Starting phenix.real_space_refine on Wed Feb 14 06:03:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op3_13012/02_2024/7op3_13012_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op3_13012/02_2024/7op3_13012.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op3_13012/02_2024/7op3_13012.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op3_13012/02_2024/7op3_13012.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op3_13012/02_2024/7op3_13012_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7op3_13012/02_2024/7op3_13012_updated.pdb" } resolution = 3.5 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= 0.082 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 54 5.16 5 C 5709 2.51 5 N 1460 2.21 5 O 1549 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 750": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1037": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1361": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1384": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8772 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1101, 8772 Unusual residues: {'SPM': 1} Classifications: {'peptide': 1100, 'undetermined': 1} Link IDs: {'PTRANS': 55, 'TRANS': 1044, None: 1} Not linked: pdbres="GLN A1394 " pdbres="SPM A1701 " Chain breaks: 5 Time building chain proxies: 5.59, per 1000 atoms: 0.64 Number of scatterers: 8772 At special positions: 0 Unit cell: (90.688, 92.352, 132.288, 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 54 16.00 O 1549 8.00 N 1460 7.00 C 5709 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=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 2.1 seconds 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2082 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 9 sheets defined 40.8% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.75 Creating SS restraints... Processing helix chain 'A' and resid 228 through 238 removed outlier: 3.595A pdb=" N ALA A 231 " --> pdb=" O ILE A 228 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL A 235 " --> pdb=" O ILE A 232 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N LEU A 236 " --> pdb=" O TYR A 233 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS A 237 " --> pdb=" O ILE A 234 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N VAL A 238 " --> pdb=" O VAL A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 247 through 250 No H-bonds generated for 'chain 'A' and resid 247 through 250' Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.512A pdb=" N LYS A 257 " --> pdb=" O LYS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 356 No H-bonds generated for 'chain 'A' and resid 353 through 356' Processing helix chain 'A' and resid 362 through 367 removed outlier: 4.434A pdb=" N LYS A 365 " --> pdb=" O GLY A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 391 removed outlier: 3.633A pdb=" N VAL A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 409 removed outlier: 3.612A pdb=" N VAL A 401 " --> pdb=" O TYR A 397 " (cutoff:3.500A) Processing helix chain 'A' and resid 414 through 445 removed outlier: 3.632A pdb=" N SER A 445 " --> pdb=" O LEU A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 518 No H-bonds generated for 'chain 'A' and resid 515 through 518' Processing helix chain 'A' and resid 530 through 535 removed outlier: 3.853A pdb=" N LYS A 534 " --> pdb=" O HIS A 530 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS A 535 " --> pdb=" O ASP A 531 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 530 through 535' Processing helix chain 'A' and resid 572 through 576 Processing helix chain 'A' and resid 588 through 617 removed outlier: 4.166A pdb=" N PHE A 593 " --> pdb=" O TYR A 589 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N LEU A 605 " --> pdb=" O CYS A 601 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ARG A 616 " --> pdb=" O VAL A 612 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 617 " --> pdb=" O ASN A 613 " (cutoff:3.500A) Processing helix chain 'A' and resid 621 through 635 removed outlier: 3.717A pdb=" N LEU A 632 " --> pdb=" O ALA A 628 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 633 " --> pdb=" O LEU A 629 " (cutoff:3.500A) Processing helix chain 'A' and resid 640 through 643 No H-bonds generated for 'chain 'A' and resid 640 through 643' Processing helix chain 'A' and resid 646 through 657 Processing helix chain 'A' and resid 666 through 673 removed outlier: 4.160A pdb=" N VAL A 670 " --> pdb=" O GLN A 666 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLY A 672 " --> pdb=" O VAL A 668 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LYS A 673 " --> pdb=" O ASN A 669 " (cutoff:3.500A) Processing helix chain 'A' and resid 749 through 758 removed outlier: 4.255A pdb=" N ALA A 758 " --> pdb=" O LEU A 754 " (cutoff:3.500A) Processing helix chain 'A' and resid 774 through 784 removed outlier: 3.979A pdb=" N LYS A 778 " --> pdb=" O PRO A 774 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N MET A 779 " --> pdb=" O LEU A 775 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N PHE A 780 " --> pdb=" O GLU A 776 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N GLU A 781 " --> pdb=" O VAL A 777 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N PHE A 782 " --> pdb=" O LYS A 778 " (cutoff:3.500A) removed outlier: 6.096A pdb=" N THR A 783 " --> pdb=" O MET A 779 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N GLY A 784 " --> pdb=" O PHE A 780 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 774 through 784' Processing helix chain 'A' and resid 868 through 871 No H-bonds generated for 'chain 'A' and resid 868 through 871' Processing helix chain 'A' and resid 883 through 890 Processing helix chain 'A' and resid 905 through 907 No H-bonds generated for 'chain 'A' and resid 905 through 907' Processing helix chain 'A' and resid 916 through 920 Processing helix chain 'A' and resid 939 through 948 Processing helix chain 'A' and resid 961 through 971 removed outlier: 3.599A pdb=" N SER A 966 " --> pdb=" O ARG A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 1043 through 1051 Processing helix chain 'A' and resid 1055 through 1064 Processing helix chain 'A' and resid 1073 through 1086 Processing helix chain 'A' and resid 1100 through 1105 Processing helix chain 'A' and resid 1130 through 1166 Proline residue: A1134 - end of helix removed outlier: 3.542A pdb=" N ILE A1137 " --> pdb=" O PRO A1134 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLU A1139 " --> pdb=" O VAL A1136 " (cutoff:3.500A) Processing helix chain 'A' and resid 1169 through 1171 No H-bonds generated for 'chain 'A' and resid 1169 through 1171' Processing helix chain 'A' and resid 1177 through 1186 removed outlier: 3.736A pdb=" N LEU A1181 " --> pdb=" O ASP A1177 " (cutoff:3.500A) Processing helix chain 'A' and resid 1189 through 1195 Processing helix chain 'A' and resid 1216 through 1242 removed outlier: 3.635A pdb=" N VAL A1220 " --> pdb=" O ARG A1216 " (cutoff:3.500A) Proline residue: A1221 - end of helix removed outlier: 3.550A pdb=" N GLN A1242 " --> pdb=" O VAL A1238 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1281 removed outlier: 3.816A pdb=" N THR A1265 " --> pdb=" O SER A1261 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU A1266 " --> pdb=" O GLU A1262 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N SER A1270 " --> pdb=" O LEU A1266 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N SER A1277 " --> pdb=" O GLU A1273 " (cutoff:3.500A) Processing helix chain 'A' and resid 1295 through 1313 removed outlier: 3.869A pdb=" N ALA A1300 " --> pdb=" O PRO A1296 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N THR A1308 " --> pdb=" O THR A1304 " (cutoff:3.500A) Processing helix chain 'A' and resid 1317 through 1323 removed outlier: 4.517A pdb=" N GLU A1321 " --> pdb=" O TRP A1318 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE A1322 " --> pdb=" O LEU A1319 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N MET A1323 " --> pdb=" O PHE A1320 " (cutoff:3.500A) Processing helix chain 'A' and resid 1330 through 1353 Processing helix chain 'A' and resid 1355 through 1366 Processing helix chain 'A' and resid 1378 through 1388 Processing sheet with id= A, first strand: chain 'A' and resid 206 through 210 removed outlier: 3.723A pdb=" N MET A 209 " --> pdb=" O ILE A 218 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE A 218 " --> pdb=" O MET A 209 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLU A 274 " --> pdb=" O ALA A 219 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N SER A 221 " --> pdb=" O VAL A 272 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL A 272 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 286 through 288 removed outlier: 4.188A pdb=" N SER A 322 " --> pdb=" O ARG A 286 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N LYS A 288 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU A 320 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N ARG A 321 " --> pdb=" O TYR A 332 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS A 338 " --> pdb=" O HIS A 333 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 472 through 474 removed outlier: 3.530A pdb=" N THR A 491 " --> pdb=" O VAL A 559 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N LEU A 561 " --> pdb=" O LEU A 489 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N LEU A 489 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 494 through 496 Processing sheet with id= E, first strand: chain 'A' and resid 660 through 662 Processing sheet with id= F, first strand: chain 'A' and resid 695 through 697 removed outlier: 4.313A pdb=" N ASP A 924 " --> pdb=" O THR A 900 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N CYS A 898 " --> pdb=" O VAL A 926 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N PHE A 928 " --> pdb=" O ILE A 896 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ILE A 896 " --> pdb=" O PHE A 928 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ILE A 930 " --> pdb=" O ARG A 894 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ARG A 894 " --> pdb=" O ILE A 930 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 981 through 984 Processing sheet with id= H, first strand: chain 'A' and resid 1091 through 1095 removed outlier: 6.142A pdb=" N VAL A1108 " --> pdb=" O PHE A1092 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLY A1094 " --> pdb=" O VAL A1108 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ILE A1110 " --> pdb=" O GLY A1094 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'A' and resid 1039 through 1041 removed outlier: 7.705A pdb=" N VAL A1041 " --> pdb=" O LYS A1066 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N TYR A1068 " --> pdb=" O VAL A1041 " (cutoff:3.500A) 291 hydrogen bonds defined for protein. 750 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: 3.08 Time building geometry restraints manager: 3.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2729 1.34 - 1.46: 2104 1.46 - 1.58: 4078 1.58 - 1.70: 0 1.70 - 1.81: 79 Bond restraints: 8990 Sorted by residual: bond pdb=" C TRP A1295 " pdb=" N PRO A1296 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.64e+00 bond pdb=" CB ARG A1366 " pdb=" CG ARG A1366 " ideal model delta sigma weight residual 1.520 1.562 -0.042 3.00e-02 1.11e+03 2.00e+00 bond pdb=" CB TYR A1037 " pdb=" CG TYR A1037 " ideal model delta sigma weight residual 1.512 1.542 -0.030 2.20e-02 2.07e+03 1.84e+00 bond pdb=" C ARG A1285 " pdb=" N PRO A1286 " ideal model delta sigma weight residual 1.335 1.351 -0.017 1.28e-02 6.10e+03 1.72e+00 bond pdb=" CA THR A 394 " pdb=" CB THR A 394 " ideal model delta sigma weight residual 1.526 1.546 -0.020 1.53e-02 4.27e+03 1.69e+00 ... (remaining 8985 not shown) Histogram of bond angle deviations from ideal: 99.79 - 106.65: 285 106.65 - 113.51: 4870 113.51 - 120.37: 3333 120.37 - 127.23: 3613 127.23 - 134.09: 106 Bond angle restraints: 12207 Sorted by residual: angle pdb=" CA THR A 394 " pdb=" CB THR A 394 " pdb=" CG2 THR A 394 " ideal model delta sigma weight residual 110.50 117.05 -6.55 1.70e+00 3.46e-01 1.48e+01 angle pdb=" N TYR A1037 " pdb=" CA TYR A1037 " pdb=" C TYR A1037 " ideal model delta sigma weight residual 111.36 115.40 -4.04 1.09e+00 8.42e-01 1.37e+01 angle pdb=" C PHE A 782 " pdb=" N THR A 783 " pdb=" CA THR A 783 " ideal model delta sigma weight residual 121.54 128.41 -6.87 1.91e+00 2.74e-01 1.29e+01 angle pdb=" N TRP A 350 " pdb=" CA TRP A 350 " pdb=" CB TRP A 350 " ideal model delta sigma weight residual 110.16 115.16 -5.00 1.48e+00 4.57e-01 1.14e+01 angle pdb=" N ARG A 292 " pdb=" CA ARG A 292 " pdb=" C ARG A 292 " ideal model delta sigma weight residual 109.81 117.27 -7.46 2.21e+00 2.05e-01 1.14e+01 ... (remaining 12202 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4768 17.62 - 35.23: 463 35.23 - 52.85: 87 52.85 - 70.47: 14 70.47 - 88.08: 8 Dihedral angle restraints: 5340 sinusoidal: 2123 harmonic: 3217 Sorted by residual: dihedral pdb=" CA VAL A 453 " pdb=" C VAL A 453 " pdb=" N PHE A 454 " pdb=" CA PHE A 454 " ideal model delta harmonic sigma weight residual 180.00 161.01 18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA ARG A1285 " pdb=" C ARG A1285 " pdb=" N PRO A1286 " pdb=" CA PRO A1286 " ideal model delta harmonic sigma weight residual -180.00 -161.11 -18.89 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CB GLU A1293 " pdb=" CG GLU A1293 " pdb=" CD GLU A1293 " pdb=" OE1 GLU A1293 " ideal model delta sinusoidal sigma weight residual 0.00 88.08 -88.08 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 5337 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 1170 0.068 - 0.135: 200 0.135 - 0.203: 15 0.203 - 0.270: 3 0.270 - 0.338: 3 Chirality restraints: 1391 Sorted by residual: chirality pdb=" CB ILE A 660 " pdb=" CA ILE A 660 " pdb=" CG1 ILE A 660 " pdb=" CG2 ILE A 660 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" CB ILE A 220 " pdb=" CA ILE A 220 " pdb=" CG1 ILE A 220 " pdb=" CG2 ILE A 220 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB THR A 263 " pdb=" CA THR A 263 " pdb=" OG1 THR A 263 " pdb=" CG2 THR A 263 " both_signs ideal model delta sigma weight residual False 2.55 2.28 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1388 not shown) Planarity restraints: 1523 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 350 " 0.028 2.00e-02 2.50e+03 3.46e-02 2.98e+01 pdb=" CG TRP A 350 " -0.091 2.00e-02 2.50e+03 pdb=" CD1 TRP A 350 " 0.049 2.00e-02 2.50e+03 pdb=" CD2 TRP A 350 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 350 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 350 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 350 " 0.011 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 350 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 350 " 0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP A 350 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1037 " 0.028 2.00e-02 2.50e+03 1.97e-02 7.79e+00 pdb=" CG TYR A1037 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TYR A1037 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR A1037 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR A1037 " 0.017 2.00e-02 2.50e+03 pdb=" CE2 TYR A1037 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A1037 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR A1037 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 868 " 0.041 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO A 869 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 869 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 869 " 0.034 5.00e-02 4.00e+02 ... (remaining 1520 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 2245 2.80 - 3.33: 8260 3.33 - 3.85: 14449 3.85 - 4.38: 16067 4.38 - 4.90: 27964 Nonbonded interactions: 68985 Sorted by model distance: nonbonded pdb=" OD1 ASN A 669 " pdb=" OG SER A1143 " model vdw 2.278 2.440 nonbonded pdb=" OH TYR A 331 " pdb=" O VAL A 371 " model vdw 2.293 2.440 nonbonded pdb=" OG SER A1001 " pdb=" O ASN A1003 " model vdw 2.293 2.440 nonbonded pdb=" O LYS A 673 " pdb=" OG SER A1089 " model vdw 2.313 2.440 nonbonded pdb=" O SER A 949 " pdb=" OG SER A 949 " model vdw 2.315 2.440 ... (remaining 68980 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.020 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: 0.000 Extract box with map and model: 9.840 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.400 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 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 0.042 8990 Z= 0.232 Angle : 0.776 8.749 12207 Z= 0.398 Chirality : 0.052 0.338 1391 Planarity : 0.006 0.061 1523 Dihedral : 14.575 88.082 3258 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -1.24 (0.24), residues: 1088 helix: 0.28 (0.24), residues: 437 sheet: -0.72 (0.52), residues: 101 loop : -1.80 (0.25), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.002 TRP A 350 HIS 0.004 0.001 HIS A1052 PHE 0.042 0.002 PHE A 780 TYR 0.042 0.002 TYR A1037 ARG 0.012 0.001 ARG A 576 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.922 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 104 average time/residue: 0.1831 time to fit residues: 27.9048 Evaluate side-chains 82 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 46 optimal weight: 0.0270 chunk 28 optimal weight: 0.3980 chunk 56 optimal weight: 20.0000 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8990 Z= 0.169 Angle : 0.524 7.481 12207 Z= 0.269 Chirality : 0.041 0.157 1391 Planarity : 0.005 0.046 1523 Dihedral : 4.749 51.848 1210 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.62 % Allowed : 8.92 % Favored : 90.46 % 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: -0.79 (0.25), residues: 1088 helix: 0.80 (0.25), residues: 444 sheet: -0.66 (0.49), residues: 110 loop : -1.69 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 350 HIS 0.006 0.001 HIS A 977 PHE 0.023 0.001 PHE A 536 TYR 0.013 0.001 TYR A1037 ARG 0.005 0.000 ARG A1070 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 91 time to evaluate : 1.038 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 96 average time/residue: 0.1880 time to fit residues: 26.7541 Evaluate side-chains 90 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 1387 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 20.0000 chunk 31 optimal weight: 0.0570 chunk 83 optimal weight: 0.5980 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 108 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1242 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8990 Z= 0.214 Angle : 0.529 7.323 12207 Z= 0.268 Chirality : 0.042 0.184 1391 Planarity : 0.004 0.036 1523 Dihedral : 4.646 55.282 1210 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.24 % Allowed : 13.17 % Favored : 85.58 % 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: -0.83 (0.25), residues: 1088 helix: 0.69 (0.25), residues: 447 sheet: -0.75 (0.48), residues: 115 loop : -1.64 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 350 HIS 0.005 0.001 HIS A 977 PHE 0.016 0.001 PHE A 780 TYR 0.015 0.001 TYR A 255 ARG 0.003 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 87 time to evaluate : 1.000 Fit side-chains REVERT: A 680 ASP cc_start: 0.7724 (t0) cc_final: 0.7478 (t70) REVERT: A 945 GLU cc_start: 0.7906 (tt0) cc_final: 0.7695 (tt0) outliers start: 12 outliers final: 6 residues processed: 94 average time/residue: 0.1717 time to fit residues: 24.6121 Evaluate side-chains 87 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 81 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 1037 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.4980 chunk 75 optimal weight: 0.8980 chunk 51 optimal weight: 0.0470 chunk 11 optimal weight: 3.9990 chunk 47 optimal weight: 0.0570 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.0870 chunk 106 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 0.0030 chunk 28 optimal weight: 8.9990 overall best weight: 0.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1242 GLN ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1241 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8990 Z= 0.122 Angle : 0.491 6.662 12207 Z= 0.247 Chirality : 0.041 0.165 1391 Planarity : 0.004 0.033 1523 Dihedral : 4.430 59.393 1210 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.66 % Allowed : 13.80 % Favored : 84.54 % 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: -0.67 (0.26), residues: 1088 helix: 0.91 (0.25), residues: 448 sheet: -0.67 (0.48), residues: 115 loop : -1.64 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 350 HIS 0.003 0.000 HIS A 977 PHE 0.021 0.001 PHE A1361 TYR 0.013 0.001 TYR A 255 ARG 0.004 0.000 ARG A1070 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 0.960 Fit side-chains REVERT: A 680 ASP cc_start: 0.7685 (t0) cc_final: 0.7461 (t0) REVERT: A 868 MET cc_start: 0.4547 (OUTLIER) cc_final: 0.4179 (mtm) REVERT: A 945 GLU cc_start: 0.7729 (tt0) cc_final: 0.7500 (tt0) REVERT: A 1187 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8299 (mp) outliers start: 16 outliers final: 8 residues processed: 109 average time/residue: 0.1865 time to fit residues: 29.9457 Evaluate side-chains 99 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 1 optimal weight: 0.0070 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 0.5980 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 54 optimal weight: 30.0000 chunk 95 optimal weight: 0.0570 chunk 26 optimal weight: 6.9990 overall best weight: 1.1320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.1550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8990 Z= 0.257 Angle : 0.539 6.752 12207 Z= 0.273 Chirality : 0.043 0.139 1391 Planarity : 0.004 0.031 1523 Dihedral : 4.563 57.876 1210 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.18 % Allowed : 14.63 % Favored : 83.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.85 (0.25), residues: 1088 helix: 0.71 (0.25), residues: 453 sheet: -0.48 (0.48), residues: 124 loop : -1.80 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 350 HIS 0.005 0.001 HIS A 977 PHE 0.016 0.001 PHE A 536 TYR 0.018 0.001 TYR A1317 ARG 0.003 0.000 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 90 time to evaluate : 0.926 Fit side-chains REVERT: A 868 MET cc_start: 0.4641 (OUTLIER) cc_final: 0.4273 (mtm) REVERT: A 945 GLU cc_start: 0.7911 (tt0) cc_final: 0.7693 (tt0) outliers start: 21 outliers final: 15 residues processed: 105 average time/residue: 0.1680 time to fit residues: 26.8413 Evaluate side-chains 100 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 533 ASP Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1133 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 3.9990 chunk 95 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 106 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 30.0000 chunk 8 optimal weight: 0.7980 chunk 55 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 351 ASN A 355 ASN A 497 ASN A 530 HIS ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1263 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8990 Z= 0.383 Angle : 0.613 6.552 12207 Z= 0.313 Chirality : 0.046 0.153 1391 Planarity : 0.005 0.033 1523 Dihedral : 4.927 57.289 1210 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 3.01 % Allowed : 16.18 % Favored : 80.81 % 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: -1.12 (0.25), residues: 1088 helix: 0.33 (0.24), residues: 449 sheet: -0.59 (0.48), residues: 124 loop : -1.78 (0.26), residues: 515 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 350 HIS 0.006 0.001 HIS A1352 PHE 0.023 0.002 PHE A1361 TYR 0.016 0.002 TYR A 397 ARG 0.004 0.000 ARG A1138 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 87 time to evaluate : 1.022 Fit side-chains REVERT: A 868 MET cc_start: 0.4755 (OUTLIER) cc_final: 0.4363 (mtm) REVERT: A 890 HIS cc_start: 0.7749 (m-70) cc_final: 0.7543 (m170) REVERT: A 1187 LEU cc_start: 0.8686 (OUTLIER) cc_final: 0.8465 (mp) REVERT: A 1263 ASN cc_start: 0.8230 (OUTLIER) cc_final: 0.7386 (t0) outliers start: 29 outliers final: 21 residues processed: 110 average time/residue: 0.1705 time to fit residues: 28.5087 Evaluate side-chains 108 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 84 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 419 ILE Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 493 ASP Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1133 VAL Chi-restraints excluded: chain A residue 1164 SER Chi-restraints excluded: chain A residue 1187 LEU Chi-restraints excluded: chain A residue 1263 ASN Chi-restraints excluded: chain A residue 1378 LEU Chi-restraints excluded: chain A residue 1387 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 89 optimal weight: 0.5980 chunk 59 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 64 optimal weight: 0.4980 chunk 48 optimal weight: 7.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8990 Z= 0.201 Angle : 0.538 7.837 12207 Z= 0.271 Chirality : 0.042 0.142 1391 Planarity : 0.004 0.033 1523 Dihedral : 4.684 55.604 1210 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.39 % Allowed : 17.22 % Favored : 80.39 % 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: -0.92 (0.25), residues: 1088 helix: 0.56 (0.25), residues: 448 sheet: -0.52 (0.48), residues: 124 loop : -1.71 (0.26), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 350 HIS 0.003 0.001 HIS A 333 PHE 0.017 0.001 PHE A 536 TYR 0.020 0.002 TYR A 887 ARG 0.002 0.000 ARG A1070 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 88 time to evaluate : 0.943 Fit side-chains REVERT: A 868 MET cc_start: 0.4675 (OUTLIER) cc_final: 0.4300 (mtm) REVERT: A 1187 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8406 (mp) outliers start: 23 outliers final: 18 residues processed: 106 average time/residue: 0.1796 time to fit residues: 28.5040 Evaluate side-chains 104 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 868 MET Chi-restraints excluded: chain A residue 887 TYR Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1187 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9990 chunk 31 optimal weight: 0.0050 chunk 20 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 9 optimal weight: 8.9990 chunk 83 optimal weight: 0.4980 chunk 96 optimal weight: 1.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 2.9990 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 890 HIS ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8990 Z= 0.182 Angle : 0.521 8.105 12207 Z= 0.261 Chirality : 0.042 0.143 1391 Planarity : 0.004 0.033 1523 Dihedral : 4.499 52.876 1210 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.59 % Allowed : 17.84 % Favored : 79.56 % 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: -0.79 (0.26), residues: 1088 helix: 0.72 (0.25), residues: 447 sheet: -0.50 (0.48), residues: 124 loop : -1.67 (0.26), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 350 HIS 0.003 0.001 HIS A 977 PHE 0.017 0.001 PHE A 536 TYR 0.015 0.001 TYR A1317 ARG 0.004 0.000 ARG A 438 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 85 time to evaluate : 1.032 Fit side-chains outliers start: 25 outliers final: 19 residues processed: 104 average time/residue: 0.1842 time to fit residues: 29.1971 Evaluate side-chains 100 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 81 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 258 LEU Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 887 TYR Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1039 ILE Chi-restraints excluded: chain A residue 1378 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.5980 chunk 101 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 43 optimal weight: 0.7980 chunk 77 optimal weight: 0.9980 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 0.0060 chunk 93 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 63 optimal weight: 6.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.2050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8990 Z= 0.159 Angle : 0.532 8.967 12207 Z= 0.262 Chirality : 0.041 0.142 1391 Planarity : 0.004 0.032 1523 Dihedral : 4.352 49.789 1210 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 1.97 % Allowed : 18.57 % Favored : 79.46 % 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: -0.68 (0.26), residues: 1088 helix: 0.88 (0.26), residues: 439 sheet: -0.50 (0.50), residues: 114 loop : -1.62 (0.26), residues: 535 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 350 HIS 0.003 0.001 HIS A 977 PHE 0.017 0.001 PHE A 536 TYR 0.016 0.001 TYR A1182 ARG 0.003 0.000 ARG A1070 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 1.175 Fit side-chains REVERT: A 1186 MET cc_start: 0.7901 (mtt) cc_final: 0.7684 (mtt) outliers start: 19 outliers final: 17 residues processed: 101 average time/residue: 0.1811 time to fit residues: 27.2624 Evaluate side-chains 99 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 482 GLN Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 754 LEU Chi-restraints excluded: chain A residue 955 MET Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 7.9990 chunk 72 optimal weight: 0.0170 chunk 109 optimal weight: 0.0470 chunk 100 optimal weight: 0.3980 chunk 87 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 69 optimal weight: 2.9990 chunk 92 optimal weight: 0.0870 chunk 26 optimal weight: 0.8980 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 530 HIS ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8990 Z= 0.143 Angle : 0.525 9.460 12207 Z= 0.256 Chirality : 0.041 0.141 1391 Planarity : 0.004 0.032 1523 Dihedral : 4.198 46.218 1210 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.76 % Allowed : 18.57 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.64 (0.26), residues: 1088 helix: 0.97 (0.26), residues: 444 sheet: -0.50 (0.49), residues: 114 loop : -1.67 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 350 HIS 0.003 0.000 HIS A 977 PHE 0.016 0.001 PHE A 536 TYR 0.014 0.001 TYR A1182 ARG 0.004 0.000 ARG A 438 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 87 time to evaluate : 1.003 Fit side-chains REVERT: A 1186 MET cc_start: 0.7819 (mtt) cc_final: 0.7543 (mtt) outliers start: 17 outliers final: 14 residues processed: 100 average time/residue: 0.1843 time to fit residues: 27.8826 Evaluate side-chains 97 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 323 ILE Chi-restraints excluded: chain A residue 488 LEU Chi-restraints excluded: chain A residue 563 VAL Chi-restraints excluded: chain A residue 575 VAL Chi-restraints excluded: chain A residue 633 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 660 ILE Chi-restraints excluded: chain A residue 662 CYS Chi-restraints excluded: chain A residue 712 VAL Chi-restraints excluded: chain A residue 961 ILE Chi-restraints excluded: chain A residue 1002 ILE Chi-restraints excluded: chain A residue 1037 TYR Chi-restraints excluded: chain A residue 1039 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 4.9990 chunk 12 optimal weight: 0.4980 chunk 24 optimal weight: 6.9990 chunk 87 optimal weight: 0.0670 chunk 36 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 63 optimal weight: 6.9990 overall best weight: 0.9120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.194590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.122343 restraints weight = 10483.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.125946 restraints weight = 6092.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.127913 restraints weight = 4452.366| |-----------------------------------------------------------------------------| r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8990 Z= 0.226 Angle : 0.550 9.532 12207 Z= 0.271 Chirality : 0.043 0.203 1391 Planarity : 0.004 0.032 1523 Dihedral : 4.442 57.546 1210 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 1.66 % Allowed : 19.09 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.25), residues: 1088 helix: 0.78 (0.25), residues: 452 sheet: -0.50 (0.50), residues: 114 loop : -1.70 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 350 HIS 0.003 0.001 HIS A1352 PHE 0.016 0.001 PHE A 536 TYR 0.017 0.001 TYR A 255 ARG 0.005 0.000 ARG A 438 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1971.63 seconds wall clock time: 36 minutes 41.17 seconds (2201.17 seconds total)