Starting phenix.real_space_refine on Wed Aug 5 18:49:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c5s_16442/08_2026/8c5s_16442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5s_16442/08_2026/8c5s_16442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8c5s_16442/08_2026/8c5s_16442.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c5s_16442/08_2026/8c5s_16442.cif" model { file = "/net/cci-nas-00/data/ceres_data/8c5s_16442/08_2026/8c5s_16442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5s_16442/08_2026/8c5s_16442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c5s_16442/08_2026/8c5s_16442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5s_16442/08_2026/8c5s_16442.map" } resolution = 3.75 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= 0.018 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 65 5.49 5 S 36 5.16 5 C 7038 2.51 5 N 1960 2.21 5 O 2213 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11312 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2758 Classifications: {'peptide': 336} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 316} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 7244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 924, 7244 Classifications: {'peptide': 924} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 44, 'TRANS': 879} Chain breaks: 2 Unresolved non-hydrogen bonds: 172 Unresolved non-hydrogen angles: 209 Unresolved non-hydrogen dihedrals: 135 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 80 Chain: "N" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 580 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "T" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 569 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNAv2': 6} Modifications used: {'rna3p_pur': 4, 'rna3p_pyr': 2} Link IDs: {'rna3p': 5} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 32 Unusual residues: {'GTP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.00, per 1000 atoms: 0.27 Number of scatterers: 11312 At special positions: 0 Unit cell: (104.76, 116.4, 119.31, 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 36 16.00 P 65 15.00 O 2213 8.00 N 1960 7.00 C 7038 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.88 Conformation dependent library (CDL) restraints added in 758.9 milliseconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2384 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 10 sheets defined 57.1% alpha, 7.5% beta 23 base pairs and 46 stacking pairs defined. Time for finding SS restraints: 1.32 Creating SS restraints... Processing helix chain 'B' and resid 7 through 14 removed outlier: 3.686A pdb=" N LEU B 14 " --> pdb=" O ASP B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 37 removed outlier: 3.607A pdb=" N TYR B 29 " --> pdb=" O ASN B 25 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASP B 37 " --> pdb=" O PHE B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 37 through 42 removed outlier: 4.122A pdb=" N THR B 41 " --> pdb=" O ASP B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 47 Processing helix chain 'B' and resid 58 through 69 Processing helix chain 'B' and resid 79 through 90 Processing helix chain 'B' and resid 104 through 113 removed outlier: 4.098A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.830A pdb=" N ILE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLY B 155 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 160 through 164 removed outlier: 3.576A pdb=" N PHE B 163 " --> pdb=" O LEU B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 190 through 200 Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 217 through 225 removed outlier: 4.070A pdb=" N GLU B 222 " --> pdb=" O SER B 218 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLU B 223 " --> pdb=" O GLN B 219 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.617A pdb=" N ILE B 234 " --> pdb=" O ALA B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 266 Processing helix chain 'B' and resid 273 through 278 removed outlier: 3.578A pdb=" N VAL B 277 " --> pdb=" O PRO B 273 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N MET B 278 " --> pdb=" O LEU B 274 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 273 through 278' Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 284 through 293 removed outlier: 3.618A pdb=" N TYR B 288 " --> pdb=" O GLY B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 300 removed outlier: 3.557A pdb=" N LEU B 299 " --> pdb=" O ASP B 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.548A pdb=" N GLU B 320 " --> pdb=" O LYS B 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 Processing helix chain 'A' and resid 397 through 421 removed outlier: 5.057A pdb=" N ASP A 414 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 442 removed outlier: 4.138A pdb=" N ALA A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 474 Proline residue: A 463 - end of helix Processing helix chain 'A' and resid 487 through 492 Processing helix chain 'A' and resid 492 through 501 Proline residue: A 498 - end of helix removed outlier: 3.525A pdb=" N THR A 501 " --> pdb=" O GLY A 497 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 517 Processing helix chain 'A' and resid 531 through 552 removed outlier: 3.571A pdb=" N LEU A 552 " --> pdb=" O SER A 548 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 Processing helix chain 'A' and resid 652 through 662 Processing helix chain 'A' and resid 703 through 717 removed outlier: 4.074A pdb=" N VAL A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 719 through 731 Processing helix chain 'A' and resid 738 through 749 Processing helix chain 'A' and resid 775 through 813 removed outlier: 3.568A pdb=" N LEU A 779 " --> pdb=" O ASP A 775 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 848 removed outlier: 3.588A pdb=" N LEU A 848 " --> pdb=" O MET A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 860 through 872 Processing helix chain 'A' and resid 879 through 889 Processing helix chain 'A' and resid 890 through 900 removed outlier: 3.526A pdb=" N ASN A 900 " --> pdb=" O ASP A 896 " (cutoff:3.500A) Processing helix chain 'A' and resid 907 through 911 Processing helix chain 'A' and resid 913 through 930 Processing helix chain 'A' and resid 948 through 959 Processing helix chain 'A' and resid 961 through 966 Processing helix chain 'A' and resid 977 through 994 Processing helix chain 'A' and resid 998 through 1004 Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 4.068A pdb=" N VAL A1013 " --> pdb=" O THR A1009 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1036 Processing helix chain 'A' and resid 1037 through 1041 removed outlier: 3.926A pdb=" N PHE A1041 " --> pdb=" O SER A1038 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1063 Processing helix chain 'A' and resid 1067 through 1085 removed outlier: 3.514A pdb=" N LEU A1071 " --> pdb=" O HIS A1067 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE A1072 " --> pdb=" O SER A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1149 through 1180 removed outlier: 3.995A pdb=" N GLN A1153 " --> pdb=" O ASN A1149 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N LYS A1154 " --> pdb=" O ALA A1150 " (cutoff:3.500A) Proline residue: A1158 - end of helix removed outlier: 3.833A pdb=" N ALA A1167 " --> pdb=" O HIS A1163 " (cutoff:3.500A) Processing helix chain 'A' and resid 1197 through 1213 Processing helix chain 'A' and resid 1216 through 1229 Processing helix chain 'A' and resid 1242 through 1257 Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.697A pdb=" N SER A1281 " --> pdb=" O GLU A1277 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1292 Processing helix chain 'A' and resid 1295 through 1300 Processing helix chain 'A' and resid 1305 through 1311 removed outlier: 3.834A pdb=" N GLU A1310 " --> pdb=" O LEU A1306 " (cutoff:3.500A) Processing helix chain 'A' and resid 1339 through 1345 removed outlier: 3.557A pdb=" N VAL A1342 " --> pdb=" O ASP A1339 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ASN A1345 " --> pdb=" O VAL A1342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.647A pdb=" N GLU B 77 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER B 74 " --> pdb=" O VAL B 50 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU B 76 " --> pdb=" O ASP B 52 " (cutoff:3.500A) removed outlier: 10.435A pdb=" N LYS B 165 " --> pdb=" O ASP B 130 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE B 132 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N LYS B 167 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA B 206 " --> pdb=" O LEU B 244 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N GLU B 246 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N LEU B 204 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N ILE B 227 " --> pdb=" O LYS B 203 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ILE B 205 " --> pdb=" O ILE B 227 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 528 through 530 Processing sheet with id=AA3, first strand: chain 'A' and resid 614 through 616 Processing sheet with id=AA4, first strand: chain 'A' and resid 818 through 819 Processing sheet with id=AA5, first strand: chain 'A' and resid 822 through 824 Processing sheet with id=AA6, first strand: chain 'A' and resid 855 through 856 removed outlier: 3.969A pdb=" N LYS A 855 " --> pdb=" O SER A 938 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER A 938 " --> pdb=" O LYS A 855 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 942 through 944 removed outlier: 3.648A pdb=" N THR A1193 " --> pdb=" O VAL A 942 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1087 through 1088 Processing sheet with id=AA9, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id=AB1, first strand: chain 'A' and resid 1127 through 1131 508 hydrogen bonds defined for protein. 1461 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 51 hydrogen bonds 102 hydrogen bond angles 0 basepair planarities 23 basepair parallelities 46 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.27 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: 3140 1.34 - 1.45: 2231 1.45 - 1.57: 6142 1.57 - 1.69: 133 1.69 - 1.81: 62 Bond restraints: 11708 Sorted by residual: bond pdb=" C3' DG N 113 " pdb=" C2' DG N 113 " ideal model delta sigma weight residual 1.516 1.623 -0.107 8.00e-03 1.56e+04 1.79e+02 bond pdb=" C3' DG N 136 " pdb=" C2' DG N 136 " ideal model delta sigma weight residual 1.516 1.620 -0.104 8.00e-03 1.56e+04 1.69e+02 bond pdb=" C3' DT N 111 " pdb=" C2' DT N 111 " ideal model delta sigma weight residual 1.516 1.619 -0.103 8.00e-03 1.56e+04 1.65e+02 bond pdb=" C3' DT T 20 " pdb=" C2' DT T 20 " ideal model delta sigma weight residual 1.516 1.608 -0.092 8.00e-03 1.56e+04 1.31e+02 bond pdb=" O3' DC T 24 " pdb=" P DG T 25 " ideal model delta sigma weight residual 1.607 1.728 -0.121 1.20e-02 6.94e+03 1.02e+02 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 15970 4.50 - 9.00: 140 9.00 - 13.50: 22 13.50 - 18.00: 5 18.00 - 22.50: 3 Bond angle restraints: 16140 Sorted by residual: angle pdb=" C3' DA T 35 " pdb=" O3' DA T 35 " pdb=" P DT T 36 " ideal model delta sigma weight residual 119.70 99.37 20.33 1.20e+00 6.94e-01 2.87e+02 angle pdb=" C3' A C 104 " pdb=" O3' A C 104 " pdb=" P A C 105 " ideal model delta sigma weight residual 119.70 101.23 18.47 1.20e+00 6.94e-01 2.37e+02 angle pdb=" C3' DC T 17 " pdb=" O3' DC T 17 " pdb=" P DA T 18 " ideal model delta sigma weight residual 119.70 135.17 -15.47 1.20e+00 6.94e-01 1.66e+02 angle pdb=" C3' DT T 19 " pdb=" O3' DT T 19 " pdb=" P DT T 20 " ideal model delta sigma weight residual 119.70 107.31 12.39 1.20e+00 6.94e-01 1.07e+02 angle pdb=" O4' DG T 16 " pdb=" C1' DG T 16 " pdb=" C2' DG T 16 " ideal model delta sigma weight residual 105.90 113.12 -7.22 8.00e-01 1.56e+00 8.16e+01 ... (remaining 16135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.06: 6428 30.06 - 60.11: 443 60.11 - 90.17: 23 90.17 - 120.22: 2 120.22 - 150.28: 4 Dihedral angle restraints: 6900 sinusoidal: 3220 harmonic: 3680 Sorted by residual: dihedral pdb=" O5' GTP C 201 " pdb=" O3A GTP C 201 " pdb=" PA GTP C 201 " pdb=" PB GTP C 201 " ideal model delta sinusoidal sigma weight residual -85.88 55.19 -141.07 1 2.00e+01 2.50e-03 4.27e+01 dihedral pdb=" O3A GTP C 201 " pdb=" O3B GTP C 201 " pdb=" PB GTP C 201 " pdb=" PG GTP C 201 " ideal model delta sinusoidal sigma weight residual 303.79 167.39 136.40 1 2.00e+01 2.50e-03 4.14e+01 dihedral pdb=" C8 GTP C 201 " pdb=" C1' GTP C 201 " pdb=" N9 GTP C 201 " pdb=" O4' GTP C 201 " ideal model delta sinusoidal sigma weight residual 104.59 -18.61 123.20 1 2.00e+01 2.50e-03 3.71e+01 ... (remaining 6897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1718 0.149 - 0.297: 31 0.297 - 0.446: 7 0.446 - 0.594: 25 0.594 - 0.743: 7 Chirality restraints: 1788 Sorted by residual: chirality pdb=" P A C 104 " pdb=" OP1 A C 104 " pdb=" OP2 A C 104 " pdb=" O5' A C 104 " both_signs ideal model delta sigma weight residual True 2.17 -2.92 -0.74 2.00e-01 2.50e+01 1.38e+01 chirality pdb=" C1' DG T 16 " pdb=" O4' DG T 16 " pdb=" C2' DG T 16 " pdb=" N9 DG T 16 " both_signs ideal model delta sigma weight residual False 2.43 1.75 0.68 2.00e-01 2.50e+01 1.16e+01 chirality pdb=" P DT N 109 " pdb=" OP1 DT N 109 " pdb=" OP2 DT N 109 " pdb=" O5' DT N 109 " both_signs ideal model delta sigma weight residual True 2.34 -2.97 -0.63 2.00e-01 2.50e+01 1.00e+01 ... (remaining 1785 not shown) Planarity restraints: 1841 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 900 " -0.056 5.00e-02 4.00e+02 8.44e-02 1.14e+01 pdb=" N PRO A 901 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO A 901 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 901 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 767 " 0.057 5.00e-02 4.00e+02 8.34e-02 1.11e+01 pdb=" N PRO A 768 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO A 768 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 768 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 462 " -0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO A 463 " 0.084 5.00e-02 4.00e+02 pdb=" CA PRO A 463 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 463 " -0.027 5.00e-02 4.00e+02 ... (remaining 1838 not shown) Histogram of nonbonded interaction distances: 1.84 - 2.45: 34 2.45 - 3.07: 7210 3.07 - 3.68: 17158 3.68 - 4.29: 25016 4.29 - 4.90: 40963 Nonbonded interactions: 90381 Sorted by model distance: nonbonded pdb=" OE1 GLN B 336 " pdb=" N2 DG T 25 " model vdw 1.842 3.120 nonbonded pdb=" O ASN A 900 " pdb=" OD1 ASN A 900 " model vdw 2.082 3.040 nonbonded pdb=" OG1 THR A1132 " pdb=" O GLN A1135 " model vdw 2.223 3.040 nonbonded pdb=" OE1 GLN A 944 " pdb=" OG SER A1351 " model vdw 2.253 3.040 nonbonded pdb=" OG SER A 794 " pdb=" N7 DG T 25 " model vdw 2.267 3.120 ... (remaining 90376 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 0.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.830 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 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 : 0.007 0.121 11709 Z= 0.566 Angle : 1.038 22.496 16140 Z= 0.594 Chirality : 0.091 0.743 1788 Planarity : 0.005 0.084 1841 Dihedral : 18.426 150.277 4516 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % 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 (0.24), residues: 1252 helix: 1.71 (0.21), residues: 649 sheet: -0.89 (0.49), residues: 111 loop : -1.04 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 264 TYR 0.024 0.001 TYR B 161 PHE 0.029 0.001 PHE A1338 TRP 0.023 0.001 TRP A 915 HIS 0.004 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00679 / 0.57 (11708) covalent geometry : angle 1.03834 / 0.59 (16140) hydrogen bonds : bond 0.14756 / 9.77 ( 559) hydrogen bonds : angle 6.18565 / 4.37 ( 1563) Misc. bond : bond 0.01822 / 0.96 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.344 Fit side-chains REVERT: A 476 LEU cc_start: 0.6034 (mt) cc_final: 0.5205 (tt) REVERT: A 1005 LYS cc_start: 0.7467 (tmmt) cc_final: 0.7193 (tttp) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.1059 time to fit residues: 28.3473 Evaluate side-chains 150 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 8.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 0.0020 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 40.0000 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 35 optimal weight: 7.9990 overall best weight: 4.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN B 187 HIS A 492 ASN A 900 ASN ** A 916 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 987 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.159848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.132108 restraints weight = 15428.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.133789 restraints weight = 11197.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.133996 restraints weight = 9608.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.134445 restraints weight = 8803.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134676 restraints weight = 8212.526| |-----------------------------------------------------------------------------| r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 11709 Z= 0.191 Angle : 0.661 9.849 16140 Z= 0.350 Chirality : 0.046 0.255 1788 Planarity : 0.005 0.056 1841 Dihedral : 20.013 162.507 2089 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 1.77 % Allowed : 8.01 % Favored : 90.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.24), residues: 1252 helix: 1.60 (0.21), residues: 662 sheet: -0.93 (0.45), residues: 129 loop : -1.18 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 79 TYR 0.027 0.002 TYR B 161 PHE 0.016 0.001 PHE B 118 TRP 0.016 0.002 TRP A 915 HIS 0.011 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (11708) covalent geometry : angle 0.66083 / 0.35 (16140) hydrogen bonds : bond 0.05508 / 3.59 ( 559) hydrogen bonds : angle 4.66976 / 3.34 ( 1563) Misc. bond : bond 0.00012 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 158 time to evaluate : 0.406 Fit side-chains REVERT: B 137 ASN cc_start: 0.9005 (OUTLIER) cc_final: 0.8563 (t0) REVERT: A 439 LYS cc_start: 0.6493 (tttt) cc_final: 0.6117 (tttt) outliers start: 19 outliers final: 12 residues processed: 169 average time/residue: 0.1022 time to fit residues: 25.1950 Evaluate side-chains 161 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 16 optimal weight: 8.9990 chunk 62 optimal weight: 6.9990 chunk 14 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 86 optimal weight: 3.9990 chunk 24 optimal weight: 7.9990 chunk 19 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 89 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN A 900 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.160249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.133286 restraints weight = 15429.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.134687 restraints weight = 11523.666| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.134983 restraints weight = 9839.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.135223 restraints weight = 9115.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.136505 restraints weight = 8442.137| |-----------------------------------------------------------------------------| r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11709 Z= 0.140 Angle : 0.593 9.456 16140 Z= 0.314 Chirality : 0.042 0.181 1788 Planarity : 0.004 0.051 1841 Dihedral : 19.735 171.128 2089 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 2.05 % Allowed : 11.28 % Favored : 86.67 % 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: 0.56 (0.24), residues: 1252 helix: 1.68 (0.21), residues: 664 sheet: -0.95 (0.44), residues: 129 loop : -1.18 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 264 TYR 0.010 0.001 TYR B 42 PHE 0.018 0.001 PHE A1338 TRP 0.016 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 (11708) covalent geometry : angle 0.59319 / 0.31 (16140) hydrogen bonds : bond 0.04856 / 3.17 ( 559) hydrogen bonds : angle 4.44825 / 3.18 ( 1563) Misc. bond : bond 0.00042 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.340 Fit side-chains REVERT: B 137 ASN cc_start: 0.8816 (OUTLIER) cc_final: 0.8259 (t0) REVERT: B 321 TRP cc_start: 0.7974 (t60) cc_final: 0.7010 (t60) outliers start: 22 outliers final: 16 residues processed: 169 average time/residue: 0.0883 time to fit residues: 21.7611 Evaluate side-chains 168 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 420 GLU Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1235 ILE Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 125 optimal weight: 40.0000 chunk 24 optimal weight: 8.9990 chunk 29 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 4 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 137 ASN A 900 ASN A 968 ASN A 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.160134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.132932 restraints weight = 15454.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133981 restraints weight = 11703.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.135176 restraints weight = 9409.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.136255 restraints weight = 8239.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.136560 restraints weight = 7315.382| |-----------------------------------------------------------------------------| r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11709 Z= 0.144 Angle : 0.597 10.415 16140 Z= 0.312 Chirality : 0.042 0.184 1788 Planarity : 0.004 0.052 1841 Dihedral : 19.381 143.609 2089 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.15 % Favored : 95.77 % Rotamer: Outliers : 2.24 % Allowed : 12.77 % Favored : 85.00 % 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: 0.57 (0.24), residues: 1252 helix: 1.71 (0.21), residues: 664 sheet: -1.03 (0.43), residues: 129 loop : -1.19 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 264 TYR 0.013 0.001 TYR A 690 PHE 0.013 0.001 PHE A 826 TRP 0.013 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.14 (11708) covalent geometry : angle 0.59748 / 0.31 (16140) hydrogen bonds : bond 0.04637 / 3.03 ( 559) hydrogen bonds : angle 4.39809 / 3.13 ( 1563) Misc. bond : bond 0.00059 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.323 Fit side-chains REVERT: B 137 ASN cc_start: 0.8901 (OUTLIER) cc_final: 0.8317 (t0) REVERT: B 247 MET cc_start: 0.8356 (mmt) cc_final: 0.7925 (tpp) REVERT: B 321 TRP cc_start: 0.7975 (t60) cc_final: 0.7244 (t60) REVERT: A 1215 VAL cc_start: 0.7652 (OUTLIER) cc_final: 0.7393 (t) outliers start: 24 outliers final: 15 residues processed: 167 average time/residue: 0.0905 time to fit residues: 21.9588 Evaluate side-chains 162 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 21 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 0.7980 chunk 80 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 chunk 89 optimal weight: 7.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 900 ASN A 987 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.160931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.133829 restraints weight = 15285.683| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.134605 restraints weight = 11835.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135922 restraints weight = 9383.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.137239 restraints weight = 8165.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.137600 restraints weight = 7236.552| |-----------------------------------------------------------------------------| r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11709 Z= 0.126 Angle : 0.578 9.724 16140 Z= 0.302 Chirality : 0.041 0.183 1788 Planarity : 0.004 0.052 1841 Dihedral : 19.174 137.880 2089 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.96 % Allowed : 14.07 % Favored : 83.97 % 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: 0.64 (0.24), residues: 1252 helix: 1.78 (0.21), residues: 664 sheet: -0.99 (0.43), residues: 129 loop : -1.18 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 264 TYR 0.010 0.001 TYR B 42 PHE 0.018 0.001 PHE A1338 TRP 0.014 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (11708) covalent geometry : angle 0.57811 / 0.30 (16140) hydrogen bonds : bond 0.04338 / 2.83 ( 559) hydrogen bonds : angle 4.29180 / 3.06 ( 1563) Misc. bond : bond 0.00072 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.306 Fit side-chains REVERT: B 321 TRP cc_start: 0.7950 (t60) cc_final: 0.7287 (t60) REVERT: A 1215 VAL cc_start: 0.7675 (OUTLIER) cc_final: 0.7412 (t) outliers start: 21 outliers final: 12 residues processed: 172 average time/residue: 0.0974 time to fit residues: 24.8117 Evaluate side-chains 164 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 1 optimal weight: 7.9990 chunk 34 optimal weight: 7.9990 chunk 49 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 61 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 52 optimal weight: 20.0000 overall best weight: 5.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN A 900 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.155418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.127871 restraints weight = 15688.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.129847 restraints weight = 13340.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.131154 restraints weight = 10908.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.131368 restraints weight = 9143.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131590 restraints weight = 8332.149| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 11709 Z= 0.212 Angle : 0.663 10.572 16140 Z= 0.346 Chirality : 0.045 0.187 1788 Planarity : 0.005 0.055 1841 Dihedral : 19.183 137.928 2089 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer: Outliers : 2.33 % Allowed : 14.54 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.24), residues: 1252 helix: 1.58 (0.21), residues: 662 sheet: -1.02 (0.43), residues: 129 loop : -1.30 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 264 TYR 0.028 0.002 TYR B 161 PHE 0.017 0.002 PHE A1349 TRP 0.018 0.002 TRP A 915 HIS 0.004 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00485 / 0.21 (11708) covalent geometry : angle 0.66283 / 0.35 (16140) hydrogen bonds : bond 0.05264 / 3.43 ( 559) hydrogen bonds : angle 4.45977 / 3.18 ( 1563) Misc. bond : bond 0.00034 / 0.02 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 150 time to evaluate : 0.508 Fit side-chains REVERT: B 114 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7590 (mp0) REVERT: B 321 TRP cc_start: 0.8117 (t60) cc_final: 0.7463 (t60) REVERT: A 461 MET cc_start: 0.8128 (ttm) cc_final: 0.7355 (ttm) REVERT: A 519 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7382 (pp) REVERT: A 1215 VAL cc_start: 0.7716 (OUTLIER) cc_final: 0.7446 (t) outliers start: 25 outliers final: 18 residues processed: 169 average time/residue: 0.1003 time to fit residues: 25.1848 Evaluate side-chains 167 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 519 LEU Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 910 THR Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 6.9990 chunk 57 optimal weight: 9.9990 chunk 38 optimal weight: 20.0000 chunk 51 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 29 optimal weight: 7.9990 chunk 13 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 105 optimal weight: 8.9990 chunk 88 optimal weight: 0.8980 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN A 900 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.157317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129245 restraints weight = 15526.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.132012 restraints weight = 12553.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.133346 restraints weight = 9128.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133720 restraints weight = 7608.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.134007 restraints weight = 7097.111| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11709 Z= 0.151 Angle : 0.607 9.326 16140 Z= 0.318 Chirality : 0.042 0.176 1788 Planarity : 0.004 0.054 1841 Dihedral : 19.098 137.299 2089 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.63 % Favored : 95.29 % Rotamer: Outliers : 2.42 % Allowed : 15.66 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.24), residues: 1252 helix: 1.62 (0.21), residues: 664 sheet: -1.08 (0.42), residues: 129 loop : -1.28 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 264 TYR 0.027 0.001 TYR B 161 PHE 0.021 0.001 PHE A1338 TRP 0.021 0.002 TRP A 915 HIS 0.003 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.15 (11708) covalent geometry : angle 0.60700 / 0.32 (16140) hydrogen bonds : bond 0.04598 / 2.98 ( 559) hydrogen bonds : angle 4.34962 / 3.11 ( 1563) Misc. bond : bond 0.00074 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 157 time to evaluate : 0.403 Fit side-chains REVERT: B 114 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7515 (mp0) REVERT: B 137 ASN cc_start: 0.9002 (t0) cc_final: 0.8522 (t0) REVERT: B 321 TRP cc_start: 0.8081 (t60) cc_final: 0.7453 (t60) REVERT: A 461 MET cc_start: 0.8171 (ttm) cc_final: 0.7478 (ttm) REVERT: A 1215 VAL cc_start: 0.7707 (OUTLIER) cc_final: 0.7441 (t) REVERT: A 1271 PHE cc_start: 0.4876 (m-80) cc_final: 0.3937 (t80) outliers start: 26 outliers final: 17 residues processed: 173 average time/residue: 0.0991 time to fit residues: 25.2526 Evaluate side-chains 171 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 152 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 2 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 1 optimal weight: 8.9990 chunk 61 optimal weight: 0.6980 chunk 125 optimal weight: 40.0000 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 46 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN A 639 GLN A 900 ASN A 987 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.157849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.130030 restraints weight = 15447.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.132328 restraints weight = 12204.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.133631 restraints weight = 9218.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.134527 restraints weight = 7736.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.134675 restraints weight = 7151.859| |-----------------------------------------------------------------------------| r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11709 Z= 0.149 Angle : 0.607 9.541 16140 Z= 0.316 Chirality : 0.042 0.177 1788 Planarity : 0.004 0.053 1841 Dihedral : 19.010 136.875 2089 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.39 % Favored : 95.53 % Rotamer: Outliers : 2.42 % Allowed : 15.94 % Favored : 81.64 % 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: 0.46 (0.24), residues: 1252 helix: 1.65 (0.21), residues: 664 sheet: -1.08 (0.42), residues: 129 loop : -1.29 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 264 TYR 0.014 0.001 TYR B 83 PHE 0.023 0.001 PHE A1338 TRP 0.024 0.002 TRP A 915 HIS 0.003 0.001 HIS A1169 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.15 (11708) covalent geometry : angle 0.60674 / 0.32 (16140) hydrogen bonds : bond 0.04488 / 2.92 ( 559) hydrogen bonds : angle 4.28905 / 3.07 ( 1563) Misc. bond : bond 0.00078 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.400 Fit side-chains REVERT: B 114 GLU cc_start: 0.7815 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: B 137 ASN cc_start: 0.9002 (t0) cc_final: 0.8562 (t0) REVERT: B 321 TRP cc_start: 0.8067 (t60) cc_final: 0.7629 (t60) REVERT: A 1215 VAL cc_start: 0.7706 (OUTLIER) cc_final: 0.7403 (t) REVERT: A 1271 PHE cc_start: 0.4946 (m-80) cc_final: 0.3985 (t80) outliers start: 26 outliers final: 19 residues processed: 171 average time/residue: 0.1002 time to fit residues: 25.2603 Evaluate side-chains 171 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 150 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 99 optimal weight: 4.9990 chunk 26 optimal weight: 9.9990 chunk 54 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 112 optimal weight: 4.9990 chunk 90 optimal weight: 20.0000 chunk 115 optimal weight: 7.9990 chunk 119 optimal weight: 40.0000 chunk 65 optimal weight: 0.9980 chunk 124 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN A 900 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.156774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129821 restraints weight = 15409.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.130494 restraints weight = 12740.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.131640 restraints weight = 10985.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.131988 restraints weight = 9755.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.132199 restraints weight = 8923.360| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11709 Z= 0.178 Angle : 0.626 9.605 16140 Z= 0.325 Chirality : 0.043 0.176 1788 Planarity : 0.004 0.053 1841 Dihedral : 19.010 136.798 2089 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 2.42 % Allowed : 16.12 % Favored : 81.45 % 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: 0.42 (0.24), residues: 1252 helix: 1.61 (0.21), residues: 662 sheet: -1.10 (0.42), residues: 129 loop : -1.30 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 264 TYR 0.027 0.002 TYR B 73 PHE 0.025 0.001 PHE A1338 TRP 0.026 0.002 TRP A 915 HIS 0.003 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00410 / 0.18 (11708) covalent geometry : angle 0.62593 / 0.33 (16140) hydrogen bonds : bond 0.04717 / 3.07 ( 559) hydrogen bonds : angle 4.34947 / 3.10 ( 1563) Misc. bond : bond 0.00063 / 0.03 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.414 Fit side-chains REVERT: B 114 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: B 137 ASN cc_start: 0.9014 (t0) cc_final: 0.8562 (t0) REVERT: B 321 TRP cc_start: 0.8100 (t60) cc_final: 0.7588 (t60) REVERT: A 1215 VAL cc_start: 0.7718 (OUTLIER) cc_final: 0.7440 (t) REVERT: A 1271 PHE cc_start: 0.4829 (m-80) cc_final: 0.3842 (t80) outliers start: 26 outliers final: 21 residues processed: 170 average time/residue: 0.1005 time to fit residues: 25.2332 Evaluate side-chains 169 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1210 ILE Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 10 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 61 optimal weight: 20.0000 chunk 93 optimal weight: 6.9990 chunk 116 optimal weight: 20.0000 chunk 115 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN A 900 ASN A 987 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.156820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129729 restraints weight = 15459.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.130777 restraints weight = 12650.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.131833 restraints weight = 11109.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.132303 restraints weight = 9274.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.132540 restraints weight = 8727.004| |-----------------------------------------------------------------------------| r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 11709 Z= 0.163 Angle : 0.624 9.334 16140 Z= 0.323 Chirality : 0.042 0.175 1788 Planarity : 0.004 0.053 1841 Dihedral : 18.994 136.572 2089 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.55 % Favored : 95.37 % Rotamer: Outliers : 2.42 % Allowed : 16.40 % Favored : 81.17 % 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: 0.42 (0.24), residues: 1252 helix: 1.60 (0.21), residues: 665 sheet: -1.10 (0.42), residues: 129 loop : -1.29 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 264 TYR 0.025 0.001 TYR B 73 PHE 0.026 0.001 PHE A1338 TRP 0.028 0.002 TRP A 915 HIS 0.003 0.001 HIS B 265 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 (11708) covalent geometry : angle 0.62450 / 0.32 (16140) hydrogen bonds : bond 0.04600 / 2.99 ( 559) hydrogen bonds : angle 4.33477 / 3.09 ( 1563) Misc. bond : bond 0.00070 / 0.04 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 154 time to evaluate : 0.404 Fit side-chains REVERT: B 114 GLU cc_start: 0.7851 (OUTLIER) cc_final: 0.7566 (mp0) REVERT: B 137 ASN cc_start: 0.8980 (t0) cc_final: 0.8526 (t0) REVERT: B 321 TRP cc_start: 0.8092 (t60) cc_final: 0.7587 (t60) REVERT: A 461 MET cc_start: 0.7891 (ttm) cc_final: 0.7024 (ttm) REVERT: A 1051 SER cc_start: 0.7496 (t) cc_final: 0.7174 (p) REVERT: A 1215 VAL cc_start: 0.7732 (OUTLIER) cc_final: 0.7455 (t) REVERT: A 1271 PHE cc_start: 0.4783 (m-80) cc_final: 0.3808 (t80) outliers start: 26 outliers final: 20 residues processed: 171 average time/residue: 0.0970 time to fit residues: 24.5539 Evaluate side-chains 172 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 692 TYR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain A residue 996 LYS Chi-restraints excluded: chain A residue 1024 VAL Chi-restraints excluded: chain A residue 1096 PHE Chi-restraints excluded: chain A residue 1146 ASN Chi-restraints excluded: chain A residue 1186 SER Chi-restraints excluded: chain A residue 1187 VAL Chi-restraints excluded: chain A residue 1189 ASP Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 125 optimal weight: 40.0000 chunk 128 optimal weight: 30.0000 chunk 12 optimal weight: 7.9990 chunk 79 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 overall best weight: 4.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 287 GLN A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.156221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.129158 restraints weight = 15505.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.130322 restraints weight = 12776.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131335 restraints weight = 11154.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.131502 restraints weight = 9370.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.133322 restraints weight = 8834.384| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7856 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 11709 Z= 0.183 Angle : 0.637 9.553 16140 Z= 0.330 Chirality : 0.043 0.175 1788 Planarity : 0.004 0.053 1841 Dihedral : 19.011 136.601 2089 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 2.24 % Allowed : 17.05 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.24), residues: 1252 helix: 1.56 (0.21), residues: 665 sheet: -1.21 (0.43), residues: 125 loop : -1.33 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 264 TYR 0.025 0.002 TYR B 73 PHE 0.025 0.002 PHE A1338 TRP 0.036 0.002 TRP A 915 HIS 0.003 0.001 HIS B 187 Details of bonding type rmsd/Z covalent geometry : bond 0.00422 / 0.18 (11708) covalent geometry : angle 0.63705 / 0.33 (16140) hydrogen bonds : bond 0.04803 / 3.12 ( 559) hydrogen bonds : angle 4.39487 / 3.14 ( 1563) Misc. bond : bond 0.00062 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1553.39 seconds wall clock time: 27 minutes 45.25 seconds (1665.25 seconds total)