Starting phenix.real_space_refine on Thu Mar 14 14:55:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk7_14757/03_2024/7zk7_14757.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk7_14757/03_2024/7zk7_14757.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk7_14757/03_2024/7zk7_14757.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk7_14757/03_2024/7zk7_14757.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk7_14757/03_2024/7zk7_14757.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zk7_14757/03_2024/7zk7_14757.pdb" } resolution = 3.2 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= 0.006 sd= 0.054 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: 4 Type Number sf(0) Gaussians S 39 5.16 5 C 5867 2.51 5 N 1541 2.21 5 O 1665 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 93": "OE1" <-> "OE2" Residue "A GLU 321": "OE1" <-> "OE2" Residue "A GLU 895": "OE1" <-> "OE2" Residue "A TYR 1129": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9112 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1161, 9112 Unusual residues: {'JIZ': 1, 'JJI': 1, 'Y01': 2} Classifications: {'peptide': 1157, 'undetermined': 4} Link IDs: {'PTRANS': 29, 'TRANS': 1127, None: 4} Not linked: pdbres="LYS A1260 " pdbres="JJI A1401 " Not linked: pdbres="JJI A1401 " pdbres="JIZ A1402 " Not linked: pdbres="JIZ A1402 " pdbres="Y01 A1403 " Not linked: pdbres="Y01 A1403 " pdbres="Y01 A1404 " Chain breaks: 1 Time building chain proxies: 5.23, per 1000 atoms: 0.57 Number of scatterers: 9112 At special positions: 0 Unit cell: (75.33, 114.669, 149.823, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 39 16.00 O 1665 8.00 N 1541 7.00 C 5867 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: 3.61 Conformation dependent library (CDL) restraints added in 1.6 seconds 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2122 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 6 sheets defined 66.8% alpha, 3.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.85 Creating SS restraints... Processing helix chain 'A' and resid 37 through 42 removed outlier: 3.957A pdb=" N TYR A 41 " --> pdb=" O MET A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 43 through 82 removed outlier: 4.243A pdb=" N LEU A 64 " --> pdb=" O HIS A 60 " (cutoff:3.500A) Proline residue: A 65 - end of helix Processing helix chain 'A' and resid 98 through 152 removed outlier: 3.659A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N TYR A 126 " --> pdb=" O LEU A 122 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 131 " --> pdb=" O ILE A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 162 removed outlier: 3.704A pdb=" N PHE A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 256 removed outlier: 4.152A pdb=" N VAL A 175 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER A 176 " --> pdb=" O THR A 172 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ILE A 186 " --> pdb=" O ILE A 182 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N PHE A 190 " --> pdb=" O ILE A 186 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLN A 191 " --> pdb=" O GLY A 187 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N TRP A 208 " --> pdb=" O PHE A 204 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N LYS A 209 " --> pdb=" O THR A 205 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 212 " --> pdb=" O TRP A 208 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Proline residue: A 219 - end of helix removed outlier: 3.704A pdb=" N GLY A 222 " --> pdb=" O SER A 218 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ALA A 246 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL A 249 " --> pdb=" O LYS A 245 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL A 253 " --> pdb=" O VAL A 249 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU A 254 " --> pdb=" O ALA A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 256 through 264 Processing helix chain 'A' and resid 265 through 319 removed outlier: 3.858A pdb=" N GLU A 269 " --> pdb=" O GLY A 265 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N GLU A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ALA A 280 " --> pdb=" O ASN A 276 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ARG A 282 " --> pdb=" O GLU A 278 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ILE A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N LEU A 316 " --> pdb=" O TYR A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 344 removed outlier: 3.756A pdb=" N VAL A 330 " --> pdb=" O GLN A 326 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER A 333 " --> pdb=" O THR A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 365 removed outlier: 3.675A pdb=" N PHE A 351 " --> pdb=" O ASN A 347 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ILE A 365 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.882A pdb=" N LYS A 401 " --> pdb=" O PRO A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 435 Processing helix chain 'A' and resid 436 through 438 No H-bonds generated for 'chain 'A' and resid 436 through 438' Processing helix chain 'A' and resid 458 through 465 Processing helix chain 'A' and resid 479 through 486 Processing helix chain 'A' and resid 492 through 501 Processing helix chain 'A' and resid 528 through 543 removed outlier: 3.841A pdb=" N ARG A 534 " --> pdb=" O GLY A 530 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 543 " --> pdb=" O ARG A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 564 through 574 Processing helix chain 'A' and resid 585 through 591 Processing helix chain 'A' and resid 694 through 701 removed outlier: 3.650A pdb=" N LYS A 698 " --> pdb=" O TRP A 694 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 737 removed outlier: 3.735A pdb=" N GLN A 721 " --> pdb=" O ASN A 717 " (cutoff:3.500A) Proline residue: A 722 - end of helix removed outlier: 3.986A pdb=" N PHE A 735 " --> pdb=" O VAL A 731 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 795 removed outlier: 4.598A pdb=" N GLN A 746 " --> pdb=" O GLU A 742 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 802 Processing helix chain 'A' and resid 806 through 816 Processing helix chain 'A' and resid 821 through 826 removed outlier: 3.761A pdb=" N THR A 825 " --> pdb=" O VAL A 821 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N GLY A 826 " --> pdb=" O LYS A 822 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 821 through 826' Processing helix chain 'A' and resid 826 through 899 removed outlier: 4.018A pdb=" N ILE A 832 " --> pdb=" O ARG A 828 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N PHE A 833 " --> pdb=" O LEU A 829 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N THR A 841 " --> pdb=" O ALA A 837 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE A 845 " --> pdb=" O THR A 841 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TRP A 851 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLN A 852 " --> pdb=" O ILE A 848 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N LEU A 853 " --> pdb=" O TYR A 849 " (cutoff:3.500A) Proline residue: A 862 - end of helix removed outlier: 4.272A pdb=" N ILE A 892 " --> pdb=" O GLY A 888 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN A 899 " --> pdb=" O GLU A 895 " (cutoff:3.500A) Processing helix chain 'A' and resid 899 through 906 Processing helix chain 'A' and resid 909 through 962 removed outlier: 3.563A pdb=" N GLU A 913 " --> pdb=" O GLU A 909 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N ILE A 922 " --> pdb=" O GLN A 918 " (cutoff:3.500A) Proline residue: A 923 - end of helix removed outlier: 3.509A pdb=" N MET A 928 " --> pdb=" O TYR A 924 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 978 Processing helix chain 'A' and resid 978 through 990 removed outlier: 3.500A pdb=" N ALA A 983 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing helix chain 'A' and resid 995 through 1010 Processing helix chain 'A' and resid 1068 through 1072 removed outlier: 3.749A pdb=" N LYS A1072 " --> pdb=" O GLY A1069 " (cutoff:3.500A) Processing helix chain 'A' and resid 1074 through 1080 removed outlier: 3.818A pdb=" N GLU A1080 " --> pdb=" O VAL A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1101 through 1107 Processing helix chain 'A' and resid 1122 through 1129 Processing helix chain 'A' and resid 1140 through 1149 Processing helix chain 'A' and resid 1150 through 1155 Processing helix chain 'A' and resid 1173 through 1188 removed outlier: 4.060A pdb=" N ARG A1188 " --> pdb=" O ARG A1184 " (cutoff:3.500A) Processing helix chain 'A' and resid 1199 through 1203 Processing helix chain 'A' and resid 1205 through 1221 removed outlier: 4.461A pdb=" N VAL A1209 " --> pdb=" O GLU A1205 " (cutoff:3.500A) Processing helix chain 'A' and resid 1229 through 1236 removed outlier: 3.528A pdb=" N ILE A1233 " --> pdb=" O ARG A1229 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1255 removed outlier: 4.027A pdb=" N GLN A1254 " --> pdb=" O HIS A1250 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 389 through 391 Processing sheet with id=AA2, first strand: chain 'A' and resid 394 through 395 removed outlier: 3.577A pdb=" N PHE A 395 " --> pdb=" O LEU A 406 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 466 through 468 Processing sheet with id=AA4, first strand: chain 'A' and resid 1031 through 1032 removed outlier: 3.718A pdb=" N PHE A1091 " --> pdb=" O GLN A1032 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1034 through 1038 removed outlier: 3.719A pdb=" N VAL A1036 " --> pdb=" O LEU A1052 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LEU A1052 " --> pdb=" O VAL A1036 " (cutoff:3.500A) removed outlier: 8.145A pdb=" N PHE A1038 " --> pdb=" O GLN A1050 " (cutoff:3.500A) removed outlier: 5.897A pdb=" N GLN A1050 " --> pdb=" O PHE A1038 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 6.142A pdb=" N LEU A1193 " --> pdb=" O ILE A1224 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N ILE A1226 " --> pdb=" O LEU A1193 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU A1195 " --> pdb=" O ILE A1226 " (cutoff:3.500A) 557 hydrogen bonds defined for protein. 1644 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.02 Time building geometry restraints manager: 3.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.32: 1523 1.32 - 1.46: 3213 1.46 - 1.60: 4481 1.60 - 1.74: 9 1.74 - 1.88: 63 Bond restraints: 9289 Sorted by residual: bond pdb=" C03 JIZ A1402 " pdb=" N02 JIZ A1402 " ideal model delta sigma weight residual 1.367 1.638 -0.271 2.00e-02 2.50e+03 1.83e+02 bond pdb=" C08 JIZ A1402 " pdb=" N04 JIZ A1402 " ideal model delta sigma weight residual 1.366 1.616 -0.250 2.00e-02 2.50e+03 1.57e+02 bond pdb=" C13 JIZ A1402 " pdb=" N06 JIZ A1402 " ideal model delta sigma weight residual 1.366 1.609 -0.243 2.00e-02 2.50e+03 1.48e+02 bond pdb=" N2 JJI A1401 " pdb=" O22 JJI A1401 " ideal model delta sigma weight residual 1.204 1.403 -0.199 2.00e-02 2.50e+03 9.92e+01 bond pdb=" N4 JJI A1401 " pdb=" O42 JJI A1401 " ideal model delta sigma weight residual 1.207 1.404 -0.197 2.00e-02 2.50e+03 9.69e+01 ... (remaining 9284 not shown) Histogram of bond angle deviations from ideal: 96.29 - 103.87: 104 103.87 - 111.46: 4011 111.46 - 119.04: 3656 119.04 - 126.63: 4708 126.63 - 134.21: 95 Bond angle restraints: 12574 Sorted by residual: angle pdb=" C18 JJI A1401 " pdb=" S04 JJI A1401 " pdb=" S JJI A1401 " ideal model delta sigma weight residual 102.75 125.80 -23.05 3.00e+00 1.11e-01 5.90e+01 angle pdb=" N VAL A 984 " pdb=" CA VAL A 984 " pdb=" C VAL A 984 " ideal model delta sigma weight residual 110.62 104.12 6.50 1.02e+00 9.61e-01 4.06e+01 angle pdb=" C SER A 989 " pdb=" CA SER A 989 " pdb=" CB SER A 989 " ideal model delta sigma weight residual 110.88 100.95 9.93 1.57e+00 4.06e-01 4.00e+01 angle pdb=" C TYR A1017 " pdb=" CA TYR A1017 " pdb=" CB TYR A1017 " ideal model delta sigma weight residual 110.06 118.74 -8.68 1.39e+00 5.18e-01 3.90e+01 angle pdb=" C GLU A1013 " pdb=" N ILE A1014 " pdb=" CA ILE A1014 " ideal model delta sigma weight residual 122.93 114.90 8.03 1.31e+00 5.83e-01 3.75e+01 ... (remaining 12569 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.17: 5430 29.17 - 58.35: 178 58.35 - 87.52: 14 87.52 - 116.69: 7 116.69 - 145.87: 4 Dihedral angle restraints: 5633 sinusoidal: 2322 harmonic: 3311 Sorted by residual: dihedral pdb=" C ASP A1015 " pdb=" N ASP A1015 " pdb=" CA ASP A1015 " pdb=" CB ASP A1015 " ideal model delta harmonic sigma weight residual -122.60 -134.32 11.72 0 2.50e+00 1.60e-01 2.20e+01 dihedral pdb=" C GLN A 795 " pdb=" N GLN A 795 " pdb=" CA GLN A 795 " pdb=" CB GLN A 795 " ideal model delta harmonic sigma weight residual -122.60 -110.98 -11.62 0 2.50e+00 1.60e-01 2.16e+01 dihedral pdb=" C SER A 989 " pdb=" N SER A 989 " pdb=" CA SER A 989 " pdb=" CB SER A 989 " ideal model delta harmonic sigma weight residual -122.60 -111.54 -11.06 0 2.50e+00 1.60e-01 1.96e+01 ... (remaining 5630 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1245 0.076 - 0.152: 146 0.152 - 0.227: 30 0.227 - 0.303: 16 0.303 - 0.379: 5 Chirality restraints: 1442 Sorted by residual: chirality pdb=" CA ASP A1015 " pdb=" N ASP A1015 " pdb=" C ASP A1015 " pdb=" CB ASP A1015 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA VAL A 797 " pdb=" N VAL A 797 " pdb=" C VAL A 797 " pdb=" CB VAL A 797 " both_signs ideal model delta sigma weight residual False 2.44 2.78 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA TYR A1017 " pdb=" N TYR A1017 " pdb=" C TYR A1017 " pdb=" CB TYR A1017 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.65e+00 ... (remaining 1439 not shown) Planarity restraints: 1590 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 794 " 0.021 2.00e-02 2.50e+03 4.25e-02 1.81e+01 pdb=" C ARG A 794 " -0.073 2.00e-02 2.50e+03 pdb=" O ARG A 794 " 0.027 2.00e-02 2.50e+03 pdb=" N GLN A 795 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A1013 " -0.021 2.00e-02 2.50e+03 4.19e-02 1.76e+01 pdb=" C GLU A1013 " 0.073 2.00e-02 2.50e+03 pdb=" O GLU A1013 " -0.026 2.00e-02 2.50e+03 pdb=" N ILE A1014 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 207 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C GLY A 207 " -0.048 2.00e-02 2.50e+03 pdb=" O GLY A 207 " 0.018 2.00e-02 2.50e+03 pdb=" N TRP A 208 " 0.016 2.00e-02 2.50e+03 ... (remaining 1587 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1248 2.75 - 3.29: 9586 3.29 - 3.83: 14689 3.83 - 4.36: 16941 4.36 - 4.90: 28355 Nonbonded interactions: 70819 Sorted by model distance: nonbonded pdb=" OD2 ASP A 160 " pdb=" OH TYR A 440 " model vdw 2.217 2.440 nonbonded pdb=" O ILE A 761 " pdb=" OG1 THR A 765 " model vdw 2.218 2.440 nonbonded pdb=" OG1 THR A 479 " pdb=" OE1 GLU A 482 " model vdw 2.234 2.440 nonbonded pdb=" OE2 GLU A 269 " pdb=" OH TYR A1129 " model vdw 2.282 2.440 nonbonded pdb=" OE1 GLU A 155 " pdb=" OG SER A 370 " model vdw 2.289 2.440 ... (remaining 70814 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 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: 4.950 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 26.990 Find NCS groups from input model: 0.230 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: 0.010 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 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 : 0.010 0.271 9289 Z= 0.730 Angle : 1.030 23.051 12574 Z= 0.628 Chirality : 0.062 0.379 1442 Planarity : 0.005 0.042 1590 Dihedral : 14.733 145.867 3511 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.55 % Favored : 94.28 % Rotamer: Outliers : 0.63 % Allowed : 1.48 % Favored : 97.89 % Cbeta Deviations : 0.85 % 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: -0.03 (0.25), residues: 1153 helix: 0.79 (0.20), residues: 728 sheet: -0.46 (0.73), residues: 56 loop : -1.50 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 158 HIS 0.004 0.001 HIS A1003 PHE 0.021 0.002 PHE A 766 TYR 0.032 0.002 TYR A1017 ARG 0.004 0.000 ARG A 828 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 236 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8551 (tp) cc_final: 0.8327 (tt) REVERT: A 67 MET cc_start: 0.7444 (tpp) cc_final: 0.7243 (tpp) REVERT: A 295 MET cc_start: 0.8602 (tpp) cc_final: 0.8325 (tpp) REVERT: A 345 SER cc_start: 0.9115 (t) cc_final: 0.8897 (p) REVERT: A 392 ASN cc_start: 0.7873 (t0) cc_final: 0.7592 (p0) REVERT: A 693 PHE cc_start: 0.5384 (t80) cc_final: 0.4884 (t80) REVERT: A 1082 PHE cc_start: 0.8735 (m-10) cc_final: 0.8485 (m-10) REVERT: A 1114 GLN cc_start: 0.8802 (tt0) cc_final: 0.8560 (mm-40) outliers start: 6 outliers final: 1 residues processed: 242 average time/residue: 0.2232 time to fit residues: 73.1644 Evaluate side-chains 150 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 149 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 ASN A 417 GLN A 566 GLN ** A 838 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1099 GLN A1149 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7532 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9289 Z= 0.205 Angle : 0.630 10.581 12574 Z= 0.317 Chirality : 0.041 0.154 1442 Planarity : 0.004 0.035 1590 Dihedral : 11.610 129.026 1434 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.03 % Favored : 94.80 % Rotamer: Outliers : 2.22 % Allowed : 10.88 % Favored : 86.91 % 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: 0.30 (0.25), residues: 1153 helix: 1.06 (0.20), residues: 741 sheet: -0.45 (0.81), residues: 49 loop : -1.49 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A1104 HIS 0.003 0.001 HIS A 60 PHE 0.024 0.001 PHE A 339 TYR 0.013 0.001 TYR A 243 ARG 0.008 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 168 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8543 (tp) cc_final: 0.8315 (tt) REVERT: A 67 MET cc_start: 0.7330 (tpp) cc_final: 0.6805 (tpp) REVERT: A 170 ARG cc_start: 0.7724 (ttm-80) cc_final: 0.7395 (ttm-80) REVERT: A 201 ILE cc_start: 0.8647 (OUTLIER) cc_final: 0.8391 (mm) REVERT: A 212 LEU cc_start: 0.7957 (OUTLIER) cc_final: 0.7694 (mm) REVERT: A 276 ASN cc_start: 0.8331 (OUTLIER) cc_final: 0.7910 (t0) REVERT: A 464 GLU cc_start: 0.8450 (pp20) cc_final: 0.7849 (tm-30) REVERT: A 482 GLU cc_start: 0.8891 (mp0) cc_final: 0.8680 (mp0) REVERT: A 1082 PHE cc_start: 0.8893 (m-10) cc_final: 0.8495 (m-10) REVERT: A 1114 GLN cc_start: 0.8921 (tt0) cc_final: 0.8527 (mm-40) outliers start: 21 outliers final: 8 residues processed: 181 average time/residue: 0.2110 time to fit residues: 52.6885 Evaluate side-chains 144 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 133 time to evaluate : 0.910 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 340 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1253 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 20.0000 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 71 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 114 optimal weight: 20.0000 chunk 93 optimal weight: 0.1980 chunk 104 optimal weight: 0.4980 chunk 35 optimal weight: 6.9990 chunk 84 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 139 GLN A 276 ASN A 392 ASN A 566 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.2670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9289 Z= 0.209 Angle : 0.604 10.701 12574 Z= 0.302 Chirality : 0.041 0.256 1442 Planarity : 0.003 0.034 1590 Dihedral : 10.374 108.341 1431 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.29 % Favored : 94.62 % Rotamer: Outliers : 2.01 % Allowed : 13.73 % Favored : 84.27 % 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: 0.36 (0.25), residues: 1153 helix: 1.18 (0.19), residues: 739 sheet: -0.29 (0.81), residues: 49 loop : -1.63 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 704 HIS 0.003 0.001 HIS A 60 PHE 0.016 0.001 PHE A 339 TYR 0.015 0.001 TYR A 243 ARG 0.005 0.000 ARG A1134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 147 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8559 (tp) cc_final: 0.8307 (tt) REVERT: A 67 MET cc_start: 0.7398 (tpp) cc_final: 0.6887 (tpp) REVERT: A 170 ARG cc_start: 0.7659 (ttm-80) cc_final: 0.7342 (ttm-80) REVERT: A 212 LEU cc_start: 0.8122 (OUTLIER) cc_final: 0.7890 (mm) REVERT: A 276 ASN cc_start: 0.8452 (OUTLIER) cc_final: 0.8087 (t0) REVERT: A 446 MET cc_start: 0.8351 (tpt) cc_final: 0.7948 (tpp) REVERT: A 464 GLU cc_start: 0.8500 (pp20) cc_final: 0.7883 (tm-30) REVERT: A 546 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7486 (tttt) REVERT: A 566 GLN cc_start: 0.8416 (tp40) cc_final: 0.8001 (tp-100) REVERT: A 1082 PHE cc_start: 0.8965 (m-10) cc_final: 0.8738 (m-10) REVERT: A 1114 GLN cc_start: 0.8914 (tt0) cc_final: 0.8518 (mm110) REVERT: A 1118 LEU cc_start: 0.6051 (OUTLIER) cc_final: 0.5683 (tt) REVERT: A 1229 ARG cc_start: 0.8063 (mmt180) cc_final: 0.7726 (mmm160) outliers start: 19 outliers final: 11 residues processed: 158 average time/residue: 0.1935 time to fit residues: 43.5480 Evaluate side-chains 144 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 129 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1253 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 54 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 70 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 112 optimal weight: 8.9990 chunk 55 optimal weight: 30.0000 chunk 100 optimal weight: 10.0000 chunk 30 optimal weight: 0.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN ** A 566 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 700 ASN A 805 ASN A1189 GLN A1250 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 9289 Z= 0.359 Angle : 0.697 10.701 12574 Z= 0.347 Chirality : 0.044 0.318 1442 Planarity : 0.004 0.043 1590 Dihedral : 10.369 107.905 1431 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.24 % Favored : 93.67 % Rotamer: Outliers : 3.48 % Allowed : 16.68 % Favored : 79.83 % 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: 0.14 (0.25), residues: 1153 helix: 0.95 (0.19), residues: 743 sheet: -0.25 (0.81), residues: 49 loop : -1.62 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 704 HIS 0.008 0.001 HIS A 60 PHE 0.017 0.002 PHE A 196 TYR 0.013 0.002 TYR A 243 ARG 0.009 0.001 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 139 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8581 (tp) cc_final: 0.8341 (tt) REVERT: A 446 MET cc_start: 0.8478 (tpt) cc_final: 0.7872 (tpp) REVERT: A 464 GLU cc_start: 0.8520 (pp20) cc_final: 0.7959 (tm-30) REVERT: A 510 MET cc_start: 0.7167 (mtt) cc_final: 0.6931 (mpp) REVERT: A 546 LYS cc_start: 0.7925 (OUTLIER) cc_final: 0.7439 (tttp) REVERT: A 551 ASP cc_start: 0.8075 (t0) cc_final: 0.7836 (t0) REVERT: A 1082 PHE cc_start: 0.9027 (m-10) cc_final: 0.8731 (m-10) REVERT: A 1118 LEU cc_start: 0.6241 (OUTLIER) cc_final: 0.5960 (tt) REVERT: A 1229 ARG cc_start: 0.8005 (mmt180) cc_final: 0.7673 (mmm160) outliers start: 33 outliers final: 23 residues processed: 163 average time/residue: 0.1905 time to fit residues: 44.6237 Evaluate side-chains 154 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 129 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 520 VAL Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1092 LEU Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1231 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 10.0000 chunk 95 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 20.0000 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.2980 overall best weight: 2.0588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 276 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 9289 Z= 0.289 Angle : 0.659 10.363 12574 Z= 0.325 Chirality : 0.042 0.312 1442 Planarity : 0.004 0.037 1590 Dihedral : 9.334 103.933 1431 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.33 % Favored : 93.58 % Rotamer: Outliers : 3.27 % Allowed : 18.69 % Favored : 78.04 % 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: 0.18 (0.25), residues: 1153 helix: 1.00 (0.19), residues: 741 sheet: -0.30 (0.82), residues: 49 loop : -1.65 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 704 HIS 0.006 0.001 HIS A 60 PHE 0.018 0.002 PHE A 196 TYR 0.014 0.001 TYR A 243 ARG 0.005 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 135 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8558 (tp) cc_final: 0.8302 (tt) REVERT: A 446 MET cc_start: 0.8416 (tpt) cc_final: 0.8019 (tpp) REVERT: A 464 GLU cc_start: 0.8524 (pp20) cc_final: 0.7962 (tm-30) REVERT: A 546 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7401 (tttp) REVERT: A 766 PHE cc_start: 0.8307 (OUTLIER) cc_final: 0.7727 (t80) REVERT: A 1082 PHE cc_start: 0.8968 (m-10) cc_final: 0.8683 (m-10) REVERT: A 1118 LEU cc_start: 0.6248 (OUTLIER) cc_final: 0.5774 (tt) REVERT: A 1229 ARG cc_start: 0.8047 (mmt180) cc_final: 0.7717 (mmm160) outliers start: 31 outliers final: 22 residues processed: 154 average time/residue: 0.1873 time to fit residues: 41.8434 Evaluate side-chains 152 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 127 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 74 MET Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1074 THR Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1231 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 0.4980 chunk 9 optimal weight: 0.8980 chunk 58 optimal weight: 20.0000 chunk 108 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.3549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9289 Z= 0.192 Angle : 0.614 11.534 12574 Z= 0.303 Chirality : 0.041 0.333 1442 Planarity : 0.003 0.037 1590 Dihedral : 8.367 97.725 1431 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.46 % Favored : 94.45 % Rotamer: Outliers : 3.06 % Allowed : 19.75 % Favored : 77.19 % 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 (0.25), residues: 1153 helix: 1.21 (0.19), residues: 740 sheet: -0.36 (0.82), residues: 49 loop : -1.61 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 704 HIS 0.003 0.001 HIS A 141 PHE 0.029 0.001 PHE A 508 TYR 0.016 0.001 TYR A 243 ARG 0.006 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 140 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6450 (m-80) cc_final: 0.5985 (m-80) REVERT: A 48 LEU cc_start: 0.8533 (tp) cc_final: 0.8314 (tp) REVERT: A 170 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7430 (ttm-80) REVERT: A 446 MET cc_start: 0.8391 (tpt) cc_final: 0.8027 (tpp) REVERT: A 464 GLU cc_start: 0.8546 (pp20) cc_final: 0.8000 (tm-30) REVERT: A 546 LYS cc_start: 0.7851 (OUTLIER) cc_final: 0.7513 (tttp) REVERT: A 576 ARG cc_start: 0.7484 (mpp80) cc_final: 0.7267 (mmm-85) REVERT: A 766 PHE cc_start: 0.8192 (OUTLIER) cc_final: 0.7732 (t80) REVERT: A 1082 PHE cc_start: 0.8893 (m-10) cc_final: 0.8618 (m-10) REVERT: A 1118 LEU cc_start: 0.6332 (OUTLIER) cc_final: 0.5925 (tt) REVERT: A 1229 ARG cc_start: 0.8012 (mmt180) cc_final: 0.7686 (mmm160) outliers start: 29 outliers final: 20 residues processed: 160 average time/residue: 0.1868 time to fit residues: 43.2204 Evaluate side-chains 151 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 128 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1113 SER Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1231 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 62 optimal weight: 0.5980 chunk 111 optimal weight: 20.0000 chunk 69 optimal weight: 0.5980 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 44 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 566 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.3625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9289 Z= 0.181 Angle : 0.623 12.981 12574 Z= 0.303 Chirality : 0.041 0.359 1442 Planarity : 0.003 0.037 1590 Dihedral : 8.231 97.204 1431 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.64 % Favored : 94.28 % Rotamer: Outliers : 2.96 % Allowed : 20.06 % Favored : 76.98 % 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: 0.47 (0.25), residues: 1153 helix: 1.26 (0.19), residues: 740 sheet: 0.06 (0.90), residues: 39 loop : -1.60 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 704 HIS 0.003 0.001 HIS A 141 PHE 0.021 0.001 PHE A 508 TYR 0.015 0.001 TYR A 243 ARG 0.007 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8526 (tp) cc_final: 0.8308 (tp) REVERT: A 170 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7326 (ttm-80) REVERT: A 446 MET cc_start: 0.8399 (tpt) cc_final: 0.8017 (tpp) REVERT: A 464 GLU cc_start: 0.8531 (pp20) cc_final: 0.7993 (tm-30) REVERT: A 493 MET cc_start: 0.8016 (tpp) cc_final: 0.7813 (tpp) REVERT: A 546 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7508 (tttp) REVERT: A 766 PHE cc_start: 0.8187 (OUTLIER) cc_final: 0.7769 (t80) REVERT: A 1082 PHE cc_start: 0.8835 (m-10) cc_final: 0.8583 (m-10) REVERT: A 1118 LEU cc_start: 0.6265 (OUTLIER) cc_final: 0.5837 (tt) REVERT: A 1229 ARG cc_start: 0.8037 (mmt180) cc_final: 0.7716 (mmm160) outliers start: 28 outliers final: 20 residues processed: 156 average time/residue: 0.2020 time to fit residues: 44.5809 Evaluate side-chains 149 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1231 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 55 optimal weight: 20.0000 chunk 10 optimal weight: 3.9990 chunk 87 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 107 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 566 GLN A1189 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9289 Z= 0.255 Angle : 0.666 13.066 12574 Z= 0.329 Chirality : 0.043 0.360 1442 Planarity : 0.004 0.038 1590 Dihedral : 8.433 100.494 1431 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.16 % Favored : 93.76 % Rotamer: Outliers : 2.85 % Allowed : 20.70 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1153 helix: 1.23 (0.19), residues: 740 sheet: -0.48 (0.81), residues: 49 loop : -1.64 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 704 HIS 0.008 0.001 HIS A 162 PHE 0.032 0.002 PHE A 979 TYR 0.014 0.001 TYR A 243 ARG 0.008 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 1.075 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8557 (tp) cc_final: 0.8324 (tp) REVERT: A 170 ARG cc_start: 0.7752 (ttm-80) cc_final: 0.7462 (ttm-80) REVERT: A 446 MET cc_start: 0.8396 (tpt) cc_final: 0.8038 (tpp) REVERT: A 464 GLU cc_start: 0.8530 (pp20) cc_final: 0.7997 (tm-30) REVERT: A 493 MET cc_start: 0.8051 (tpp) cc_final: 0.7845 (tpp) REVERT: A 546 LYS cc_start: 0.7915 (OUTLIER) cc_final: 0.7502 (tttp) REVERT: A 766 PHE cc_start: 0.8241 (OUTLIER) cc_final: 0.7764 (t80) REVERT: A 1078 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8764 (mp) REVERT: A 1082 PHE cc_start: 0.8838 (m-10) cc_final: 0.8583 (m-10) REVERT: A 1118 LEU cc_start: 0.6338 (OUTLIER) cc_final: 0.5924 (tt) REVERT: A 1229 ARG cc_start: 0.8054 (mmt180) cc_final: 0.7736 (mmm160) outliers start: 27 outliers final: 23 residues processed: 151 average time/residue: 0.1844 time to fit residues: 39.7590 Evaluate side-chains 157 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 130 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 546 LYS Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 858 LEU Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1231 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 chunk 103 optimal weight: 10.0000 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 566 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9289 Z= 0.205 Angle : 0.646 13.530 12574 Z= 0.316 Chirality : 0.042 0.365 1442 Planarity : 0.003 0.038 1590 Dihedral : 8.315 99.273 1431 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.90 % Favored : 94.02 % Rotamer: Outliers : 2.75 % Allowed : 21.22 % Favored : 76.03 % 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: 0.41 (0.25), residues: 1153 helix: 1.22 (0.19), residues: 743 sheet: -0.45 (0.82), residues: 49 loop : -1.63 (0.32), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 158 HIS 0.006 0.001 HIS A 162 PHE 0.029 0.001 PHE A 979 TYR 0.015 0.001 TYR A 243 ARG 0.008 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 134 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LEU cc_start: 0.8536 (tp) cc_final: 0.8309 (tp) REVERT: A 170 ARG cc_start: 0.7733 (ttm-80) cc_final: 0.7445 (ttm-80) REVERT: A 446 MET cc_start: 0.8390 (tpt) cc_final: 0.8031 (tpp) REVERT: A 464 GLU cc_start: 0.8529 (pp20) cc_final: 0.8020 (tm-30) REVERT: A 493 MET cc_start: 0.8045 (tpp) cc_final: 0.7825 (tpp) REVERT: A 507 ASP cc_start: 0.6789 (OUTLIER) cc_final: 0.5860 (t70) REVERT: A 766 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7747 (t80) REVERT: A 1078 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8748 (mp) REVERT: A 1082 PHE cc_start: 0.8818 (m-10) cc_final: 0.8567 (m-10) REVERT: A 1118 LEU cc_start: 0.6335 (OUTLIER) cc_final: 0.5887 (tt) REVERT: A 1229 ARG cc_start: 0.8065 (mmt180) cc_final: 0.7372 (mmp80) outliers start: 26 outliers final: 22 residues processed: 154 average time/residue: 0.1755 time to fit residues: 39.3920 Evaluate side-chains 155 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 129 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 936 ILE Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1122 SER Chi-restraints excluded: chain A residue 1231 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 10.0000 chunk 76 optimal weight: 0.4980 chunk 115 optimal weight: 0.7980 chunk 106 optimal weight: 0.0370 chunk 92 optimal weight: 40.0000 chunk 9 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 73 optimal weight: 0.6980 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 566 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.3854 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9289 Z= 0.180 Angle : 0.641 13.803 12574 Z= 0.311 Chirality : 0.042 0.367 1442 Planarity : 0.003 0.038 1590 Dihedral : 8.098 96.862 1431 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 2.64 % Allowed : 21.44 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.48 (0.25), residues: 1153 helix: 1.27 (0.19), residues: 743 sheet: -0.06 (0.88), residues: 39 loop : -1.60 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 158 HIS 0.004 0.001 HIS A 162 PHE 0.034 0.001 PHE A 508 TYR 0.015 0.001 TYR A 243 ARG 0.009 0.000 ARG A 589 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2306 Ramachandran restraints generated. 1153 Oldfield, 0 Emsley, 1153 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 134 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 TYR cc_start: 0.6386 (m-80) cc_final: 0.6163 (m-80) REVERT: A 48 LEU cc_start: 0.8524 (tp) cc_final: 0.8308 (tp) REVERT: A 170 ARG cc_start: 0.7614 (ttm-80) cc_final: 0.7332 (ttm-80) REVERT: A 446 MET cc_start: 0.8397 (tpt) cc_final: 0.8053 (tpp) REVERT: A 464 GLU cc_start: 0.8526 (pp20) cc_final: 0.8019 (tm-30) REVERT: A 493 MET cc_start: 0.8037 (tpp) cc_final: 0.7799 (tpp) REVERT: A 507 ASP cc_start: 0.6817 (OUTLIER) cc_final: 0.5685 (t70) REVERT: A 766 PHE cc_start: 0.8175 (OUTLIER) cc_final: 0.7761 (t80) REVERT: A 1078 LEU cc_start: 0.9057 (OUTLIER) cc_final: 0.8751 (mp) REVERT: A 1082 PHE cc_start: 0.8790 (m-10) cc_final: 0.8547 (m-10) REVERT: A 1118 LEU cc_start: 0.6281 (OUTLIER) cc_final: 0.5856 (tt) REVERT: A 1229 ARG cc_start: 0.8060 (mmt180) cc_final: 0.7367 (mmp80) outliers start: 25 outliers final: 21 residues processed: 152 average time/residue: 0.1938 time to fit residues: 42.8959 Evaluate side-chains 155 residues out of total 947 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 130 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 MET Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 68 MET Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 166 GLU Chi-restraints excluded: chain A residue 195 THR Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 237 ASP Chi-restraints excluded: chain A residue 276 ASN Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 335 CYS Chi-restraints excluded: chain A residue 392 ASN Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 462 LEU Chi-restraints excluded: chain A residue 478 THR Chi-restraints excluded: chain A residue 507 ASP Chi-restraints excluded: chain A residue 566 GLN Chi-restraints excluded: chain A residue 765 THR Chi-restraints excluded: chain A residue 766 PHE Chi-restraints excluded: chain A residue 791 SER Chi-restraints excluded: chain A residue 989 SER Chi-restraints excluded: chain A residue 1076 VAL Chi-restraints excluded: chain A residue 1078 LEU Chi-restraints excluded: chain A residue 1118 LEU Chi-restraints excluded: chain A residue 1122 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 2.9990 chunk 13 optimal weight: 0.0870 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 20.0000 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 0.0770 chunk 5 optimal weight: 0.0980 chunk 66 optimal weight: 0.6980 overall best weight: 0.3716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 HIS A 566 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.170105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.127118 restraints weight = 16634.942| |-----------------------------------------------------------------------------| r_work (start): 0.3889 rms_B_bonded: 3.30 r_work: 0.3708 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9289 Z= 0.168 Angle : 0.629 13.878 12574 Z= 0.304 Chirality : 0.041 0.367 1442 Planarity : 0.003 0.038 1590 Dihedral : 7.892 95.478 1431 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.81 % Favored : 94.10 % Rotamer: Outliers : 2.32 % Allowed : 21.75 % Favored : 75.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 (0.25), residues: 1153 helix: 1.31 (0.19), residues: 743 sheet: -0.04 (0.87), residues: 39 loop : -1.55 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 158 HIS 0.004 0.001 HIS A 141 PHE 0.024 0.001 PHE A 900 TYR 0.014 0.001 TYR A 243 ARG 0.009 0.000 ARG A 589 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2279.41 seconds wall clock time: 41 minutes 28.91 seconds (2488.91 seconds total)