Starting phenix.real_space_refine on Wed May 14 02:29:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c5s_16442/05_2025/8c5s_16442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c5s_16442/05_2025/8c5s_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8c5s_16442/05_2025/8c5s_16442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c5s_16442/05_2025/8c5s_16442.map" model { file = "/net/cci-nas-00/data/ceres_data/8c5s_16442/05_2025/8c5s_16442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c5s_16442/05_2025/8c5s_16442.cif" } resolution = 3.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 2, 'GLU:plan': 9, 'ARG:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 6} 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: {'RNA': 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: 6.89, per 1000 atoms: 0.61 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: 3.25 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 4.10 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: 4.70 Time building geometry restraints manager: 3.72 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=" O3' DC T 24 " pdb=" P DG T 25 " ideal model delta sigma weight residual 1.607 1.728 -0.121 1.50e-02 4.44e+03 6.56e+01 bond pdb=" O3' DT N 135 " pdb=" P DG N 136 " ideal model delta sigma weight residual 1.607 1.495 0.112 1.50e-02 4.44e+03 5.56e+01 bond pdb=" O3' DC T 17 " pdb=" P DA T 18 " ideal model delta sigma weight residual 1.607 1.499 0.108 1.50e-02 4.44e+03 5.16e+01 bond pdb=" O3' DA T 31 " pdb=" P DT T 32 " ideal model delta sigma weight residual 1.607 1.506 0.101 1.50e-02 4.44e+03 4.56e+01 bond pdb=" O3' DA T 34 " pdb=" P DA T 35 " ideal model delta sigma weight residual 1.607 1.523 0.084 1.50e-02 4.44e+03 3.15e+01 ... (remaining 11703 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.50: 15979 4.50 - 9.00: 129 9.00 - 13.50: 24 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 120.20 99.37 20.83 1.50e+00 4.44e-01 1.93e+02 angle pdb=" C3' A C 104 " pdb=" O3' A C 104 " pdb=" P A C 105 " ideal model delta sigma weight residual 120.20 101.23 18.97 1.50e+00 4.44e-01 1.60e+02 angle pdb=" C3' DC T 17 " pdb=" O3' DC T 17 " pdb=" P DA T 18 " ideal model delta sigma weight residual 120.20 135.17 -14.97 1.50e+00 4.44e-01 9.96e+01 angle pdb=" O3' DG N 136 " pdb=" C3' DG N 136 " pdb=" C2' DG N 136 " ideal model delta sigma weight residual 111.50 98.40 13.10 1.50e+00 4.44e-01 7.62e+01 angle pdb=" C3' DT T 19 " pdb=" O3' DT T 19 " pdb=" P DT T 20 " ideal model delta sigma weight residual 120.20 107.31 12.89 1.50e+00 4.44e-01 7.38e+01 ... (remaining 16135 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.06: 6440 30.06 - 60.11: 443 60.11 - 90.17: 25 90.17 - 120.22: 2 120.22 - 150.28: 4 Dihedral angle restraints: 6914 sinusoidal: 3234 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 6911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1716 0.134 - 0.268: 32 0.268 - 0.402: 7 0.402 - 0.536: 25 0.536 - 0.670: 8 Chirality restraints: 1788 Sorted by residual: 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 2.42 1.75 0.67 2.00e-01 2.50e+01 1.12e+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 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.69e+00 chirality pdb=" P DC T 10 " pdb=" OP1 DC T 10 " pdb=" OP2 DC T 10 " pdb=" O5' DC T 10 " both_signs ideal model delta sigma weight residual True 2.35 -2.97 -0.62 2.00e-01 2.50e+01 9.64e+00 ... (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: 0.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 31.960 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 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= 0.348 Angle : 1.037 22.496 16140 Z= 0.543 Chirality : 0.087 0.670 1788 Planarity : 0.005 0.084 1841 Dihedral : 18.483 150.277 4530 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.023 0.001 TRP A 915 HIS 0.004 0.001 HIS A1169 PHE 0.029 0.001 PHE A1338 TYR 0.024 0.001 TYR B 161 ARG 0.004 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.14756 ( 559) hydrogen bonds : angle 6.18565 ( 1563) covalent geometry : bond 0.00658 (11708) covalent geometry : angle 1.03711 (16140) Misc. bond : bond 0.01822 ( 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 : 1.191 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: 0.2561 time to fit residues: 67.6713 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 : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 117 optimal weight: 20.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 187 HIS A 492 ASN A 900 ASN A 987 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.161971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.135179 restraints weight = 15171.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.135638 restraints weight = 11385.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.137217 restraints weight = 9394.916| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11709 Z= 0.138 Angle : 0.570 9.573 16140 Z= 0.303 Chirality : 0.039 0.142 1788 Planarity : 0.005 0.057 1841 Dihedral : 19.943 167.118 2103 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.77 % Allowed : 7.27 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.25), residues: 1252 helix: 1.72 (0.21), residues: 667 sheet: -0.83 (0.45), residues: 129 loop : -1.10 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 915 HIS 0.010 0.001 HIS B 187 PHE 0.013 0.001 PHE B 118 TYR 0.026 0.001 TYR B 161 ARG 0.003 0.000 ARG A 883 Details of bonding type rmsd hydrogen bonds : bond 0.05021 ( 559) hydrogen bonds : angle 4.48062 ( 1563) covalent geometry : bond 0.00310 (11708) covalent geometry : angle 0.56999 (16140) Misc. bond : bond 0.00122 ( 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 182 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 1.182 Fit side-chains REVERT: A 439 LYS cc_start: 0.6558 (tttt) cc_final: 0.6166 (tttt) REVERT: A 476 LEU cc_start: 0.6071 (mt) cc_final: 0.5189 (tt) outliers start: 19 outliers final: 12 residues processed: 172 average time/residue: 0.2428 time to fit residues: 59.1818 Evaluate side-chains 164 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 896 ASP 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 1235 ILE Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 116 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 28 optimal weight: 9.9990 chunk 98 optimal weight: 9.9990 chunk 73 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 42 optimal weight: 30.0000 chunk 34 optimal weight: 0.8980 chunk 50 optimal weight: 9.9990 chunk 52 optimal weight: 20.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 265 HIS A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.156808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.129350 restraints weight = 15563.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.130904 restraints weight = 12897.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.132278 restraints weight = 11072.278| |-----------------------------------------------------------------------------| r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.1557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 11709 Z= 0.242 Angle : 0.651 8.770 16140 Z= 0.342 Chirality : 0.043 0.157 1788 Planarity : 0.005 0.055 1841 Dihedral : 19.511 141.910 2103 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.03 % Favored : 94.89 % Rotamer: Outliers : 2.05 % Allowed : 11.65 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1252 helix: 1.56 (0.21), residues: 662 sheet: -1.00 (0.44), residues: 129 loop : -1.27 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 915 HIS 0.004 0.001 HIS A 868 PHE 0.022 0.002 PHE B 318 TYR 0.024 0.002 TYR B 161 ARG 0.003 0.001 ARG A 731 Details of bonding type rmsd hydrogen bonds : bond 0.05434 ( 559) hydrogen bonds : angle 4.57307 ( 1563) covalent geometry : bond 0.00570 (11708) covalent geometry : angle 0.65106 (16140) Misc. bond : bond 0.00052 ( 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 172 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 150 time to evaluate : 1.205 Fit side-chains REVERT: B 247 MET cc_start: 0.8385 (mmt) cc_final: 0.8052 (tpp) REVERT: B 321 TRP cc_start: 0.8110 (t60) cc_final: 0.7449 (t60) outliers start: 22 outliers final: 17 residues processed: 164 average time/residue: 0.2352 time to fit residues: 55.9849 Evaluate side-chains 160 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 143 time to evaluate : 1.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 3.9990 chunk 32 optimal weight: 0.0070 chunk 47 optimal weight: 3.9990 chunk 59 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 101 optimal weight: 7.9990 chunk 114 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 73 optimal weight: 0.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN A 900 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.158612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.131904 restraints weight = 15373.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.133003 restraints weight = 11300.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.132997 restraints weight = 9587.957| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.1635 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= 0.141 Angle : 0.568 9.222 16140 Z= 0.298 Chirality : 0.039 0.143 1788 Planarity : 0.004 0.054 1841 Dihedral : 19.074 136.401 2103 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.23 % Favored : 95.69 % Rotamer: Outliers : 2.05 % Allowed : 14.07 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.24), residues: 1252 helix: 1.66 (0.21), residues: 664 sheet: -1.02 (0.43), residues: 129 loop : -1.22 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 PHE 0.015 0.001 PHE A 826 TYR 0.023 0.001 TYR B 161 ARG 0.003 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04353 ( 559) hydrogen bonds : angle 4.28638 ( 1563) covalent geometry : bond 0.00324 (11708) covalent geometry : angle 0.56814 (16140) Misc. bond : bond 0.00077 ( 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 182 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.183 Fit side-chains REVERT: B 114 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: B 137 ASN cc_start: 0.8992 (OUTLIER) cc_final: 0.8524 (t0) REVERT: B 321 TRP cc_start: 0.8049 (t60) cc_final: 0.7518 (t60) REVERT: A 1215 VAL cc_start: 0.7623 (OUTLIER) cc_final: 0.7341 (t) outliers start: 22 outliers final: 15 residues processed: 173 average time/residue: 0.2224 time to fit residues: 55.9950 Evaluate side-chains 163 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 145 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU 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 683 VAL Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain A residue 927 VAL 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 1215 VAL Chi-restraints excluded: chain A residue 1296 THR Chi-restraints excluded: chain A residue 1350 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 6.9990 chunk 120 optimal weight: 0.0060 chunk 112 optimal weight: 8.9990 chunk 74 optimal weight: 9.9990 chunk 52 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 12 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 20 optimal weight: 20.0000 chunk 90 optimal weight: 20.0000 overall best weight: 6.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN A 900 ASN A 968 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.155419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.128166 restraints weight = 15394.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.128879 restraints weight = 12752.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.129965 restraints weight = 11439.713| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 11709 Z= 0.218 Angle : 0.628 9.830 16140 Z= 0.329 Chirality : 0.041 0.146 1788 Planarity : 0.005 0.056 1841 Dihedral : 19.087 136.421 2103 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.27 % Favored : 94.65 % Rotamer: Outliers : 2.61 % Allowed : 14.82 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.24), residues: 1252 helix: 1.56 (0.21), residues: 662 sheet: -1.07 (0.43), residues: 129 loop : -1.30 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 915 HIS 0.003 0.001 HIS B 187 PHE 0.018 0.002 PHE A1338 TYR 0.026 0.002 TYR B 161 ARG 0.004 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04981 ( 559) hydrogen bonds : angle 4.44261 ( 1563) covalent geometry : bond 0.00515 (11708) covalent geometry : angle 0.62750 (16140) Misc. bond : bond 0.00041 ( 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 174 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 146 time to evaluate : 1.369 Fit side-chains REVERT: B 114 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7582 (mp0) REVERT: B 137 ASN cc_start: 0.9030 (OUTLIER) cc_final: 0.8493 (t0) REVERT: B 321 TRP cc_start: 0.8101 (t60) cc_final: 0.7639 (t60) REVERT: A 1215 VAL cc_start: 0.7669 (OUTLIER) cc_final: 0.7407 (t) REVERT: A 1271 PHE cc_start: 0.4892 (m-80) cc_final: 0.3928 (t80) outliers start: 28 outliers final: 18 residues processed: 166 average time/residue: 0.2390 time to fit residues: 57.9243 Evaluate side-chains 159 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 138 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain A residue 395 LEU 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 683 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 20.0000 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 49 optimal weight: 30.0000 chunk 124 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 16 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 GLN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.153362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.125635 restraints weight = 15733.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.127691 restraints weight = 13227.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.128765 restraints weight = 11123.070| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 11709 Z= 0.253 Angle : 0.662 10.904 16140 Z= 0.348 Chirality : 0.043 0.151 1788 Planarity : 0.005 0.057 1841 Dihedral : 19.156 136.594 2103 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.59 % Favored : 94.25 % Rotamer: Outliers : 3.17 % Allowed : 14.82 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.24), residues: 1252 helix: 1.42 (0.21), residues: 661 sheet: -1.13 (0.43), residues: 129 loop : -1.37 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 235 HIS 0.004 0.001 HIS B 187 PHE 0.019 0.002 PHE A1349 TYR 0.022 0.002 TYR B 161 ARG 0.003 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.05325 ( 559) hydrogen bonds : angle 4.56823 ( 1563) covalent geometry : bond 0.00596 (11708) covalent geometry : angle 0.66243 (16140) Misc. bond : bond 0.00027 ( 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 173 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.204 Fit side-chains REVERT: B 114 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: B 137 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8764 (t0) REVERT: A 461 MET cc_start: 0.8042 (ttm) cc_final: 0.7220 (ttm) REVERT: A 1051 SER cc_start: 0.7590 (t) cc_final: 0.7264 (p) REVERT: A 1215 VAL cc_start: 0.7658 (OUTLIER) cc_final: 0.7425 (t) REVERT: A 1271 PHE cc_start: 0.4879 (m-80) cc_final: 0.3795 (t80) outliers start: 34 outliers final: 22 residues processed: 165 average time/residue: 0.2207 time to fit residues: 53.2165 Evaluate side-chains 161 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 136 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 512 THR Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 683 VAL 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 55 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 107 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 64 optimal weight: 4.9990 chunk 5 optimal weight: 0.0060 chunk 50 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 106 optimal weight: 0.9980 chunk 100 optimal weight: 0.0370 chunk 104 optimal weight: 4.9990 overall best weight: 1.8078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 GLN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.158446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.131171 restraints weight = 15628.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.132407 restraints weight = 11821.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.133761 restraints weight = 9431.296| |-----------------------------------------------------------------------------| r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11709 Z= 0.127 Angle : 0.569 9.226 16140 Z= 0.298 Chirality : 0.038 0.142 1788 Planarity : 0.004 0.055 1841 Dihedral : 18.974 135.448 2103 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.52 % Allowed : 16.22 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1252 helix: 1.65 (0.21), residues: 664 sheet: -1.10 (0.42), residues: 129 loop : -1.31 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 915 HIS 0.003 0.001 HIS A1169 PHE 0.019 0.001 PHE A1338 TYR 0.026 0.001 TYR B 73 ARG 0.003 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04212 ( 559) hydrogen bonds : angle 4.27985 ( 1563) covalent geometry : bond 0.00287 (11708) covalent geometry : angle 0.56888 (16140) Misc. bond : bond 0.00075 ( 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 181 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 154 time to evaluate : 1.318 Fit side-chains REVERT: B 114 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: B 137 ASN cc_start: 0.8913 (OUTLIER) cc_final: 0.8700 (t0) REVERT: B 321 TRP cc_start: 0.8068 (t60) cc_final: 0.7762 (t60) REVERT: A 607 MET cc_start: 0.7478 (ttm) cc_final: 0.7278 (mtm) REVERT: A 1051 SER cc_start: 0.7386 (t) cc_final: 0.7076 (p) REVERT: A 1215 VAL cc_start: 0.7687 (OUTLIER) cc_final: 0.7397 (t) REVERT: A 1271 PHE cc_start: 0.4790 (m-80) cc_final: 0.3779 (t80) outliers start: 27 outliers final: 19 residues processed: 171 average time/residue: 0.2367 time to fit residues: 58.0544 Evaluate side-chains 167 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 304 ILE Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 414 ASP Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 651 ILE Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 755 LEU 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 1269 ILE Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 122 optimal weight: 20.0000 chunk 40 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 86 optimal weight: 9.9990 chunk 81 optimal weight: 0.5980 chunk 32 optimal weight: 0.0770 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 20.0000 chunk 47 optimal weight: 0.0980 chunk 102 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 overall best weight: 1.5542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 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 = 0.3746 r_free = 0.3746 target = 0.159713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.132703 restraints weight = 15505.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.133637 restraints weight = 11396.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.135141 restraints weight = 9639.185| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1994 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= 0.123 Angle : 0.570 9.673 16140 Z= 0.295 Chirality : 0.038 0.153 1788 Planarity : 0.004 0.054 1841 Dihedral : 18.867 134.848 2103 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 2.33 % Allowed : 17.33 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1252 helix: 1.70 (0.21), residues: 665 sheet: -1.10 (0.43), residues: 124 loop : -1.30 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 915 HIS 0.004 0.001 HIS A1169 PHE 0.018 0.001 PHE A1338 TYR 0.025 0.001 TYR B 161 ARG 0.004 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.03987 ( 559) hydrogen bonds : angle 4.17226 ( 1563) covalent geometry : bond 0.00280 (11708) covalent geometry : angle 0.57036 (16140) Misc. bond : bond 0.00073 ( 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: 25 poor density : 155 time to evaluate : 1.171 Fit side-chains REVERT: B 137 ASN cc_start: 0.8873 (OUTLIER) cc_final: 0.8418 (t0) REVERT: B 321 TRP cc_start: 0.8066 (t60) cc_final: 0.7785 (t60) REVERT: A 1051 SER cc_start: 0.7375 (t) cc_final: 0.7063 (p) REVERT: A 1215 VAL cc_start: 0.7704 (OUTLIER) cc_final: 0.7416 (t) REVERT: A 1271 PHE cc_start: 0.4850 (m-80) cc_final: 0.3953 (t80) outliers start: 25 outliers final: 20 residues processed: 170 average time/residue: 0.2156 time to fit residues: 53.1601 Evaluate side-chains 168 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 146 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 304 ILE 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 651 ILE Chi-restraints excluded: chain A residue 665 ILE Chi-restraints excluded: chain A residue 755 LEU 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 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 1269 ILE Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 8 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 75 optimal weight: 9.9990 chunk 80 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 118 optimal weight: 10.0000 chunk 100 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 GLN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.161084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.134233 restraints weight = 15394.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.135659 restraints weight = 11013.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.136829 restraints weight = 8876.499| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11709 Z= 0.121 Angle : 0.566 8.720 16140 Z= 0.292 Chirality : 0.038 0.161 1788 Planarity : 0.004 0.053 1841 Dihedral : 18.791 134.413 2103 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 2.42 % Allowed : 17.61 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.24), residues: 1252 helix: 1.70 (0.21), residues: 672 sheet: -1.08 (0.43), residues: 125 loop : -1.25 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP A 915 HIS 0.004 0.001 HIS A1169 PHE 0.017 0.001 PHE A1338 TYR 0.031 0.001 TYR B 161 ARG 0.004 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 559) hydrogen bonds : angle 4.10468 ( 1563) covalent geometry : bond 0.00275 (11708) covalent geometry : angle 0.56570 (16140) Misc. bond : bond 0.00067 ( 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 179 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 153 time to evaluate : 1.249 Fit side-chains REVERT: B 114 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7531 (mp0) REVERT: B 137 ASN cc_start: 0.8892 (OUTLIER) cc_final: 0.8590 (t0) REVERT: B 321 TRP cc_start: 0.8049 (t60) cc_final: 0.7546 (t60) REVERT: A 503 ILE cc_start: 0.7793 (OUTLIER) cc_final: 0.7586 (mp) REVERT: A 1051 SER cc_start: 0.7368 (t) cc_final: 0.7051 (p) REVERT: A 1215 VAL cc_start: 0.7748 (OUTLIER) cc_final: 0.7468 (t) REVERT: A 1271 PHE cc_start: 0.4948 (m-80) cc_final: 0.4136 (t80) outliers start: 26 outliers final: 16 residues processed: 169 average time/residue: 0.2300 time to fit residues: 56.3958 Evaluate side-chains 168 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 307 THR Chi-restraints excluded: chain A residue 472 CYS Chi-restraints excluded: chain A residue 503 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 755 LEU 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 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 1215 VAL Chi-restraints excluded: chain A residue 1269 ILE Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 0 optimal weight: 20.0000 chunk 18 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 70 optimal weight: 9.9990 chunk 32 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 83 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 GLN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.158388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.131426 restraints weight = 15470.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.132946 restraints weight = 11290.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.133781 restraints weight = 9193.664| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.2080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11709 Z= 0.166 Angle : 0.592 9.033 16140 Z= 0.307 Chirality : 0.040 0.161 1788 Planarity : 0.004 0.054 1841 Dihedral : 18.840 134.787 2103 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.87 % Favored : 95.05 % Rotamer: Outliers : 2.42 % Allowed : 17.61 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.24), residues: 1252 helix: 1.65 (0.21), residues: 672 sheet: -1.11 (0.43), residues: 125 loop : -1.25 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 915 HIS 0.003 0.001 HIS A1169 PHE 0.025 0.001 PHE A1338 TYR 0.030 0.001 TYR B 161 ARG 0.004 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04251 ( 559) hydrogen bonds : angle 4.18523 ( 1563) covalent geometry : bond 0.00390 (11708) covalent geometry : angle 0.59204 (16140) Misc. bond : bond 0.00049 ( 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 175 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.180 Fit side-chains REVERT: B 114 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7477 (mp0) REVERT: B 137 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8442 (t0) REVERT: B 321 TRP cc_start: 0.8106 (t60) cc_final: 0.7788 (t60) REVERT: A 503 ILE cc_start: 0.7950 (OUTLIER) cc_final: 0.7741 (mp) REVERT: A 1051 SER cc_start: 0.7477 (t) cc_final: 0.7135 (p) REVERT: A 1215 VAL cc_start: 0.7872 (OUTLIER) cc_final: 0.7588 (t) REVERT: A 1271 PHE cc_start: 0.4943 (m-80) cc_final: 0.4085 (t80) outliers start: 26 outliers final: 20 residues processed: 165 average time/residue: 0.2258 time to fit residues: 54.2112 Evaluate side-chains 170 residues out of total 1125 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 114 GLU Chi-restraints excluded: chain B residue 137 ASN Chi-restraints excluded: chain B residue 174 SER Chi-restraints excluded: chain B residue 304 ILE 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 503 ILE Chi-restraints excluded: chain A residue 602 SER Chi-restraints excluded: chain A residue 607 MET Chi-restraints excluded: chain A residue 683 VAL Chi-restraints excluded: chain A residue 755 LEU 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 1215 VAL Chi-restraints excluded: chain A residue 1269 ILE Chi-restraints excluded: chain A residue 1296 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 5.9990 chunk 98 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 94 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 11 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 118 optimal weight: 20.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 137 ASN B 287 GLN A 900 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.157178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.129999 restraints weight = 15471.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.131103 restraints weight = 12757.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.132289 restraints weight = 10920.498| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7681 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11709 Z= 0.181 Angle : 0.605 8.954 16140 Z= 0.314 Chirality : 0.040 0.163 1788 Planarity : 0.005 0.055 1841 Dihedral : 18.884 135.098 2103 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.79 % Favored : 95.13 % Rotamer: Outliers : 2.42 % Allowed : 17.61 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.24), residues: 1252 helix: 1.61 (0.21), residues: 672 sheet: -1.14 (0.43), residues: 125 loop : -1.28 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 915 HIS 0.003 0.001 HIS B 187 PHE 0.025 0.002 PHE A1338 TYR 0.029 0.002 TYR B 161 ARG 0.004 0.000 ARG B 264 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 559) hydrogen bonds : angle 4.24986 ( 1563) covalent geometry : bond 0.00429 (11708) covalent geometry : angle 0.60479 (16140) Misc. bond : bond 0.00046 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3010.96 seconds wall clock time: 53 minutes 46.60 seconds (3226.60 seconds total)