Starting phenix.real_space_refine on Sat Jul 20 14:03:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atv_15664/07_2024/8atv_15664.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atv_15664/07_2024/8atv_15664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atv_15664/07_2024/8atv_15664.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atv_15664/07_2024/8atv_15664.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atv_15664/07_2024/8atv_15664.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8atv_15664/07_2024/8atv_15664.cif" } resolution = 3.39 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= 0.024 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 61 5.49 5 S 35 5.16 5 C 6950 2.51 5 N 1943 2.21 5 O 2172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 212": "OE1" <-> "OE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 1272": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 11161 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2733 Classifications: {'peptide': 334} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 19, 'TRANS': 314} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "A" Number of atoms: 7199 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 923, 7191 Classifications: {'peptide': 923} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 44, 'TRANS': 878} Chain breaks: 2 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 Conformer: "B" Number of residues, atoms: 923, 7191 Classifications: {'peptide': 923} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 63} Link IDs: {'PTRANS': 44, 'TRANS': 878} Chain breaks: 2 Unresolved non-hydrogen bonds: 218 Unresolved non-hydrogen angles: 266 Unresolved non-hydrogen dihedrals: 172 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 2, 'ASP:plan': 12, 'PHE:plan': 1, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 95 bond proxies already assigned to first conformer: 7343 Chain: "N" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 560 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "T" Number of atoms: 548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 548 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Classifications: {'RNA': 4} Modifications used: {'rna3p_pur': 4} Link IDs: {'rna3p': 3} 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: 10.57, per 1000 atoms: 0.95 Number of scatterers: 11161 At special positions: 0 Unit cell: (102.82, 117.37, 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 35 16.00 P 61 15.00 O 2172 8.00 N 1943 7.00 C 6950 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 - 3.50 Amino acid : False - 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: 4.98 Conformation dependent library (CDL) restraints added in 3.0 seconds 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 11 sheets defined 58.3% alpha, 8.9% beta 21 base pairs and 40 stacking pairs defined. Time for finding SS restraints: 3.79 Creating SS restraints... Processing helix chain 'B' and resid 7 through 12 Processing helix chain 'B' and resid 25 through 37 Processing helix chain 'B' and resid 37 through 42 removed outlier: 4.161A 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 91 Processing helix chain 'B' and resid 104 through 113 removed outlier: 4.308A pdb=" N TYR B 108 " --> pdb=" O ASP B 104 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER B 109 " --> pdb=" O TRP B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 143 through 157 removed outlier: 3.782A pdb=" N ILE B 147 " --> pdb=" O SER B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 181 Processing helix chain 'B' and resid 190 through 199 Processing helix chain 'B' and resid 212 through 216 removed outlier: 3.504A pdb=" N GLY B 215 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 Processing helix chain 'B' and resid 230 through 234 removed outlier: 3.663A pdb=" N GLU B 233 " --> pdb=" O SER B 230 " (cutoff:3.500A) Processing helix chain 'B' and resid 255 through 267 Processing helix chain 'B' and resid 273 through 282 removed outlier: 5.741A pdb=" N MET B 278 " --> pdb=" O ASN B 275 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ASP B 279 " --> pdb=" O THR B 276 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLY B 282 " --> pdb=" O ASP B 279 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 293 Processing helix chain 'B' and resid 296 through 300 Processing helix chain 'B' and resid 307 through 321 Processing helix chain 'A' and resid 388 through 395 Processing helix chain 'A' and resid 397 through 412 Processing helix chain 'A' and resid 412 through 421 Processing helix chain 'A' and resid 422 through 441 Processing helix chain 'A' and resid 448 through 478 Proline residue: A 463 - end of helix removed outlier: 3.870A pdb=" N GLU A 478 " --> pdb=" O SER A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 497 removed outlier: 3.820A pdb=" N THR A 491 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASN A 492 " --> pdb=" O LYS A 488 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLY A 495 " --> pdb=" O THR A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 519 Processing helix chain 'A' and resid 531 through 555 removed outlier: 3.645A pdb=" N ILE A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 593 through 612 Processing helix chain 'A' and resid 652 through 660 removed outlier: 4.207A pdb=" N GLN A 658 " --> pdb=" O THR A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 668 Processing helix chain 'A' and resid 703 through 717 removed outlier: 3.864A pdb=" N VAL A 707 " --> pdb=" O SER A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 720 through 731 Processing helix chain 'A' and resid 737 through 751 removed outlier: 3.853A pdb=" N GLY A 751 " --> pdb=" O VAL A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 813 removed outlier: 3.500A pdb=" N THR A 803 " --> pdb=" O ASN A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 842 through 848 Processing helix chain 'A' and resid 860 through 873 Processing helix chain 'A' and resid 879 through 890 Processing helix chain 'A' and resid 890 through 900 Processing helix chain 'A' and resid 907 through 911 Processing helix chain 'A' and resid 913 through 929 Processing helix chain 'A' and resid 932 through 935 Processing helix chain 'A' and resid 948 through 959 Processing helix chain 'A' and resid 960 through 967 Processing helix chain 'A' and resid 977 through 994 Processing helix chain 'A' and resid 998 through 1004 removed outlier: 3.720A pdb=" N LEU A1004 " --> pdb=" O ASN A1000 " (cutoff:3.500A) Processing helix chain 'A' and resid 1009 through 1021 removed outlier: 4.145A pdb=" N VAL A1021 " --> pdb=" O VAL A1017 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1038 removed outlier: 3.687A pdb=" N GLN A1036 " --> pdb=" O GLN A1032 " (cutoff:3.500A) Processing helix chain 'A' and resid 1047 through 1066 Processing helix chain 'A' and resid 1067 through 1085 Processing helix chain 'A' and resid 1090 through 1094 removed outlier: 3.545A pdb=" N GLU A1093 " --> pdb=" O ASP A1090 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LYS A1094 " --> pdb=" O VAL A1091 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1090 through 1094' Processing helix chain 'A' and resid 1149 through 1180 Proline residue: A1158 - end of helix removed outlier: 3.629A pdb=" N ILE A1162 " --> pdb=" O PRO A1158 " (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 1260 removed outlier: 3.596A pdb=" N ILE A1248 " --> pdb=" O LEU A1244 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE A1249 " --> pdb=" O ALA A1245 " (cutoff:3.500A) Processing helix chain 'A' and resid 1264 through 1281 removed outlier: 3.581A pdb=" N LEU A1279 " --> pdb=" O ARG A1275 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1293 Processing helix chain 'A' and resid 1297 through 1301 Processing helix chain 'A' and resid 1339 through 1346 removed outlier: 3.506A pdb=" N LEU A1343 " --> pdb=" O VAL A1340 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A1345 " --> pdb=" O VAL A1342 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.924A pdb=" N TYR B 73 " --> pdb=" O GLN B 96 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N LEU B 98 " --> pdb=" O TYR B 73 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU B 75 " --> pdb=" O LEU B 98 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N LYS B 49 " --> pdb=" O LEU B 133 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N VAL B 135 " --> pdb=" O LYS B 49 " (cutoff:3.500A) removed outlier: 6.143A pdb=" N LEU B 51 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 8.081A pdb=" N ASN B 137 " --> pdb=" O LEU B 51 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LEU B 53 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS B 167 " --> pdb=" O PHE B 132 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLU B 246 " --> pdb=" O LEU B 204 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N LEU B 204 " --> pdb=" O GLU B 246 " (cutoff:3.500A) removed outlier: 7.196A pdb=" N ASP B 248 " --> pdb=" O THR B 202 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N THR B 202 " --> pdb=" O ASP B 248 " (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 613 through 619 removed outlier: 3.637A pdb=" N GLY A 629 " --> pdb=" O VAL A 616 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 680 through 684 removed outlier: 4.485A pdb=" N TRP A 682 " --> pdb=" O SER A 687 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N SER A 687 " --> pdb=" O TRP A 682 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 698 through 699 Processing sheet with id=AA6, first strand: chain 'A' and resid 734 through 736 Processing sheet with id=AA7, first strand: chain 'A' and resid 855 through 856 Processing sheet with id=AA8, first strand: chain 'A' and resid 942 through 945 Processing sheet with id=AA9, first strand: chain 'A' and resid 1087 through 1088 removed outlier: 3.546A pdb=" N LEU A1238 " --> pdb=" O MET A1321 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N MET A1321 " --> pdb=" O LEU A1238 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1109 through 1111 Processing sheet with id=AB2, first strand: chain 'A' and resid 1127 through 1131 removed outlier: 3.521A pdb=" N ILE A1139 " --> pdb=" O LYS A1128 " (cutoff:3.500A) 539 hydrogen bonds defined for protein. 1544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 47 hydrogen bonds 94 hydrogen bond angles 0 basepair planarities 21 basepair parallelities 40 stacking parallelities Total time for adding SS restraints: 4.66 Time building geometry restraints manager: 5.40 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: 3129 1.34 - 1.45: 2167 1.45 - 1.57: 6081 1.57 - 1.69: 112 1.69 - 1.81: 59 Bond restraints: 11548 Sorted by residual: bond pdb=" O3' DT T 14 " pdb=" P DG T 15 " ideal model delta sigma weight residual 1.607 1.471 0.136 1.50e-02 4.44e+03 8.26e+01 bond pdb=" O3' DA T 13 " pdb=" P DT T 14 " ideal model delta sigma weight residual 1.607 1.494 0.113 1.50e-02 4.44e+03 5.67e+01 bond pdb=" O3' DC T 25 " pdb=" P DA T 26 " ideal model delta sigma weight residual 1.607 1.510 0.097 1.50e-02 4.44e+03 4.17e+01 bond pdb=" O3' DT N 112 " pdb=" P DG N 113 " ideal model delta sigma weight residual 1.607 1.687 -0.080 1.50e-02 4.44e+03 2.86e+01 bond pdb=" O3' DA N 133 " pdb=" P DT N 134 " ideal model delta sigma weight residual 1.607 1.528 0.079 1.50e-02 4.44e+03 2.77e+01 ... (remaining 11543 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.15: 623 106.15 - 113.13: 6271 113.13 - 120.11: 4007 120.11 - 127.09: 4718 127.09 - 134.06: 295 Bond angle restraints: 15914 Sorted by residual: angle pdb=" C5' DA N 130 " pdb=" C4' DA N 130 " pdb=" O4' DA N 130 " ideal model delta sigma weight residual 109.40 117.79 -8.39 1.50e+00 4.44e-01 3.13e+01 angle pdb=" C5' DT T 34 " pdb=" C4' DT T 34 " pdb=" O4' DT T 34 " ideal model delta sigma weight residual 109.40 116.99 -7.59 1.50e+00 4.44e-01 2.56e+01 angle pdb=" C LEU A 755 " pdb=" CA LEU A 755 " pdb=" CB LEU A 755 " ideal model delta sigma weight residual 117.23 110.74 6.49 1.36e+00 5.41e-01 2.28e+01 angle pdb=" C3' DT T 14 " pdb=" O3' DT T 14 " pdb=" P DG T 15 " ideal model delta sigma weight residual 120.20 127.00 -6.80 1.50e+00 4.44e-01 2.06e+01 angle pdb=" C3' DT N 112 " pdb=" O3' DT N 112 " pdb=" P DG N 113 " ideal model delta sigma weight residual 120.20 126.82 -6.62 1.50e+00 4.44e-01 1.95e+01 ... (remaining 15909 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.58: 6265 27.58 - 55.17: 488 55.17 - 82.75: 51 82.75 - 110.34: 6 110.34 - 137.92: 2 Dihedral angle restraints: 6812 sinusoidal: 3137 harmonic: 3675 Sorted by residual: 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 303.79 165.87 137.92 1 2.00e+01 2.50e-03 4.18e+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 -12.68 117.28 1 2.00e+01 2.50e-03 3.50e+01 dihedral pdb=" O3B GTP C 201 " pdb=" O3A GTP C 201 " pdb=" PB GTP C 201 " pdb=" PA GTP C 201 " ideal model delta sinusoidal sigma weight residual -68.92 -166.09 97.17 1 2.00e+01 2.50e-03 2.70e+01 ... (remaining 6809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 1711 0.106 - 0.212: 45 0.212 - 0.318: 3 0.318 - 0.424: 2 0.424 - 0.530: 1 Chirality restraints: 1762 Sorted by residual: chirality pdb=" P DT N 127 " pdb=" OP1 DT N 127 " pdb=" OP2 DT N 127 " pdb=" O5' DT N 127 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.01e+00 chirality pdb=" C4' DA N 130 " pdb=" C5' DA N 130 " pdb=" O4' DA N 130 " pdb=" C3' DA N 130 " both_signs ideal model delta sigma weight residual False -2.53 -2.11 -0.42 2.00e-01 2.50e+01 4.37e+00 chirality pdb=" C3' DG N 108 " pdb=" C4' DG N 108 " pdb=" O3' DG N 108 " pdb=" C2' DG N 108 " both_signs ideal model delta sigma weight residual False -2.66 -2.32 -0.34 2.00e-01 2.50e+01 2.84e+00 ... (remaining 1759 not shown) Planarity restraints: 1828 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 119 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.84e+00 pdb=" N PRO B 120 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO B 120 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 120 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 703 " -0.027 5.00e-02 4.00e+02 4.11e-02 2.70e+00 pdb=" N PRO A 704 " 0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 704 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 704 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 775 " 0.026 5.00e-02 4.00e+02 3.90e-02 2.43e+00 pdb=" N PRO A 776 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 776 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO A 776 " 0.022 5.00e-02 4.00e+02 ... (remaining 1825 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 399 2.72 - 3.26: 10573 3.26 - 3.81: 18947 3.81 - 4.35: 23018 4.35 - 4.90: 38372 Nonbonded interactions: 91309 Sorted by model distance: nonbonded pdb=" O ASN A 487 " pdb=" OG1 THR A 491 " model vdw 2.173 2.440 nonbonded pdb=" OD1 ASP B 257 " pdb=" N ASN B 258 " model vdw 2.177 2.520 nonbonded pdb=" O PRO B 102 " pdb=" OH TYR B 108 " model vdw 2.214 2.440 nonbonded pdb=" NE2 GLN A 416 " pdb=" OE1 GLU A 420 " model vdw 2.261 2.520 nonbonded pdb=" O PHE B 90 " pdb=" OG SER B 93 " model vdw 2.264 2.440 ... (remaining 91304 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.130 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: 0.450 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 42.490 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.060 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 11548 Z= 0.259 Angle : 0.695 13.149 15914 Z= 0.372 Chirality : 0.048 0.530 1762 Planarity : 0.004 0.042 1828 Dihedral : 18.012 137.923 4432 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.00 (0.24), residues: 1250 helix: 1.67 (0.20), residues: 697 sheet: 0.70 (0.54), residues: 93 loop : -0.92 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 864 HIS 0.007 0.001 HIS A1057 PHE 0.012 0.001 PHE A 886 TYR 0.014 0.001 TYR B 161 ARG 0.003 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 163 time to evaluate : 1.202 Fit side-chains REVERT: A 467 GLU cc_start: 0.6632 (tp30) cc_final: 0.6321 (tp30) outliers start: 0 outliers final: 0 residues processed: 163 average time/residue: 0.2405 time to fit residues: 55.6125 Evaluate side-chains 138 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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: 10.0000 chunk 97 optimal weight: 7.9990 chunk 54 optimal weight: 0.1980 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 117 optimal weight: 30.0000 overall best weight: 3.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 966 GLN A1231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.0753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11548 Z= 0.216 Angle : 0.571 8.590 15914 Z= 0.306 Chirality : 0.040 0.189 1762 Planarity : 0.004 0.042 1828 Dihedral : 18.228 109.516 2047 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.85 % Allowed : 5.78 % Favored : 93.37 % 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: 1.14 (0.24), residues: 1250 helix: 1.83 (0.20), residues: 689 sheet: 0.74 (0.52), residues: 103 loop : -0.92 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1110 HIS 0.006 0.001 HIS A1057 PHE 0.013 0.001 PHE A 886 TYR 0.018 0.002 TYR A1229 ARG 0.002 0.000 ARG A1250 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 150 time to evaluate : 1.175 Fit side-chains REVERT: B 116 ARG cc_start: 0.6849 (mmm-85) cc_final: 0.6646 (mmm-85) REVERT: A 461 MET cc_start: 0.8710 (tmm) cc_final: 0.8051 (ttt) REVERT: A 467 GLU cc_start: 0.6653 (tp30) cc_final: 0.6391 (tp30) REVERT: A 533 ARG cc_start: 0.7338 (ttt180) cc_final: 0.7070 (tpt-90) outliers start: 9 outliers final: 6 residues processed: 151 average time/residue: 0.2597 time to fit residues: 54.8315 Evaluate side-chains 146 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 140 time to evaluate : 1.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 1054 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 79 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 117 optimal weight: 20.0000 chunk 126 optimal weight: 10.0000 chunk 104 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 94 optimal weight: 7.9990 overall best weight: 5.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 96 GLN A1231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 11548 Z= 0.290 Angle : 0.614 9.242 15914 Z= 0.326 Chirality : 0.042 0.203 1762 Planarity : 0.005 0.046 1828 Dihedral : 18.544 109.995 2047 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.92 % Favored : 96.00 % Rotamer: Outliers : 1.33 % Allowed : 7.20 % Favored : 91.48 % 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: 0.84 (0.24), residues: 1250 helix: 1.59 (0.20), residues: 688 sheet: 0.58 (0.53), residues: 103 loop : -1.06 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 864 HIS 0.009 0.002 HIS A 943 PHE 0.015 0.002 PHE B 229 TYR 0.017 0.002 TYR A 496 ARG 0.002 0.000 ARG A1250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 1.180 Fit side-chains REVERT: A 461 MET cc_start: 0.8772 (tmm) cc_final: 0.8198 (ttt) REVERT: A 1105 MET cc_start: 0.8124 (mmm) cc_final: 0.7711 (mmp) outliers start: 14 outliers final: 11 residues processed: 147 average time/residue: 0.2547 time to fit residues: 52.5547 Evaluate side-chains 149 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1231 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 20.0000 chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 chunk 117 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 overall best weight: 3.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11548 Z= 0.206 Angle : 0.558 8.683 15914 Z= 0.298 Chirality : 0.039 0.155 1762 Planarity : 0.004 0.042 1828 Dihedral : 18.505 109.375 2047 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.60 % Favored : 96.32 % Rotamer: Outliers : 1.04 % Allowed : 8.33 % Favored : 90.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.01 (0.24), residues: 1250 helix: 1.76 (0.20), residues: 689 sheet: 0.61 (0.52), residues: 103 loop : -1.03 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 864 HIS 0.006 0.001 HIS A1057 PHE 0.012 0.001 PHE A 886 TYR 0.016 0.002 TYR A 496 ARG 0.003 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 1.206 Fit side-chains REVERT: B 214 LYS cc_start: 0.8080 (mmtm) cc_final: 0.7809 (mmtm) REVERT: A 461 MET cc_start: 0.8781 (tmm) cc_final: 0.8213 (ttt) REVERT: A 926 GLU cc_start: 0.6889 (tt0) cc_final: 0.6678 (tt0) REVERT: A 1105 MET cc_start: 0.8192 (mmm) cc_final: 0.7835 (mmp) outliers start: 11 outliers final: 9 residues processed: 141 average time/residue: 0.2517 time to fit residues: 50.2423 Evaluate side-chains 148 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 139 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1054 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 8.9990 chunk 70 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 51 optimal weight: 0.7980 chunk 106 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 31 optimal weight: 1.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7580 moved from start: 0.1352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 11548 Z= 0.249 Angle : 0.573 9.017 15914 Z= 0.306 Chirality : 0.040 0.152 1762 Planarity : 0.004 0.044 1828 Dihedral : 18.666 109.271 2047 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.76 % Favored : 96.16 % Rotamer: Outliers : 1.23 % Allowed : 9.94 % Favored : 88.83 % 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: 0.89 (0.24), residues: 1250 helix: 1.66 (0.20), residues: 689 sheet: 0.49 (0.52), residues: 103 loop : -1.06 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 864 HIS 0.006 0.001 HIS A 943 PHE 0.015 0.001 PHE B 229 TYR 0.016 0.002 TYR A 496 ARG 0.002 0.000 ARG A 441 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.192 Fit side-chains REVERT: B 116 ARG cc_start: 0.6934 (mmm-85) cc_final: 0.6492 (mmm-85) REVERT: B 168 MET cc_start: 0.7345 (mmm) cc_final: 0.6999 (tpt) REVERT: B 214 LYS cc_start: 0.8024 (mmtm) cc_final: 0.7791 (mmtm) REVERT: A 461 MET cc_start: 0.8834 (tmm) cc_final: 0.8389 (ttt) REVERT: A 533 ARG cc_start: 0.7488 (ttt180) cc_final: 0.7223 (tpt-90) REVERT: A 1201 MET cc_start: 0.8588 (ttp) cc_final: 0.8379 (ttp) outliers start: 13 outliers final: 10 residues processed: 143 average time/residue: 0.2502 time to fit residues: 50.3401 Evaluate side-chains 146 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1231 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 10.0000 chunk 112 optimal weight: 7.9990 chunk 24 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 57 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 120 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 890 HIS A1231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11548 Z= 0.185 Angle : 0.536 8.646 15914 Z= 0.287 Chirality : 0.038 0.144 1762 Planarity : 0.004 0.039 1828 Dihedral : 18.522 108.477 2047 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.48 % Rotamer: Outliers : 1.23 % Allowed : 10.61 % Favored : 88.16 % 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: 1.07 (0.24), residues: 1250 helix: 1.82 (0.20), residues: 689 sheet: 0.54 (0.51), residues: 103 loop : -0.99 (0.27), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 455 HIS 0.006 0.001 HIS A1057 PHE 0.012 0.001 PHE A 886 TYR 0.015 0.001 TYR A 496 ARG 0.003 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 1.250 Fit side-chains REVERT: B 116 ARG cc_start: 0.6841 (mmm-85) cc_final: 0.6502 (mmm-85) REVERT: B 168 MET cc_start: 0.7280 (mmm) cc_final: 0.6969 (tpt) REVERT: A 461 MET cc_start: 0.8810 (tmm) cc_final: 0.8385 (ttt) REVERT: A 533 ARG cc_start: 0.7411 (ttt180) cc_final: 0.7210 (tpt-90) REVERT: A 1201 MET cc_start: 0.8550 (ttp) cc_final: 0.8323 (ttp) outliers start: 13 outliers final: 11 residues processed: 142 average time/residue: 0.2556 time to fit residues: 51.3224 Evaluate side-chains 144 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 630 GLU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1231 ASN Chi-restraints excluded: chain A residue 1233 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 chunk 91 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 77 optimal weight: 2.9990 chunk 75 optimal weight: 0.0470 chunk 57 optimal weight: 6.9990 chunk 76 optimal weight: 9.9990 overall best weight: 2.8086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11548 Z= 0.191 Angle : 0.531 8.653 15914 Z= 0.285 Chirality : 0.039 0.142 1762 Planarity : 0.004 0.045 1828 Dihedral : 18.511 107.962 2047 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.44 % Favored : 96.48 % Rotamer: Outliers : 1.52 % Allowed : 11.74 % Favored : 86.74 % 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: 1.09 (0.24), residues: 1250 helix: 1.83 (0.20), residues: 689 sheet: 0.54 (0.51), residues: 103 loop : -0.97 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 864 HIS 0.006 0.001 HIS A1057 PHE 0.013 0.001 PHE A 886 TYR 0.016 0.001 TYR A 496 ARG 0.003 0.000 ARG A1228 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.190 Fit side-chains REVERT: B 116 ARG cc_start: 0.6858 (mmm-85) cc_final: 0.6540 (mmm-85) REVERT: B 168 MET cc_start: 0.7262 (mmm) cc_final: 0.6981 (tpt) REVERT: B 267 MET cc_start: 0.8195 (mmm) cc_final: 0.7977 (mmm) REVERT: A 461 MET cc_start: 0.8796 (tmm) cc_final: 0.8388 (ttt) REVERT: A 533 ARG cc_start: 0.7413 (ttt180) cc_final: 0.7187 (tpt-90) REVERT: A 926 GLU cc_start: 0.6793 (tt0) cc_final: 0.6463 (tt0) REVERT: A 1201 MET cc_start: 0.8533 (ttp) cc_final: 0.8288 (ttp) outliers start: 16 outliers final: 11 residues processed: 140 average time/residue: 0.2532 time to fit residues: 50.3275 Evaluate side-chains 145 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 134 time to evaluate : 1.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1054 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 5.9990 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 79 optimal weight: 0.6980 chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 7.9990 chunk 11 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 9.9990 chunk 119 optimal weight: 0.0980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 286 GLN A1231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7510 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11548 Z= 0.162 Angle : 0.504 8.352 15914 Z= 0.270 Chirality : 0.037 0.139 1762 Planarity : 0.004 0.048 1828 Dihedral : 18.344 106.342 2047 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.85 % Allowed : 12.41 % Favored : 86.74 % 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: 1.29 (0.24), residues: 1250 helix: 2.00 (0.21), residues: 690 sheet: 0.56 (0.51), residues: 103 loop : -0.89 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 24 HIS 0.007 0.001 HIS A1057 PHE 0.012 0.001 PHE A 826 TYR 0.016 0.001 TYR A 496 ARG 0.002 0.000 ARG A1220 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 1.219 Fit side-chains REVERT: B 85 PHE cc_start: 0.7799 (t80) cc_final: 0.7554 (t80) REVERT: B 116 ARG cc_start: 0.6774 (mmm-85) cc_final: 0.6501 (mmm-85) REVERT: B 267 MET cc_start: 0.8192 (mmm) cc_final: 0.7992 (mmm) REVERT: A 461 MET cc_start: 0.8755 (tmm) cc_final: 0.8421 (ttt) REVERT: A 533 ARG cc_start: 0.7394 (ttt180) cc_final: 0.7172 (tpt-90) REVERT: A 926 GLU cc_start: 0.6765 (tt0) cc_final: 0.6434 (tt0) REVERT: A 1201 MET cc_start: 0.8485 (ttp) cc_final: 0.8235 (ttp) REVERT: A 1272 GLU cc_start: 0.4383 (tp30) cc_final: 0.3909 (tp30) outliers start: 9 outliers final: 8 residues processed: 143 average time/residue: 0.2644 time to fit residues: 53.3114 Evaluate side-chains 142 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 134 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1231 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 20.0000 chunk 115 optimal weight: 20.0000 chunk 119 optimal weight: 4.9990 chunk 69 optimal weight: 9.9990 chunk 50 optimal weight: 10.0000 chunk 90 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 122 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 11548 Z= 0.378 Angle : 0.661 11.031 15914 Z= 0.349 Chirality : 0.044 0.182 1762 Planarity : 0.005 0.050 1828 Dihedral : 18.664 108.889 2047 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.08 % Favored : 95.84 % Rotamer: Outliers : 1.14 % Allowed : 12.69 % Favored : 86.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.60 (0.24), residues: 1250 helix: 1.40 (0.20), residues: 690 sheet: 0.47 (0.51), residues: 101 loop : -1.16 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 24 HIS 0.011 0.002 HIS A 943 PHE 0.019 0.002 PHE B 229 TYR 0.017 0.003 TYR A 496 ARG 0.005 0.001 ARG A1228 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.212 Fit side-chains REVERT: A 533 ARG cc_start: 0.7519 (ttt180) cc_final: 0.7091 (tpt-90) REVERT: A 1201 MET cc_start: 0.8623 (ttp) cc_final: 0.8347 (ttp) outliers start: 12 outliers final: 12 residues processed: 144 average time/residue: 0.2609 time to fit residues: 52.9966 Evaluate side-chains 148 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 277 VAL Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 490 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1054 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 9.9990 chunk 58 optimal weight: 5.9990 chunk 85 optimal weight: 4.9990 chunk 128 optimal weight: 8.9990 chunk 118 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 79 optimal weight: 0.0060 chunk 62 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 109 optimal weight: 7.9990 overall best weight: 2.9802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1231 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7558 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11548 Z= 0.205 Angle : 0.552 8.713 15914 Z= 0.296 Chirality : 0.039 0.161 1762 Planarity : 0.004 0.049 1828 Dihedral : 18.431 107.946 2047 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.28 % Favored : 96.64 % Rotamer: Outliers : 1.04 % Allowed : 12.69 % Favored : 86.27 % 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: 0.90 (0.24), residues: 1250 helix: 1.71 (0.20), residues: 689 sheet: 0.53 (0.51), residues: 101 loop : -1.12 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 24 HIS 0.006 0.001 HIS A1057 PHE 0.012 0.001 PHE A 886 TYR 0.015 0.001 TYR A 496 ARG 0.002 0.000 ARG A1220 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2500 Ramachandran restraints generated. 1250 Oldfield, 0 Emsley, 1250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 1.114 Fit side-chains REVERT: B 116 ARG cc_start: 0.6964 (mmm-85) cc_final: 0.6612 (mmm-85) REVERT: A 533 ARG cc_start: 0.7398 (ttt180) cc_final: 0.7014 (tpt-90) REVERT: A 926 GLU cc_start: 0.6710 (tt0) cc_final: 0.6431 (tt0) REVERT: A 1201 MET cc_start: 0.8563 (ttp) cc_final: 0.8297 (ttp) outliers start: 11 outliers final: 11 residues processed: 141 average time/residue: 0.2672 time to fit residues: 53.1132 Evaluate side-chains 147 residues out of total 1121 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 136 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 THR Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 208 SER Chi-restraints excluded: chain B residue 276 THR Chi-restraints excluded: chain B residue 302 CYS Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 696 THR Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1054 LEU Chi-restraints excluded: chain A residue 1231 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 10.0000 chunk 102 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 105 optimal weight: 10.0000 chunk 12 optimal weight: 0.0770 chunk 18 optimal weight: 0.3980 chunk 89 optimal weight: 9.9990 chunk 5 optimal weight: 0.0870 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1129 GLN A1231 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.167475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.134601 restraints weight = 26661.045| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.67 r_work: 0.3179 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3166 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3166 r_free = 0.3166 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3166 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.058 11548 Z= 0.155 Angle : 0.512 8.286 15914 Z= 0.275 Chirality : 0.037 0.138 1762 Planarity : 0.004 0.052 1828 Dihedral : 18.186 106.001 2047 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 0.76 % Allowed : 13.26 % Favored : 85.98 % 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: 1.28 (0.25), residues: 1250 helix: 2.02 (0.21), residues: 689 sheet: 0.55 (0.51), residues: 101 loop : -0.92 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 24 HIS 0.007 0.001 HIS A1057 PHE 0.013 0.001 PHE A 826 TYR 0.042 0.001 TYR A1232 ARG 0.003 0.000 ARG A1088 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2294.90 seconds wall clock time: 41 minutes 46.66 seconds (2506.66 seconds total)