Starting phenix.real_space_refine on Sat Jul 4 06:27:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9oe6_70388/07_2026/9oe6_70388_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9oe6_70388/07_2026/9oe6_70388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.31 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9oe6_70388/07_2026/9oe6_70388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9oe6_70388/07_2026/9oe6_70388.map" model { file = "/net/cci-nas-00/data/ceres_data/9oe6_70388/07_2026/9oe6_70388_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9oe6_70388/07_2026/9oe6_70388_trim.cif" } resolution = 3.31 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= 0.011 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: 7 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 48 5.16 5 C 5738 2.51 5 N 1524 2.21 5 O 1666 1.98 5 H 9031 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 18015 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 17951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1151, 17951 Classifications: {'peptide': 1151} Link IDs: {'PTRANS': 27, 'TRANS': 1123} Chain breaks: 2 Chain: "A" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 64 Unusual residues: {' MG': 2, 'AGS': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 3.05, per 1000 atoms: 0.17 Number of scatterers: 18015 At special positions: 0 Unit cell: (69.72, 121.18, 138.61, 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) S 48 16.00 P 6 15.00 Mg 2 11.99 O 1666 8.00 N 1524 7.00 C 5738 6.00 H 9031 1.00 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: 1.53 Conformation dependent library (CDL) restraints added in 596.3 milliseconds 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 69.2% alpha, 5.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 42 through 46 Processing helix chain 'A' and resid 49 through 70 removed outlier: 3.942A pdb=" N LEU A 70 " --> pdb=" O ASN A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 79 Processing helix chain 'A' and resid 118 through 163 removed outlier: 3.632A pdb=" N LYS A 151 " --> pdb=" O ARG A 147 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLN A 163 " --> pdb=" O SER A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 171 Processing helix chain 'A' and resid 172 through 191 removed outlier: 4.604A pdb=" N VAL A 184 " --> pdb=" O LEU A 180 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N TYR A 185 " --> pdb=" O THR A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 192 through 216 removed outlier: 3.861A pdb=" N GLY A 196 " --> pdb=" O GLY A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 232 Proline residue: A 228 - end of helix removed outlier: 4.054A pdb=" N GLY A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 236 Processing helix chain 'A' and resid 237 through 244 removed outlier: 3.859A pdb=" N MET A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 245 through 247 No H-bonds generated for 'chain 'A' and resid 245 through 247' Processing helix chain 'A' and resid 251 through 265 removed outlier: 4.459A pdb=" N ALA A 255 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 258 " --> pdb=" O LYS A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 273 removed outlier: 3.512A pdb=" N PHE A 272 " --> pdb=" O THR A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 323 removed outlier: 4.002A pdb=" N GLU A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 351 Processing helix chain 'A' and resid 352 through 376 removed outlier: 4.494A pdb=" N ASN A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N HIS A 368 " --> pdb=" O ARG A 364 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 444 removed outlier: 3.561A pdb=" N GLN A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 473 Processing helix chain 'A' and resid 489 through 495 Processing helix chain 'A' and resid 501 through 512 Processing helix chain 'A' and resid 514 through 520 Processing helix chain 'A' and resid 537 through 552 removed outlier: 3.778A pdb=" N ARG A 552 " --> pdb=" O ARG A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 582 Processing helix chain 'A' and resid 596 through 600 Processing helix chain 'A' and resid 616 through 624 Processing helix chain 'A' and resid 625 through 638 Processing helix chain 'A' and resid 695 through 703 removed outlier: 3.847A pdb=" N ASN A 703 " --> pdb=" O VAL A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 735 removed outlier: 3.658A pdb=" N GLN A 724 " --> pdb=" O ASN A 720 " (cutoff:3.500A) Proline residue: A 725 - end of helix removed outlier: 3.517A pdb=" N ALA A 728 " --> pdb=" O GLN A 724 " (cutoff:3.500A) Processing helix chain 'A' and resid 736 through 740 Processing helix chain 'A' and resid 742 through 794 removed outlier: 3.805A pdb=" N GLN A 771 " --> pdb=" O THR A 767 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 804 removed outlier: 4.074A pdb=" N TYR A 802 " --> pdb=" O ASP A 798 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ASP A 804 " --> pdb=" O ALA A 800 " (cutoff:3.500A) Processing helix chain 'A' and resid 808 through 818 Processing helix chain 'A' and resid 818 through 823 removed outlier: 3.627A pdb=" N VAL A 823 " --> pdb=" O ASP A 819 " (cutoff:3.500A) Processing helix chain 'A' and resid 823 through 828 removed outlier: 3.845A pdb=" N THR A 827 " --> pdb=" O VAL A 823 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLY A 828 " --> pdb=" O GLN A 824 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 823 through 828' Processing helix chain 'A' and resid 828 through 886 removed outlier: 7.903A pdb=" N GLN A 854 " --> pdb=" O VAL A 850 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N LEU A 855 " --> pdb=" O TYR A 851 " (cutoff:3.500A) Proline residue: A 864 - end of helix Processing helix chain 'A' and resid 891 through 901 removed outlier: 3.691A pdb=" N ALA A 895 " --> pdb=" O ALA A 891 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR A 896 " --> pdb=" O GLY A 892 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 908 Processing helix chain 'A' and resid 910 through 922 removed outlier: 3.987A pdb=" N PHE A 914 " --> pdb=" O ARG A 910 " (cutoff:3.500A) Processing helix chain 'A' and resid 923 through 964 removed outlier: 3.550A pdb=" N LYS A 927 " --> pdb=" O ILE A 923 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 929 " --> pdb=" O PRO A 925 " (cutoff:3.500A) Processing helix chain 'A' and resid 968 through 992 removed outlier: 3.745A pdb=" N VAL A 979 " --> pdb=" O VAL A 975 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1012 Processing helix chain 'A' and resid 1074 through 1082 Processing helix chain 'A' and resid 1098 through 1102 Processing helix chain 'A' and resid 1103 through 1110 removed outlier: 3.683A pdb=" N SER A1109 " --> pdb=" O HIS A1105 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1133 removed outlier: 3.515A pdb=" N ASP A1133 " --> pdb=" O ALA A1130 " (cutoff:3.500A) Processing helix chain 'A' and resid 1139 through 1150 Processing helix chain 'A' and resid 1152 through 1159 Processing helix chain 'A' and resid 1174 through 1190 removed outlier: 3.616A pdb=" N GLN A1180 " --> pdb=" O GLY A1176 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG A1181 " --> pdb=" O GLY A1177 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A1184 " --> pdb=" O GLN A1180 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG A1190 " --> pdb=" O ARG A1186 " (cutoff:3.500A) Processing helix chain 'A' and resid 1200 through 1205 removed outlier: 4.322A pdb=" N ALA A1203 " --> pdb=" O ALA A1200 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP A1205 " --> pdb=" O SER A1202 " (cutoff:3.500A) Processing helix chain 'A' and resid 1206 through 1220 removed outlier: 3.769A pdb=" N GLN A1213 " --> pdb=" O GLU A1209 " (cutoff:3.500A) Processing helix chain 'A' and resid 1231 through 1236 removed outlier: 3.767A pdb=" N ILE A1235 " --> pdb=" O ARG A1231 " (cutoff:3.500A) Processing helix chain 'A' and resid 1254 through 1262 removed outlier: 3.730A pdb=" N GLN A1261 " --> pdb=" O GLN A1257 " (cutoff:3.500A) Processing helix chain 'A' and resid 1262 through 1274 removed outlier: 3.600A pdb=" N TYR A1266 " --> pdb=" O GLN A1262 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 397 through 398 Processing sheet with id=AA2, first strand: chain 'A' and resid 402 through 404 removed outlier: 4.628A pdb=" N ILE A 402 " --> pdb=" O GLY A 417 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N LEU A 415 " --> pdb=" O PHE A 404 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 475 through 478 removed outlier: 6.792A pdb=" N LEU A 557 " --> pdb=" O ILE A 588 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N VAL A 590 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU A 559 " --> pdb=" O VAL A 590 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N ILE A 428 " --> pdb=" O VAL A 589 " (cutoff:3.500A) removed outlier: 5.981A pdb=" N ALA A 429 " --> pdb=" O ALA A 604 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N PHE A 606 " --> pdb=" O ALA A 429 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLU A 613 " --> pdb=" O GLY A 605 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N GLN A 607 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N ILE A 611 " --> pdb=" O GLN A 607 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 487 through 488 removed outlier: 3.588A pdb=" N THR A 487 " --> pdb=" O VAL A 529 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1051 through 1055 removed outlier: 4.608A pdb=" N VAL A1038 " --> pdb=" O GLY A1053 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N LYS A1055 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLU A1036 " --> pdb=" O LYS A1055 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N GLY A1034 " --> pdb=" O MET A1093 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG A1091 " --> pdb=" O GLU A1036 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N VAL A1038 " --> pdb=" O GLN A1089 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N GLN A1089 " --> pdb=" O VAL A1038 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1066 through 1067 removed outlier: 6.125A pdb=" N VAL A1067 " --> pdb=" O VAL A1244 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N ILE A1241 " --> pdb=" O GLN A1252 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLN A1252 " --> pdb=" O ILE A1241 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL A1243 " --> pdb=" O VAL A1250 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1111 through 1114 removed outlier: 7.257A pdb=" N GLY A1112 " --> pdb=" O LEU A1196 " (cutoff:3.500A) 559 hydrogen bonds defined for protein. 1635 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.19 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.06: 9022 1.06 - 1.28: 1484 1.28 - 1.50: 3785 1.50 - 1.73: 3795 1.73 - 1.95: 85 Bond restraints: 18171 Sorted by residual: bond pdb=" O2G AGS A1303 " pdb=" PG AGS A1303 " ideal model delta sigma weight residual 1.604 1.503 0.101 2.00e-02 2.50e+03 2.56e+01 bond pdb=" O3B AGS A1301 " pdb=" PB AGS A1301 " ideal model delta sigma weight residual 1.673 1.581 0.092 2.00e-02 2.50e+03 2.10e+01 bond pdb=" O3A AGS A1301 " pdb=" PA AGS A1301 " ideal model delta sigma weight residual 1.664 1.585 0.079 2.00e-02 2.50e+03 1.57e+01 bond pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sigma weight residual 1.673 1.596 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" O3G AGS A1303 " pdb=" PG AGS A1303 " ideal model delta sigma weight residual 1.570 1.501 0.069 2.00e-02 2.50e+03 1.19e+01 ... (remaining 18166 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.94: 32817 5.94 - 11.89: 10 11.89 - 17.83: 0 17.83 - 23.78: 4 23.78 - 29.72: 8 Bond angle restraints: 32839 Sorted by residual: angle pdb=" HZ1 LYS A1100 " pdb=" NZ LYS A1100 " pdb=" HZ2 LYS A1100 " ideal model delta sigma weight residual 109.00 79.28 29.72 3.00e+00 1.11e-01 9.81e+01 angle pdb=" HZ1 LYS A1100 " pdb=" NZ LYS A1100 " pdb=" HZ3 LYS A1100 " ideal model delta sigma weight residual 109.00 79.34 29.66 3.00e+00 1.11e-01 9.77e+01 angle pdb=" CG LEU A 702 " pdb=" CD2 LEU A 702 " pdb="HD23 LEU A 702 " ideal model delta sigma weight residual 109.00 79.57 29.43 3.00e+00 1.11e-01 9.62e+01 angle pdb=" CG LEU A 702 " pdb=" CD2 LEU A 702 " pdb="HD21 LEU A 702 " ideal model delta sigma weight residual 109.00 79.85 29.15 3.00e+00 1.11e-01 9.44e+01 angle pdb="HD22 LEU A 702 " pdb=" CD2 LEU A 702 " pdb="HD23 LEU A 702 " ideal model delta sigma weight residual 110.00 81.12 28.88 3.00e+00 1.11e-01 9.27e+01 ... (remaining 32834 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.47: 8150 35.47 - 70.94: 345 70.94 - 106.41: 19 106.41 - 141.88: 4 141.88 - 177.35: 2 Dihedral angle restraints: 8520 sinusoidal: 4674 harmonic: 3846 Sorted by residual: dihedral pdb=" O3A AGS A1303 " pdb=" O3B AGS A1303 " pdb=" PB AGS A1303 " pdb=" PG AGS A1303 " ideal model delta sinusoidal sigma weight residual 252.61 75.26 177.35 1 3.00e+01 1.11e-03 2.13e+01 dihedral pdb=" O2A AGS A1301 " pdb=" O3A AGS A1301 " pdb=" PA AGS A1301 " pdb=" PB AGS A1301 " ideal model delta sinusoidal sigma weight residual -52.28 115.44 -167.72 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" O1A AGS A1303 " pdb=" O3A AGS A1303 " pdb=" PA AGS A1303 " pdb=" PB AGS A1303 " ideal model delta sinusoidal sigma weight residual 82.37 -53.38 135.75 1 3.00e+01 1.11e-03 1.83e+01 ... (remaining 8517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 1313 0.067 - 0.134: 113 0.134 - 0.201: 1 0.201 - 0.268: 1 0.268 - 0.335: 1 Chirality restraints: 1429 Sorted by residual: chirality pdb=" C3' AGS A1303 " pdb=" C2' AGS A1303 " pdb=" C4' AGS A1303 " pdb=" O3' AGS A1303 " both_signs ideal model delta sigma weight residual False -2.37 -2.71 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C3' AGS A1301 " pdb=" C2' AGS A1301 " pdb=" C4' AGS A1301 " pdb=" O3' AGS A1301 " both_signs ideal model delta sigma weight residual False -2.37 -2.62 0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA ILE A 556 " pdb=" N ILE A 556 " pdb=" C ILE A 556 " pdb=" CB ILE A 556 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.60e-01 ... (remaining 1426 not shown) Planarity restraints: 2670 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 797 " -0.112 2.00e-02 2.50e+03 1.25e-01 2.33e+02 pdb=" CD GLN A 797 " -0.001 2.00e-02 2.50e+03 pdb=" OE1 GLN A 797 " 0.118 2.00e-02 2.50e+03 pdb=" NE2 GLN A 797 " -0.011 2.00e-02 2.50e+03 pdb="HE21 GLN A 797 " 0.186 2.00e-02 2.50e+03 pdb="HE22 GLN A 797 " -0.179 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 801 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.33e+00 pdb=" C TRP A 801 " -0.036 2.00e-02 2.50e+03 pdb=" O TRP A 801 " 0.013 2.00e-02 2.50e+03 pdb=" N TYR A 802 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 802 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.95e+00 pdb=" N ASP A 803 " -0.034 2.00e-02 2.50e+03 pdb=" CA ASP A 803 " 0.009 2.00e-02 2.50e+03 pdb=" H ASP A 803 " 0.015 2.00e-02 2.50e+03 ... (remaining 2667 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1323 2.21 - 2.81: 38482 2.81 - 3.40: 50204 3.40 - 4.00: 64323 4.00 - 4.60: 100349 Nonbonded interactions: 254681 Sorted by model distance: nonbonded pdb=" H ILE A 458 " pdb=" O HIS A 461 " model vdw 1.611 2.450 nonbonded pdb=" OE1 GLN A1052 " pdb="HD22 ASN A1246 " model vdw 1.622 2.450 nonbonded pdb=" HG SER A 439 " pdb=" O2A AGS A1301 " model vdw 1.623 2.450 nonbonded pdb=" OD1 ASN A1191 " pdb="HH21 ARG A1223 " model vdw 1.624 2.450 nonbonded pdb=" O TRP A 801 " pdb="HD21 ASN A 807 " model vdw 1.625 2.450 ... (remaining 254676 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.010 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: 0.070 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.540 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 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 : 0.004 0.101 9140 Z= 0.202 Angle : 0.627 10.718 12366 Z= 0.331 Chirality : 0.039 0.335 1429 Planarity : 0.003 0.031 1562 Dihedral : 18.959 177.350 3389 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.58 % Allowed : 18.49 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.01 (0.25), residues: 1145 helix: 0.85 (0.19), residues: 732 sheet: -3.45 (1.39), residues: 12 loop : -1.47 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 623 TYR 0.016 0.001 TYR A 802 PHE 0.028 0.001 PHE A 308 TRP 0.006 0.001 TRP A 853 HIS 0.002 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.20 ( 9140) covalent geometry : angle 0.62711 / 0.33 (12366) hydrogen bonds : bond 0.14479 / 9.87 ( 559) hydrogen bonds : angle 6.56564 / 4.80 ( 1635) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 697 LEU cc_start: 0.8857 (mm) cc_final: 0.8608 (pp) outliers start: 15 outliers final: 14 residues processed: 72 average time/residue: 0.1880 time to fit residues: 20.2240 Evaluate side-chains 72 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 843 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1097 ASN Chi-restraints excluded: chain A residue 1124 SER Chi-restraints excluded: chain A residue 1169 ASP Chi-restraints excluded: chain A residue 1204 LEU Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 628 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 797 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.083238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.061964 restraints weight = 73015.700| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 3.59 r_work: 0.2913 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 9140 Z= 0.285 Angle : 0.602 8.528 12366 Z= 0.328 Chirality : 0.041 0.142 1429 Planarity : 0.004 0.046 1562 Dihedral : 14.090 169.466 1329 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.52 % Allowed : 17.86 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.25), residues: 1145 helix: 0.86 (0.19), residues: 750 sheet: -2.56 (1.36), residues: 17 loop : -1.69 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1181 TYR 0.014 0.001 TYR A1085 PHE 0.018 0.002 PHE A 308 TRP 0.008 0.001 TRP A 801 HIS 0.004 0.001 HIS A1255 Details of bonding type rmsd/Z covalent geometry : bond 0.00610 / 0.29 ( 9140) covalent geometry : angle 0.60176 / 0.33 (12366) hydrogen bonds : bond 0.04705 / 3.10 ( 559) hydrogen bonds : angle 5.13413 / 3.76 ( 1635) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 60 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 819 ASP cc_start: 0.8627 (m-30) cc_final: 0.8420 (m-30) outliers start: 24 outliers final: 18 residues processed: 84 average time/residue: 0.1611 time to fit residues: 20.5971 Evaluate side-chains 77 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 59 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 311 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 550 LEU Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1097 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 92 optimal weight: 5.9990 chunk 101 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 60 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 114 optimal weight: 5.9990 chunk 104 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.084488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.063266 restraints weight = 71847.301| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 3.59 r_work: 0.2944 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.0797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 9140 Z= 0.167 Angle : 0.510 7.986 12366 Z= 0.274 Chirality : 0.038 0.132 1429 Planarity : 0.003 0.038 1562 Dihedral : 12.658 166.521 1321 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.84 % Allowed : 17.44 % Favored : 79.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.25), residues: 1145 helix: 1.18 (0.19), residues: 752 sheet: -2.98 (1.11), residues: 22 loop : -1.48 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1181 TYR 0.010 0.001 TYR A1085 PHE 0.013 0.001 PHE A 308 TRP 0.006 0.001 TRP A 853 HIS 0.002 0.001 HIS A1255 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.17 ( 9140) covalent geometry : angle 0.51031 / 0.27 (12366) hydrogen bonds : bond 0.04382 / 2.92 ( 559) hydrogen bonds : angle 4.73225 / 3.47 ( 1635) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 61 time to evaluate : 0.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LEU cc_start: 0.9301 (mt) cc_final: 0.8857 (mt) REVERT: A 697 LEU cc_start: 0.8852 (mm) cc_final: 0.8574 (pp) REVERT: A 819 ASP cc_start: 0.8577 (m-30) cc_final: 0.8364 (m-30) outliers start: 27 outliers final: 23 residues processed: 86 average time/residue: 0.1488 time to fit residues: 20.0323 Evaluate side-chains 83 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 602 VAL Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 897 GLU Chi-restraints excluded: chain A residue 923 ILE Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 45 optimal weight: 4.9990 chunk 60 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 113 optimal weight: 3.9990 chunk 90 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 = 0.3565 r_free = 0.3565 target = 0.085010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.063923 restraints weight = 71265.157| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 3.56 r_work: 0.2960 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.0988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9140 Z= 0.139 Angle : 0.489 7.102 12366 Z= 0.261 Chirality : 0.037 0.132 1429 Planarity : 0.003 0.033 1562 Dihedral : 12.076 161.185 1319 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.15 % Allowed : 17.54 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.26), residues: 1145 helix: 1.37 (0.19), residues: 752 sheet: -2.86 (1.11), residues: 22 loop : -1.37 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1181 TYR 0.009 0.001 TYR A1085 PHE 0.010 0.001 PHE A 308 TRP 0.006 0.001 TRP A 853 HIS 0.001 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 9140) covalent geometry : angle 0.48896 / 0.26 (12366) hydrogen bonds : bond 0.04005 / 2.67 ( 559) hydrogen bonds : angle 4.47116 / 3.29 ( 1635) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 61 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 415 LEU cc_start: 0.9271 (mt) cc_final: 0.8842 (mt) REVERT: A 610 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8776 (mp0) REVERT: A 697 LEU cc_start: 0.8818 (mm) cc_final: 0.8539 (pp) REVERT: A 819 ASP cc_start: 0.8527 (m-30) cc_final: 0.8322 (m-30) outliers start: 30 outliers final: 22 residues processed: 89 average time/residue: 0.1503 time to fit residues: 20.6620 Evaluate side-chains 83 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 60 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 25 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 17 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.085367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.064221 restraints weight = 70864.135| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 3.57 r_work: 0.2968 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9140 Z= 0.129 Angle : 0.475 7.454 12366 Z= 0.253 Chirality : 0.037 0.130 1429 Planarity : 0.003 0.034 1562 Dihedral : 11.873 158.991 1316 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.73 % Allowed : 18.28 % Favored : 78.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.26), residues: 1145 helix: 1.47 (0.19), residues: 752 sheet: -2.82 (1.11), residues: 22 loop : -1.33 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1181 TYR 0.009 0.001 TYR A1085 PHE 0.010 0.001 PHE A 308 TRP 0.006 0.001 TRP A 853 HIS 0.001 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.13 ( 9140) covalent geometry : angle 0.47533 / 0.25 (12366) hydrogen bonds : bond 0.03871 / 2.58 ( 559) hydrogen bonds : angle 4.32876 / 3.19 ( 1635) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 60 time to evaluate : 0.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8331 (tpp) cc_final: 0.7968 (tpp) REVERT: A 610 GLU cc_start: 0.9076 (OUTLIER) cc_final: 0.8795 (mp0) REVERT: A 697 LEU cc_start: 0.8816 (mm) cc_final: 0.8546 (pp) outliers start: 26 outliers final: 22 residues processed: 83 average time/residue: 0.1462 time to fit residues: 19.1074 Evaluate side-chains 80 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 397 ILE Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 85 optimal weight: 1.9990 chunk 113 optimal weight: 4.9990 chunk 25 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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 = 0.3581 r_free = 0.3581 target = 0.084584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.063558 restraints weight = 71368.087| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.43 r_work: 0.2985 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9140 Z= 0.149 Angle : 0.490 7.814 12366 Z= 0.259 Chirality : 0.037 0.131 1429 Planarity : 0.003 0.034 1562 Dihedral : 11.796 157.592 1315 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.94 % Allowed : 18.17 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1145 helix: 1.51 (0.19), residues: 752 sheet: -2.80 (1.11), residues: 22 loop : -1.33 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.009 0.001 TYR A1085 PHE 0.011 0.001 PHE A 308 TRP 0.006 0.001 TRP A 853 HIS 0.002 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.15 ( 9140) covalent geometry : angle 0.48993 / 0.26 (12366) hydrogen bonds : bond 0.03867 / 2.58 ( 559) hydrogen bonds : angle 4.29192 / 3.17 ( 1635) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.518 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8421 (tpp) cc_final: 0.8058 (tpp) REVERT: A 610 GLU cc_start: 0.9063 (OUTLIER) cc_final: 0.8805 (mp0) REVERT: A 697 LEU cc_start: 0.8814 (mm) cc_final: 0.8558 (pp) outliers start: 28 outliers final: 25 residues processed: 83 average time/residue: 0.1589 time to fit residues: 20.5540 Evaluate side-chains 82 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 29 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 98 optimal weight: 1.9990 chunk 49 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- 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 = 0.3577 r_free = 0.3577 target = 0.084302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.063136 restraints weight = 72287.318| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 3.50 r_work: 0.2969 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9140 Z= 0.168 Angle : 0.494 8.266 12366 Z= 0.263 Chirality : 0.037 0.131 1429 Planarity : 0.003 0.034 1562 Dihedral : 11.753 156.548 1315 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.98 % Favored : 94.93 % Rotamer: Outliers : 2.94 % Allowed : 17.86 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.26), residues: 1145 helix: 1.49 (0.19), residues: 752 sheet: -2.73 (1.13), residues: 22 loop : -1.34 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.010 0.001 TYR A1085 PHE 0.011 0.001 PHE A 308 TRP 0.006 0.001 TRP A 853 HIS 0.002 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00358 / 0.17 ( 9140) covalent geometry : angle 0.49430 / 0.26 (12366) hydrogen bonds : bond 0.03899 / 2.59 ( 559) hydrogen bonds : angle 4.30210 / 3.18 ( 1635) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 55 time to evaluate : 0.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 610 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8808 (mp0) REVERT: A 697 LEU cc_start: 0.8822 (mm) cc_final: 0.8563 (pp) outliers start: 28 outliers final: 26 residues processed: 81 average time/residue: 0.1610 time to fit residues: 20.1015 Evaluate side-chains 82 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 55 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 718 THR Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 90 optimal weight: 0.5980 chunk 47 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 = 0.3589 r_free = 0.3589 target = 0.085050 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.064053 restraints weight = 71231.899| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 3.48 r_work: 0.2991 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2991 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9140 Z= 0.123 Angle : 0.475 7.474 12366 Z= 0.249 Chirality : 0.037 0.129 1429 Planarity : 0.003 0.031 1562 Dihedral : 11.663 153.947 1315 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 2.84 % Allowed : 17.96 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.26), residues: 1145 helix: 1.62 (0.19), residues: 752 sheet: -2.66 (1.13), residues: 22 loop : -1.26 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 409 TYR 0.013 0.001 TYR A 981 PHE 0.010 0.001 PHE A 308 TRP 0.006 0.001 TRP A 853 HIS 0.002 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 ( 9140) covalent geometry : angle 0.47516 / 0.25 (12366) hydrogen bonds : bond 0.03730 / 2.49 ( 559) hydrogen bonds : angle 4.14966 / 3.07 ( 1635) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8374 (tpp) cc_final: 0.8100 (tpp) REVERT: A 610 GLU cc_start: 0.9032 (OUTLIER) cc_final: 0.8791 (mp0) REVERT: A 697 LEU cc_start: 0.8818 (mm) cc_final: 0.8567 (pp) REVERT: A 1093 MET cc_start: 0.8704 (ttp) cc_final: 0.7917 (tpt) outliers start: 27 outliers final: 24 residues processed: 82 average time/residue: 0.1721 time to fit residues: 21.6257 Evaluate side-chains 80 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 55 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 770 LEU Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 87 optimal weight: 0.0060 chunk 49 optimal weight: 10.0000 chunk 113 optimal weight: 9.9990 chunk 56 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.084656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.063573 restraints weight = 71419.906| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.49 r_work: 0.2984 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9140 Z= 0.139 Angle : 0.482 8.522 12366 Z= 0.253 Chirality : 0.037 0.129 1429 Planarity : 0.003 0.031 1562 Dihedral : 11.577 151.044 1315 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.37 % Rotamer: Outliers : 2.73 % Allowed : 18.17 % Favored : 79.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.26), residues: 1145 helix: 1.64 (0.19), residues: 752 sheet: -2.60 (1.14), residues: 22 loop : -1.22 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 409 TYR 0.009 0.001 TYR A 981 PHE 0.012 0.001 PHE A 308 TRP 0.006 0.001 TRP A 853 HIS 0.002 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.14 ( 9140) covalent geometry : angle 0.48234 / 0.25 (12366) hydrogen bonds : bond 0.03721 / 2.48 ( 559) hydrogen bonds : angle 4.15691 / 3.08 ( 1635) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 57 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8404 (tpp) cc_final: 0.8091 (tpp) REVERT: A 610 GLU cc_start: 0.9037 (OUTLIER) cc_final: 0.8808 (mp0) REVERT: A 697 LEU cc_start: 0.8818 (mm) cc_final: 0.8568 (pp) outliers start: 26 outliers final: 24 residues processed: 81 average time/residue: 0.1652 time to fit residues: 20.4941 Evaluate side-chains 81 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 610 GLU Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 764 SER Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 856 THR Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 91 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 114 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 56 optimal weight: 0.9980 chunk 49 optimal weight: 8.9990 chunk 77 optimal weight: 0.4980 chunk 87 optimal weight: 0.0770 overall best weight: 0.8340 ------------------------------------------------------------------------------- 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 = 0.3595 r_free = 0.3595 target = 0.085347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.064238 restraints weight = 71034.743| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 3.50 r_work: 0.2997 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9140 Z= 0.111 Angle : 0.473 8.318 12366 Z= 0.245 Chirality : 0.037 0.130 1429 Planarity : 0.003 0.030 1562 Dihedral : 11.493 151.636 1315 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.21 % Allowed : 18.91 % Favored : 78.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.26), residues: 1145 helix: 1.74 (0.19), residues: 752 sheet: -2.57 (1.14), residues: 22 loop : -1.17 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 623 TYR 0.007 0.001 TYR A1085 PHE 0.010 0.001 PHE A 308 TRP 0.006 0.001 TRP A 853 HIS 0.002 0.000 HIS A 934 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.11 ( 9140) covalent geometry : angle 0.47261 / 0.25 (12366) hydrogen bonds : bond 0.03619 / 2.42 ( 559) hydrogen bonds : angle 4.04943 / 3.00 ( 1635) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2290 Ramachandran restraints generated. 1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 313 MET cc_start: 0.8395 (tpp) cc_final: 0.8111 (tpp) REVERT: A 697 LEU cc_start: 0.8812 (mm) cc_final: 0.8548 (pp) outliers start: 21 outliers final: 21 residues processed: 75 average time/residue: 0.1420 time to fit residues: 16.5215 Evaluate side-chains 77 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 56 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 73 MET Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 298 ILE Chi-restraints excluded: chain A residue 314 SER Chi-restraints excluded: chain A residue 323 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 527 THR Chi-restraints excluded: chain A residue 587 THR Chi-restraints excluded: chain A residue 628 HIS Chi-restraints excluded: chain A residue 732 SER Chi-restraints excluded: chain A residue 762 VAL Chi-restraints excluded: chain A residue 797 GLN Chi-restraints excluded: chain A residue 862 ILE Chi-restraints excluded: chain A residue 868 VAL Chi-restraints excluded: chain A residue 943 SER Chi-restraints excluded: chain A residue 1067 VAL Chi-restraints excluded: chain A residue 1098 ASP Chi-restraints excluded: chain A residue 1225 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 115 random chunks: chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 28 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.083399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.061958 restraints weight = 71712.392| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 3.46 r_work: 0.2962 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9140 Z= 0.198 Angle : 0.513 8.937 12366 Z= 0.273 Chirality : 0.038 0.132 1429 Planarity : 0.003 0.032 1562 Dihedral : 11.493 152.153 1315 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.63 % Allowed : 18.70 % Favored : 78.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1145 helix: 1.58 (0.19), residues: 753 sheet: -2.52 (1.15), residues: 22 loop : -1.30 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 623 TYR 0.014 0.001 TYR A 981 PHE 0.012 0.001 PHE A 308 TRP 0.005 0.001 TRP A 853 HIS 0.003 0.001 HIS A 158 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 ( 9140) covalent geometry : angle 0.51335 / 0.27 (12366) hydrogen bonds : bond 0.03851 / 2.56 ( 559) hydrogen bonds : angle 4.22855 / 3.14 ( 1635) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3378.84 seconds wall clock time: 58 minutes 6.53 seconds (3486.53 seconds total)