydrogen bonds : angle 3.19877 / 2.29 ( 2289) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: E 120 MET cc_start: 0.8382 (mmp) cc_final: 0.7767 (mmm) REVERT: K 1193 MET cc_start: 0.7571 (tpt) cc_final: 0.7348 (tpt) REVERT: K 1691 MET cc_start: 0.7239 (ptp) cc_final: 0.6141 (tmm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.0817 time to fit residues: 4.5143 Evaluate side-chains 25 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 98 optimal weight: 7.9990 chunk 37 optimal weight: 0.3980 chunk 11 optimal weight: 10.0000 chunk 110 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 125 optimal weight: 20.0000 chunk 61 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 46 optimal weight: 1.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 63 ASN H 67 ASN ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.045623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.032240 restraints weight = 209833.353| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.032651 restraints weight = 116605.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.033044 restraints weight = 81834.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.033180 restraints weight = 65458.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 59)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.033317 restraints weight = 58769.397| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.3585 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17106 Z= 0.153 Angle : 0.589 7.234 24363 Z= 0.338 Chirality : 0.039 0.316 2714 Planarity : 0.004 0.033 2077 Dihedral : 29.845 171.280 4705 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.00 % Allowed : 0.74 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.64 (0.23), residues: 1230 helix: 2.46 (0.18), residues: 765 sheet: -0.03 (0.63), residues: 68 loop : 0.78 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K1498 TYR 0.014 0.002 TYR B 88 PHE 0.021 0.001 PHE K1397 TRP 0.024 0.002 TRP K1502 HIS 0.007 0.001 HIS K1351 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (17106) covalent geometry : angle 0.58887 / 0.34 (24363) hydrogen bonds : bond 0.05430 / 3.72 ( 867) hydrogen bonds : angle 3.23426 / 2.33 ( 2289) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: D 59 MET cc_start: 0.8616 (tpp) cc_final: 0.8406 (tpp) REVERT: E 120 MET cc_start: 0.8356 (mmp) cc_final: 0.7740 (mmm) REVERT: K 1193 MET cc_start: 0.7406 (tpt) cc_final: 0.7181 (tpt) REVERT: K 1691 MET cc_start: 0.7209 (ptp) cc_final: 0.6090 (tmm) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 0.0959 time to fit residues: 4.7127 Evaluate side-chains 25 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 89 optimal weight: 7.9990 chunk 106 optimal weight: 7.9990 chunk 136 optimal weight: 50.0000 chunk 139 optimal weight: 30.0000 chunk 130 optimal weight: 40.0000 chunk 101 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 119 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 39 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN F 93 GLN H 63 ASN H 67 ASN ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1547 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.043909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.031264 restraints weight = 227545.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 75)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.031630 restraints weight = 124376.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.031871 restraints weight = 83587.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.032063 restraints weight = 67432.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.032092 restraints weight = 59568.887| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17106 Z= 0.259 Angle : 0.769 9.471 24363 Z= 0.424 Chirality : 0.046 0.307 2714 Planarity : 0.006 0.058 2077 Dihedral : 30.588 171.089 4705 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.23), residues: 1230 helix: 1.55 (0.18), residues: 765 sheet: -0.40 (0.61), residues: 68 loop : 0.48 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG H 33 TYR 0.022 0.003 TYR K1539 PHE 0.014 0.002 PHE H 65 TRP 0.032 0.003 TRP K1502 HIS 0.011 0.002 HIS K1413 Details of bonding type rmsd/Z covalent geometry : bond 0.00499 / 0.26 (17106) covalent geometry : angle 0.76868 / 0.42 (24363) hydrogen bonds : bond 0.09806 / 6.80 ( 867) hydrogen bonds : angle 3.93606 / 2.84 ( 2289) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: E 120 MET cc_start: 0.8616 (mmp) cc_final: 0.8047 (mmm) REVERT: K 1193 MET cc_start: 0.7262 (tpt) cc_final: 0.7026 (tpt) REVERT: K 1691 MET cc_start: 0.7483 (ptp) cc_final: 0.6363 (tmm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1317 time to fit residues: 5.7106 Evaluate side-chains 24 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 124 optimal weight: 20.0000 chunk 43 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 141 optimal weight: 30.0000 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 chunk 82 optimal weight: 1.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 131 optimal weight: 20.0000 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS H 63 ASN ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K1487 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.044600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.031735 restraints weight = 222130.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 69)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.032185 restraints weight = 122362.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.032495 restraints weight = 81442.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.032665 restraints weight = 64584.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.032716 restraints weight = 57420.598| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7918 moved from start: 0.4854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17106 Z= 0.157 Angle : 0.631 8.492 24363 Z= 0.359 Chirality : 0.042 0.306 2714 Planarity : 0.004 0.033 2077 Dihedral : 30.605 172.389 4705 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.05 (0.23), residues: 1230 helix: 1.99 (0.18), residues: 766 sheet: -0.00 (0.65), residues: 63 loop : 0.48 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 19 TYR 0.014 0.002 TYR K1539 PHE 0.009 0.001 PHE K1399 TRP 0.032 0.002 TRP K1502 HIS 0.011 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.16 (17106) covalent geometry : angle 0.63107 / 0.36 (24363) hydrogen bonds : bond 0.06057 / 4.16 ( 867) hydrogen bonds : angle 3.52377 / 2.55 ( 2289) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.493 Fit side-chains revert: symmetry clash REVERT: E 120 MET cc_start: 0.8540 (mmp) cc_final: 0.8045 (mmm) REVERT: K 1193 MET cc_start: 0.7604 (tpt) cc_final: 0.7301 (tpt) REVERT: K 1691 MET cc_start: 0.7371 (ptp) cc_final: 0.6286 (tmm) outliers start: 0 outliers final: 0 residues processed: 29 average time/residue: 0.1172 time to fit residues: 5.9522 Evaluate side-chains 25 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 25 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 97 optimal weight: 30.0000 chunk 122 optimal weight: 50.0000 chunk 5 optimal weight: 10.0000 chunk 22 optimal weight: 9.9990 chunk 140 optimal weight: 20.0000 chunk 2 optimal weight: 7.9990 chunk 55 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 108 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 63 ASN ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K1438 HIS K1487 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.043881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.031175 restraints weight = 225793.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.031637 restraints weight = 123679.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.031849 restraints weight = 82116.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.032021 restraints weight = 66188.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.032068 restraints weight = 59820.191| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 17106 Z= 0.188 Angle : 0.657 7.847 24363 Z= 0.371 Chirality : 0.042 0.288 2714 Planarity : 0.005 0.034 2077 Dihedral : 30.635 172.708 4705 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 14.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.15 (0.24), residues: 1230 helix: 2.09 (0.18), residues: 764 sheet: -0.31 (0.63), residues: 68 loop : 0.56 (0.32), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K1233 TYR 0.015 0.002 TYR K1539 PHE 0.013 0.001 PHE K1511 TRP 0.035 0.002 TRP K1502 HIS 0.009 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00353 / 0.19 (17106) covalent geometry : angle 0.65708 / 0.37 (24363) hydrogen bonds : bond 0.06884 / 4.75 ( 867) hydrogen bonds : angle 3.56830 / 2.59 ( 2289) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2460 Ramachandran restraints generated. 1230 Oldfield, 0 Emsley, 1230 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 26 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: E 120 MET cc_start: 0.8515 (mmp) cc_final: 0.7929 (mmm) REVERT: K 1193 MET cc_start: 0.7169 (tpt) cc_final: 0.6928 (tpt) REVERT: K 1691 MET cc_start: 0.7498 (ptp) cc_final: 0.6401 (tmm) outliers start: 0 outliers final: 0 residues processed: 26 average time/residue: 0.1152 time to fit residues: 5.1466 Evaluate side-chains 24 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 24 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 1 optimal weight: 0.8980 chunk 81 optimal weight: 5.9990 chunk 79 optimal weight: 2.9990 chunk 134 optimal weight: 40.0000 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 58 optimal weight: 9.9990 chunk 8 optimal weight: 1.9990 chunk 127 optimal weight: 30.0000 chunk 68 optimal weight: 0.0980 chunk 93 optimal weight: 7.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 63 ASN ** K1297 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.043567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.030038 restraints weight = 213485.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.030450 restraints weight = 122488.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.030707 restraints weight = 85439.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.030915 restraints weight = 70636.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.031006 restraints weight = 63851.202| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 17106 Z= 0.144 Angle : 0.606 7.404 24363 Z= 0.348 Chirality : 0.041 0.292 2714 Planarity : 0.004 0.033 2077 Dihedral : 30.636 174.152 4705 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.77 % 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: 2.27 (0.24), residues: 1230 helix: 2.18 (0.18), residues: 765 sheet: -0.03 (0.66), residues: 63 loop : 0.55 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 88 TYR 0.012 0.002 TYR K1539 PHE 0.008 0.001 PHE K1111 TRP 0.027 0.002 TRP K1502 HIS 0.009 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.14 (17106) covalent geometry : angle 0.60623 / 0.35 (24363) hydrogen bonds : bond 0.05308 / 3.63 ( 867) hydrogen bonds : angle 3.38482 / 2.46 ( 2289) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3015.00 seconds wall clock time: 52 minutes 41.25 seconds (3161.25 seconds total)