Starting phenix.real_space_refine on Wed Sep 17 23:11:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9eda_47942/09_2025/9eda_47942.cif Found real_map, /net/cci-nas-00/data/ceres_data/9eda_47942/09_2025/9eda_47942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9eda_47942/09_2025/9eda_47942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9eda_47942/09_2025/9eda_47942.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9eda_47942/09_2025/9eda_47942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9eda_47942/09_2025/9eda_47942.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 138 5.49 5 S 17 5.16 5 C 7190 2.51 5 N 2110 2.21 5 O 2624 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12079 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1995 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 50, 'rna3p_pyr': 31} Link IDs: {'rna2p': 12, 'rna3p': 80} Chain: "C" Number of atoms: 346 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 346 Classifications: {'DNA': 17} Link IDs: {'rna3p': 16} Chain: "D" Number of atoms: 332 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 332 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "c" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 239 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 9166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1150, 9166 Classifications: {'peptide': 1150} Incomplete info: {'truncation_to_alanine': 53} Link IDs: {'PTRANS': 32, 'TRANS': 1117} Chain breaks: 4 Unresolved non-hydrogen bonds: 221 Unresolved non-hydrogen angles: 261 Unresolved non-hydrogen dihedrals: 190 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 12, 'ARG:plan': 6, 'ASN:plan1': 1, 'ASP:plan': 4, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 122 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 2.73, per 1000 atoms: 0.23 Number of scatterers: 12079 At special positions: 0 Unit cell: (85.8196, 136.645, 124.147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 17 16.00 P 138 15.00 O 2624 8.00 N 2110 7.00 C 7190 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 479.1 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2188 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 6 sheets defined 54.4% alpha, 7.6% beta 51 base pairs and 88 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 59 through 95 removed outlier: 5.046A pdb=" N ASN A 88 " --> pdb=" O GLU A 84 " (cutoff:3.500A) removed outlier: 5.644A pdb=" N GLU A 89 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS A 92 " --> pdb=" O ASN A 88 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ASP A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 103 Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 134 through 145 removed outlier: 3.778A pdb=" N LEU A 138 " --> pdb=" O THR A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 164 Processing helix chain 'A' and resid 180 through 196 removed outlier: 3.537A pdb=" N LEU A 184 " --> pdb=" O ASP A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 213 Processing helix chain 'A' and resid 217 through 229 Processing helix chain 'A' and resid 236 through 247 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.556A pdb=" N PHE A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 283 Processing helix chain 'A' and resid 286 through 304 removed outlier: 3.784A pdb=" N ASP A 304 " --> pdb=" O ILE A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 343 Processing helix chain 'A' and resid 344 through 346 No H-bonds generated for 'chain 'A' and resid 344 through 346' Processing helix chain 'A' and resid 347 through 352 Processing helix chain 'A' and resid 358 through 364 Processing helix chain 'A' and resid 368 through 382 Proline residue: A 378 - end of helix Processing helix chain 'A' and resid 386 through 395 Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.724A pdb=" N GLY A 408 " --> pdb=" O PHE A 405 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N SER A 409 " --> pdb=" O ASP A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 427 removed outlier: 4.129A pdb=" N HIS A 415 " --> pdb=" O PRO A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 436 removed outlier: 4.017A pdb=" N LYS A 434 " --> pdb=" O TYR A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 446 Processing helix chain 'A' and resid 477 through 482 Processing helix chain 'A' and resid 483 through 496 removed outlier: 3.984A pdb=" N MET A 495 " --> pdb=" O PHE A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 512 through 525 Processing helix chain 'A' and resid 541 through 556 removed outlier: 3.684A pdb=" N PHE A 553 " --> pdb=" O VAL A 549 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LYS A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 568 Processing helix chain 'A' and resid 591 through 602 Processing helix chain 'A' and resid 612 through 626 Processing helix chain 'A' and resid 628 through 637 removed outlier: 4.194A pdb=" N ARG A 635 " --> pdb=" O MET A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 640 No H-bonds generated for 'chain 'A' and resid 638 through 640' Processing helix chain 'A' and resid 644 through 654 Processing helix chain 'A' and resid 663 through 668 removed outlier: 3.700A pdb=" N ILE A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 685 Processing helix chain 'A' and resid 692 through 697 Processing helix chain 'A' and resid 703 through 714 Processing helix chain 'A' and resid 719 through 726 Processing helix chain 'A' and resid 730 through 751 removed outlier: 3.582A pdb=" N MET A 751 " --> pdb=" O LEU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 926 through 940 Processing helix chain 'A' and resid 959 through 969 removed outlier: 3.822A pdb=" N VAL A 963 " --> pdb=" O LYS A 959 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE A 966 " --> pdb=" O LEU A 962 " (cutoff:3.500A) Processing helix chain 'A' and resid 981 through 1001 Processing helix chain 'A' and resid 1078 through 1088 Processing helix chain 'A' and resid 1127 through 1132 Processing helix chain 'A' and resid 1170 through 1177 removed outlier: 3.685A pdb=" N ASN A1177 " --> pdb=" O SER A1173 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1186 Processing helix chain 'A' and resid 1191 through 1195 Processing helix chain 'A' and resid 1229 through 1240 Processing helix chain 'A' and resid 1248 through 1262 Processing helix chain 'A' and resid 1263 through 1280 removed outlier: 4.335A pdb=" N ASP A1267 " --> pdb=" O LYS A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1283 through 1297 Processing helix chain 'A' and resid 1301 through 1312 Processing helix chain 'A' and resid 1313 through 1316 Processing helix chain 'A' and resid 1341 through 1344 Processing helix chain 'A' and resid 1363 through 1365 No H-bonds generated for 'chain 'A' and resid 1363 through 1365' Processing sheet with id=AA1, first strand: chain 'A' and resid 955 through 957 removed outlier: 6.211A pdb=" N ILE A 759 " --> pdb=" O ILE A 956 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ILE A 7 " --> pdb=" O VAL A 760 " (cutoff:3.500A) removed outlier: 8.186A pdb=" N GLU A 762 " --> pdb=" O ILE A 7 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N LEU A 9 " --> pdb=" O GLU A 762 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 42 through 46 removed outlier: 9.907A pdb=" N GLU A1357 " --> pdb=" O LYS A 31 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LYS A 33 " --> pdb=" O GLU A1357 " (cutoff:3.500A) removed outlier: 7.834A pdb=" N ARG A1359 " --> pdb=" O LYS A 33 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N LEU A 35 " --> pdb=" O ARG A1359 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N ASP A1361 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU A1203 " --> pdb=" O ILE A1348 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 538 through 539 removed outlier: 3.835A pdb=" N TYR A 529 " --> pdb=" O ALA A 538 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1063 through 1064 removed outlier: 3.967A pdb=" N TRP A1074 " --> pdb=" O GLU A1064 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1156 through 1167 Processing sheet with id=AA6, first strand: chain 'A' and resid 1324 through 1326 removed outlier: 3.587A pdb=" N PHE A1324 " --> pdb=" O ILE A1331 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 123 hydrogen bonds 242 hydrogen bond angles 0 basepair planarities 51 basepair parallelities 88 stacking parallelities Total time for adding SS restraints: 2.73 Time building geometry restraints manager: 1.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2562 1.33 - 1.46: 3593 1.46 - 1.58: 6131 1.58 - 1.70: 274 1.70 - 1.83: 32 Bond restraints: 12592 Sorted by residual: bond pdb=" N ASN A 726 " pdb=" CA ASN A 726 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.32e-02 5.74e+03 8.26e+00 bond pdb=" N ILE A 226 " pdb=" CA ILE A 226 " ideal model delta sigma weight residual 1.459 1.496 -0.037 1.30e-02 5.92e+03 8.06e+00 bond pdb=" N ILE A 927 " pdb=" CA ILE A 927 " ideal model delta sigma weight residual 1.461 1.493 -0.032 1.19e-02 7.06e+03 7.35e+00 bond pdb=" N LYS A1156 " pdb=" CA LYS A1156 " ideal model delta sigma weight residual 1.454 1.487 -0.032 1.27e-02 6.20e+03 6.49e+00 bond pdb=" N MET A 694 " pdb=" CA MET A 694 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.23e-02 6.61e+03 6.43e+00 ... (remaining 12587 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.58: 17173 2.58 - 5.15: 359 5.15 - 7.73: 78 7.73 - 10.31: 17 10.31 - 12.88: 8 Bond angle restraints: 17635 Sorted by residual: angle pdb=" CA LYS A1192 " pdb=" CB LYS A1192 " pdb=" CG LYS A1192 " ideal model delta sigma weight residual 114.10 124.86 -10.76 2.00e+00 2.50e-01 2.89e+01 angle pdb=" CA GLN A1364 " pdb=" CB GLN A1364 " pdb=" CG GLN A1364 " ideal model delta sigma weight residual 114.10 123.73 -9.63 2.00e+00 2.50e-01 2.32e+01 angle pdb=" N GLU A 24 " pdb=" CA GLU A 24 " pdb=" C GLU A 24 " ideal model delta sigma weight residual 113.20 107.56 5.64 1.21e+00 6.83e-01 2.18e+01 angle pdb=" CA TYR A 451 " pdb=" CB TYR A 451 " pdb=" CG TYR A 451 " ideal model delta sigma weight residual 113.90 122.29 -8.39 1.80e+00 3.09e-01 2.17e+01 angle pdb=" CB GLN A1364 " pdb=" CG GLN A1364 " pdb=" CD GLN A1364 " ideal model delta sigma weight residual 112.60 120.42 -7.82 1.70e+00 3.46e-01 2.12e+01 ... (remaining 17630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.06: 6361 18.06 - 36.11: 736 36.11 - 54.17: 306 54.17 - 72.23: 139 72.23 - 90.28: 28 Dihedral angle restraints: 7570 sinusoidal: 4197 harmonic: 3373 Sorted by residual: dihedral pdb=" CA GLU A 627 " pdb=" C GLU A 627 " pdb=" N ASP A 628 " pdb=" CA ASP A 628 " ideal model delta harmonic sigma weight residual 180.00 153.75 26.25 0 5.00e+00 4.00e-02 2.76e+01 dihedral pdb=" CA PRO A 449 " pdb=" C PRO A 449 " pdb=" N TYR A 450 " pdb=" CA TYR A 450 " ideal model delta harmonic sigma weight residual 180.00 155.55 24.45 0 5.00e+00 4.00e-02 2.39e+01 dihedral pdb=" CA LEU A 625 " pdb=" C LEU A 625 " pdb=" N PHE A 626 " pdb=" CA PHE A 626 " ideal model delta harmonic sigma weight residual -180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 ... (remaining 7567 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.124: 2002 0.124 - 0.248: 46 0.248 - 0.371: 2 0.371 - 0.495: 3 0.495 - 0.619: 7 Chirality restraints: 2060 Sorted by residual: chirality pdb=" P DT c 4 " pdb=" OP1 DT c 4 " pdb=" OP2 DT c 4 " pdb=" O5' DT c 4 " both_signs ideal model delta sigma weight residual True 2.35 -2.96 -0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" P DT c 9 " pdb=" OP1 DT c 9 " pdb=" OP2 DT c 9 " pdb=" O5' DT c 9 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" P DA c 8 " pdb=" OP1 DA c 8 " pdb=" OP2 DA c 8 " pdb=" O5' DA c 8 " both_signs ideal model delta sigma weight residual True 2.35 -2.88 -0.53 2.00e-01 2.50e+01 7.04e+00 ... (remaining 2057 not shown) Planarity restraints: 1751 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 655 " -0.480 9.50e-02 1.11e+02 2.15e-01 2.84e+01 pdb=" NE ARG A 655 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A 655 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 655 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 655 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 661 " -0.361 9.50e-02 1.11e+02 1.62e-01 1.61e+01 pdb=" NE ARG A 661 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 661 " 0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG A 661 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 661 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 518 " -0.012 2.00e-02 2.50e+03 2.33e-02 9.53e+00 pdb=" CG PHE A 518 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE A 518 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE A 518 " -0.024 2.00e-02 2.50e+03 pdb=" CE1 PHE A 518 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 518 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 518 " 0.004 2.00e-02 2.50e+03 ... (remaining 1748 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 892 2.73 - 3.28: 11375 3.28 - 3.82: 21732 3.82 - 4.36: 26854 4.36 - 4.90: 40655 Nonbonded interactions: 101508 Sorted by model distance: nonbonded pdb=" OH TYR A 451 " pdb=" OD2 ASP A 628 " model vdw 2.193 3.040 nonbonded pdb=" O2' A B 47 " pdb=" O LEU A 101 " model vdw 2.207 3.040 nonbonded pdb=" OG SER A 512 " pdb=" OE2 GLU A 617 " model vdw 2.217 3.040 nonbonded pdb=" O ILE A 667 " pdb=" OG1 THR A 678 " model vdw 2.225 3.040 nonbonded pdb=" CG2 VAL A 530 " pdb=" CB PRO A 537 " model vdw 2.241 3.860 ... (remaining 101503 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 12.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 13.140 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:9.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7594 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 : 0.006 0.062 12592 Z= 0.272 Angle : 0.981 12.883 17635 Z= 0.521 Chirality : 0.060 0.619 2060 Planarity : 0.009 0.215 1751 Dihedral : 19.256 90.285 5382 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 0.41 % Allowed : 27.33 % Favored : 72.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.21 (0.23), residues: 1140 helix: -0.50 (0.20), residues: 560 sheet: -0.30 (0.48), residues: 117 loop : -1.16 (0.26), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 586 TYR 0.041 0.003 TYR A 271 PHE 0.052 0.003 PHE A 518 TRP 0.024 0.002 TRP A 659 HIS 0.012 0.002 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00553 (12592) covalent geometry : angle 0.98108 (17635) hydrogen bonds : bond 0.14734 ( 567) hydrogen bonds : angle 6.22377 ( 1535) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 118 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7204 (mtpp) cc_final: 0.6886 (ptpp) REVERT: A 209 LYS cc_start: 0.8911 (ttmm) cc_final: 0.8536 (tptp) REVERT: A 284 ASP cc_start: 0.8286 (p0) cc_final: 0.7728 (t0) REVERT: A 288 ASP cc_start: 0.8716 (m-30) cc_final: 0.8301 (t0) REVERT: A 383 MET cc_start: 0.7425 (mtp) cc_final: 0.7040 (mtm) REVERT: A 599 LYS cc_start: 0.8904 (mptt) cc_final: 0.8596 (mmtm) REVERT: A 618 ASP cc_start: 0.8019 (t0) cc_final: 0.7609 (t0) REVERT: A 702 LEU cc_start: 0.6082 (mm) cc_final: 0.5767 (mm) REVERT: A 762 GLU cc_start: 0.7398 (pt0) cc_final: 0.6698 (tt0) REVERT: A 1151 LYS cc_start: 0.8044 (ttmm) cc_final: 0.7777 (mttm) REVERT: A 1170 GLU cc_start: 0.8414 (mt-10) cc_final: 0.8091 (mt-10) REVERT: A 1176 LYS cc_start: 0.8511 (ttmm) cc_final: 0.8104 (tmmt) REVERT: A 1177 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.8142 (t0) REVERT: A 1258 PHE cc_start: 0.6027 (t80) cc_final: 0.5687 (t80) REVERT: A 1261 GLN cc_start: 0.8830 (pt0) cc_final: 0.8570 (pt0) outliers start: 4 outliers final: 1 residues processed: 121 average time/residue: 0.5177 time to fit residues: 68.3629 Evaluate side-chains 94 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 1177 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 108 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 0.3980 chunk 113 optimal weight: 0.6980 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 65 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0050 overall best weight: 0.3732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 160 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 235 ASN A 709 GLN A1364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.145479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.106098 restraints weight = 21799.160| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.30 r_work: 0.3364 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12592 Z= 0.133 Angle : 0.567 7.327 17635 Z= 0.303 Chirality : 0.037 0.144 2060 Planarity : 0.004 0.035 1751 Dihedral : 19.161 91.101 3126 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 4.20 % Allowed : 22.52 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.24 (0.24), residues: 1140 helix: 0.48 (0.21), residues: 575 sheet: -0.17 (0.49), residues: 117 loop : -0.88 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 586 TYR 0.031 0.001 TYR A 451 PHE 0.016 0.002 PHE A 518 TRP 0.010 0.001 TRP A1074 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00285 (12592) covalent geometry : angle 0.56668 (17635) hydrogen bonds : bond 0.03915 ( 567) hydrogen bonds : angle 4.34375 ( 1535) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 114 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7073 (mtpp) cc_final: 0.6819 (ptpp) REVERT: A 103 GLU cc_start: 0.6896 (OUTLIER) cc_final: 0.6098 (pt0) REVERT: A 118 ILE cc_start: 0.7918 (OUTLIER) cc_final: 0.7652 (mm) REVERT: A 122 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7524 (mp) REVERT: A 161 MET cc_start: 0.8163 (mtt) cc_final: 0.7631 (mtt) REVERT: A 209 LYS cc_start: 0.8908 (ttmm) cc_final: 0.8524 (tptp) REVERT: A 288 ASP cc_start: 0.8801 (m-30) cc_final: 0.8489 (t0) REVERT: A 290 PHE cc_start: 0.7871 (m-80) cc_final: 0.7642 (m-80) REVERT: A 383 MET cc_start: 0.7563 (mtp) cc_final: 0.7091 (mtm) REVERT: A 618 ASP cc_start: 0.8444 (t0) cc_final: 0.7831 (t0) REVERT: A 702 LEU cc_start: 0.5815 (mm) cc_final: 0.5464 (mm) REVERT: A 762 GLU cc_start: 0.7224 (pt0) cc_final: 0.6680 (tt0) REVERT: A 1177 ASN cc_start: 0.8530 (OUTLIER) cc_final: 0.7793 (p0) REVERT: A 1261 GLN cc_start: 0.8780 (pt0) cc_final: 0.8534 (pt0) outliers start: 41 outliers final: 10 residues processed: 146 average time/residue: 0.4803 time to fit residues: 77.0211 Evaluate side-chains 100 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 614 ASP Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1339 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 35 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 73 optimal weight: 0.8980 chunk 89 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 235 ASN A1272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.141123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.100296 restraints weight = 21685.202| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.24 r_work: 0.3284 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3170 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12592 Z= 0.163 Angle : 0.560 6.105 17635 Z= 0.299 Chirality : 0.037 0.204 2060 Planarity : 0.004 0.033 1751 Dihedral : 19.138 92.763 3124 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 3.79 % Allowed : 23.85 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.25), residues: 1140 helix: 0.79 (0.22), residues: 576 sheet: 0.34 (0.53), residues: 98 loop : -0.68 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 976 TYR 0.021 0.002 TYR A 451 PHE 0.017 0.002 PHE A1105 TRP 0.010 0.001 TRP A1074 HIS 0.009 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00352 (12592) covalent geometry : angle 0.56047 (17635) hydrogen bonds : bond 0.03933 ( 567) hydrogen bonds : angle 4.24951 ( 1535) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 100 time to evaluate : 0.339 Fit side-chains REVERT: A 26 LYS cc_start: 0.6998 (mtpp) cc_final: 0.6573 (ptpp) REVERT: A 179 SER cc_start: 0.8139 (p) cc_final: 0.7906 (m) REVERT: A 195 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8266 (mm) REVERT: A 209 LYS cc_start: 0.8882 (ttmm) cc_final: 0.8582 (tptp) REVERT: A 288 ASP cc_start: 0.8798 (m-30) cc_final: 0.8512 (t0) REVERT: A 290 PHE cc_start: 0.7846 (m-80) cc_final: 0.7596 (m-80) REVERT: A 331 ASP cc_start: 0.8828 (t0) cc_final: 0.8585 (t0) REVERT: A 383 MET cc_start: 0.7688 (mtp) cc_final: 0.7145 (mtm) REVERT: A 404 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.7884 (p) REVERT: A 406 ASP cc_start: 0.8607 (m-30) cc_final: 0.8351 (m-30) REVERT: A 618 ASP cc_start: 0.8606 (t0) cc_final: 0.8124 (t0) REVERT: A 681 ASP cc_start: 0.7536 (m-30) cc_final: 0.7174 (t0) REVERT: A 702 LEU cc_start: 0.5968 (OUTLIER) cc_final: 0.5369 (mm) REVERT: A 708 ILE cc_start: 0.7931 (pt) cc_final: 0.7660 (pp) REVERT: A 762 GLU cc_start: 0.7305 (pt0) cc_final: 0.6814 (tt0) REVERT: A 976 ARG cc_start: 0.7804 (ptp90) cc_final: 0.7343 (ptp90) REVERT: A 1177 ASN cc_start: 0.8572 (OUTLIER) cc_final: 0.7844 (p0) REVERT: A 1261 GLN cc_start: 0.8805 (pt0) cc_final: 0.8578 (pt0) REVERT: A 1307 GLU cc_start: 0.6696 (tt0) cc_final: 0.6180 (pt0) outliers start: 37 outliers final: 13 residues processed: 125 average time/residue: 0.4907 time to fit residues: 67.5311 Evaluate side-chains 104 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 597 LEU Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1213 MET Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1318 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 101 optimal weight: 0.2980 chunk 29 optimal weight: 0.0050 chunk 28 optimal weight: 1.9990 chunk 116 optimal weight: 0.2980 chunk 110 optimal weight: 0.9980 chunk 65 optimal weight: 10.0000 chunk 122 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 709 GLN A1272 GLN A1364 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.141591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.101150 restraints weight = 21543.569| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 2.23 r_work: 0.3302 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3189 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.3182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12592 Z= 0.132 Angle : 0.518 6.589 17635 Z= 0.276 Chirality : 0.036 0.193 2060 Planarity : 0.004 0.076 1751 Dihedral : 19.060 93.340 3124 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.07 % Allowed : 23.34 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.25), residues: 1140 helix: 1.11 (0.22), residues: 576 sheet: 0.39 (0.54), residues: 100 loop : -0.58 (0.29), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 221 TYR 0.015 0.001 TYR A 271 PHE 0.021 0.002 PHE A 518 TRP 0.008 0.001 TRP A1074 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00284 (12592) covalent geometry : angle 0.51826 (17635) hydrogen bonds : bond 0.03373 ( 567) hydrogen bonds : angle 4.07108 ( 1535) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 90 time to evaluate : 0.382 Fit side-chains REVERT: A 26 LYS cc_start: 0.7111 (mtpp) cc_final: 0.6632 (ptpp) REVERT: A 103 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6601 (pt0) REVERT: A 209 LYS cc_start: 0.8780 (ttmm) cc_final: 0.8483 (tptp) REVERT: A 221 ARG cc_start: 0.7778 (ttm110) cc_final: 0.7552 (ttm110) REVERT: A 288 ASP cc_start: 0.8802 (m-30) cc_final: 0.8536 (t0) REVERT: A 290 PHE cc_start: 0.7859 (m-80) cc_final: 0.7611 (m-80) REVERT: A 298 ASP cc_start: 0.7271 (m-30) cc_final: 0.6984 (m-30) REVERT: A 331 ASP cc_start: 0.8826 (t0) cc_final: 0.8454 (t0) REVERT: A 383 MET cc_start: 0.7585 (mtp) cc_final: 0.7109 (mtm) REVERT: A 404 THR cc_start: 0.8322 (OUTLIER) cc_final: 0.7922 (p) REVERT: A 599 LYS cc_start: 0.8789 (mptt) cc_final: 0.8462 (mmtm) REVERT: A 618 ASP cc_start: 0.8631 (t0) cc_final: 0.8180 (t0) REVERT: A 681 ASP cc_start: 0.7589 (m-30) cc_final: 0.7354 (m-30) REVERT: A 702 LEU cc_start: 0.6004 (OUTLIER) cc_final: 0.5526 (mm) REVERT: A 708 ILE cc_start: 0.7997 (pt) cc_final: 0.7721 (pp) REVERT: A 762 GLU cc_start: 0.7239 (pt0) cc_final: 0.6810 (tt0) REVERT: A 976 ARG cc_start: 0.7816 (ptp90) cc_final: 0.7393 (ptp90) REVERT: A 1177 ASN cc_start: 0.8505 (OUTLIER) cc_final: 0.7776 (p0) outliers start: 30 outliers final: 9 residues processed: 112 average time/residue: 0.4477 time to fit residues: 55.7411 Evaluate side-chains 92 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1338 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 54 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 44 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1262 HIS A1272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.141777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.100188 restraints weight = 21781.444| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.18 r_work: 0.3285 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12592 Z= 0.224 Angle : 0.586 6.667 17635 Z= 0.312 Chirality : 0.039 0.164 2060 Planarity : 0.004 0.042 1751 Dihedral : 19.303 95.081 3124 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 3.99 % Allowed : 22.62 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (0.25), residues: 1140 helix: 1.06 (0.22), residues: 578 sheet: 0.08 (0.53), residues: 100 loop : -0.63 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 403 TYR 0.021 0.002 TYR A 155 PHE 0.020 0.002 PHE A1105 TRP 0.012 0.001 TRP A1074 HIS 0.007 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00499 (12592) covalent geometry : angle 0.58558 (17635) hydrogen bonds : bond 0.04203 ( 567) hydrogen bonds : angle 4.16287 ( 1535) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 92 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7626 (mtpp) cc_final: 0.7060 (ptpp) REVERT: A 103 GLU cc_start: 0.7570 (OUTLIER) cc_final: 0.7185 (pt0) REVERT: A 209 LYS cc_start: 0.8954 (ttmm) cc_final: 0.8625 (tptp) REVERT: A 290 PHE cc_start: 0.8013 (m-80) cc_final: 0.7719 (m-80) REVERT: A 298 ASP cc_start: 0.7604 (m-30) cc_final: 0.7243 (m-30) REVERT: A 383 MET cc_start: 0.8000 (mtp) cc_final: 0.7598 (mtp) REVERT: A 404 THR cc_start: 0.8673 (OUTLIER) cc_final: 0.8423 (p) REVERT: A 479 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8261 (mp0) REVERT: A 702 LEU cc_start: 0.6144 (mm) cc_final: 0.5658 (mm) REVERT: A 708 ILE cc_start: 0.8354 (pt) cc_final: 0.8078 (pp) REVERT: A 762 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.7245 (tt0) REVERT: A 976 ARG cc_start: 0.8092 (ptp90) cc_final: 0.7684 (ptp90) REVERT: A 1089 MET cc_start: 0.8826 (ttm) cc_final: 0.8351 (ttm) REVERT: A 1105 PHE cc_start: 0.8512 (OUTLIER) cc_final: 0.7761 (p90) REVERT: A 1177 ASN cc_start: 0.8602 (OUTLIER) cc_final: 0.8083 (p0) REVERT: A 1307 GLU cc_start: 0.7038 (tt0) cc_final: 0.6451 (pt0) outliers start: 39 outliers final: 10 residues processed: 121 average time/residue: 0.5012 time to fit residues: 66.4779 Evaluate side-chains 98 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1105 PHE Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 11 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 49 optimal weight: 0.3980 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 126 optimal weight: 1.9990 chunk 111 optimal weight: 0.8980 chunk 87 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 695 GLN A1272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.142706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.101203 restraints weight = 21713.323| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 2.18 r_work: 0.3319 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12592 Z= 0.170 Angle : 0.547 8.399 17635 Z= 0.290 Chirality : 0.037 0.149 2060 Planarity : 0.003 0.048 1751 Dihedral : 19.202 94.395 3124 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.38 % Allowed : 23.85 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.25), residues: 1140 helix: 1.19 (0.22), residues: 578 sheet: 0.02 (0.52), residues: 101 loop : -0.64 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 221 TYR 0.014 0.001 TYR A 155 PHE 0.017 0.001 PHE A1105 TRP 0.009 0.001 TRP A1074 HIS 0.006 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00373 (12592) covalent geometry : angle 0.54702 (17635) hydrogen bonds : bond 0.03616 ( 567) hydrogen bonds : angle 4.08758 ( 1535) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7642 (mtpp) cc_final: 0.7039 (ptpp) REVERT: A 43 ILE cc_start: 0.8701 (OUTLIER) cc_final: 0.8371 (tt) REVERT: A 103 GLU cc_start: 0.7545 (OUTLIER) cc_final: 0.7136 (pt0) REVERT: A 209 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8590 (tptp) REVERT: A 221 ARG cc_start: 0.7728 (ttm110) cc_final: 0.7446 (ttm110) REVERT: A 290 PHE cc_start: 0.7946 (m-80) cc_final: 0.7688 (m-80) REVERT: A 298 ASP cc_start: 0.7557 (m-30) cc_final: 0.7139 (m-30) REVERT: A 383 MET cc_start: 0.7961 (mtp) cc_final: 0.7611 (mtp) REVERT: A 404 THR cc_start: 0.8623 (OUTLIER) cc_final: 0.8381 (p) REVERT: A 479 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8265 (mp0) REVERT: A 642 LEU cc_start: 0.7984 (OUTLIER) cc_final: 0.7468 (tp) REVERT: A 682 PHE cc_start: 0.7064 (m-10) cc_final: 0.6854 (m-10) REVERT: A 697 ILE cc_start: 0.9231 (pp) cc_final: 0.8981 (pp) REVERT: A 702 LEU cc_start: 0.6297 (mm) cc_final: 0.5801 (mm) REVERT: A 708 ILE cc_start: 0.8368 (pt) cc_final: 0.8116 (pp) REVERT: A 762 GLU cc_start: 0.7540 (OUTLIER) cc_final: 0.7211 (tt0) REVERT: A 954 LYS cc_start: 0.7828 (mptm) cc_final: 0.7605 (tppt) REVERT: A 976 ARG cc_start: 0.8068 (ptp90) cc_final: 0.7650 (ptp90) REVERT: A 1089 MET cc_start: 0.8821 (ttm) cc_final: 0.8350 (ttm) REVERT: A 1177 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8071 (p0) REVERT: A 1307 GLU cc_start: 0.6930 (tt0) cc_final: 0.6439 (pt0) outliers start: 33 outliers final: 14 residues processed: 114 average time/residue: 0.5092 time to fit residues: 63.6570 Evaluate side-chains 99 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 652 LYS Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1357 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 101 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 30 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.141940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.100509 restraints weight = 21645.081| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.17 r_work: 0.3310 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3196 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.4314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 12592 Z= 0.170 Angle : 0.553 7.170 17635 Z= 0.293 Chirality : 0.037 0.176 2060 Planarity : 0.003 0.046 1751 Dihedral : 19.185 94.592 3124 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.58 % Allowed : 23.64 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.54 (0.25), residues: 1140 helix: 1.28 (0.22), residues: 576 sheet: -0.03 (0.52), residues: 101 loop : -0.68 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 221 TYR 0.014 0.001 TYR A 155 PHE 0.017 0.002 PHE A1105 TRP 0.008 0.001 TRP A1074 HIS 0.007 0.001 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00373 (12592) covalent geometry : angle 0.55344 (17635) hydrogen bonds : bond 0.03688 ( 567) hydrogen bonds : angle 4.04668 ( 1535) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 83 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7597 (mtpp) cc_final: 0.6996 (ptpp) REVERT: A 103 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7151 (pt0) REVERT: A 145 SER cc_start: 0.8624 (OUTLIER) cc_final: 0.8300 (t) REVERT: A 209 LYS cc_start: 0.8928 (ttmm) cc_final: 0.8626 (tptp) REVERT: A 290 PHE cc_start: 0.7958 (m-80) cc_final: 0.7666 (m-80) REVERT: A 298 ASP cc_start: 0.7536 (m-30) cc_final: 0.7135 (m-30) REVERT: A 383 MET cc_start: 0.7933 (mtp) cc_final: 0.7581 (mtp) REVERT: A 390 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8459 (mm) REVERT: A 404 THR cc_start: 0.8642 (OUTLIER) cc_final: 0.8400 (p) REVERT: A 479 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8274 (mp0) REVERT: A 524 LEU cc_start: 0.9122 (OUTLIER) cc_final: 0.8897 (tt) REVERT: A 642 LEU cc_start: 0.8022 (OUTLIER) cc_final: 0.7451 (tp) REVERT: A 702 LEU cc_start: 0.6369 (mm) cc_final: 0.5876 (mm) REVERT: A 708 ILE cc_start: 0.8465 (pt) cc_final: 0.8212 (pp) REVERT: A 762 GLU cc_start: 0.7504 (OUTLIER) cc_final: 0.7178 (tt0) REVERT: A 976 ARG cc_start: 0.8064 (ptp90) cc_final: 0.7640 (ptp90) REVERT: A 1089 MET cc_start: 0.8798 (ttm) cc_final: 0.8337 (ttm) REVERT: A 1307 GLU cc_start: 0.6952 (tt0) cc_final: 0.6538 (mt-10) outliers start: 35 outliers final: 16 residues processed: 111 average time/residue: 0.5645 time to fit residues: 68.1743 Evaluate side-chains 103 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 79 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 524 LEU Chi-restraints excluded: chain A residue 642 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1357 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 50 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 chunk 36 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 104 optimal weight: 0.2980 chunk 63 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 64 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.135488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094311 restraints weight = 21611.861| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.21 r_work: 0.3192 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.4636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 12592 Z= 0.247 Angle : 0.614 8.789 17635 Z= 0.326 Chirality : 0.040 0.175 2060 Planarity : 0.004 0.048 1751 Dihedral : 19.390 95.485 3122 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.89 % Allowed : 23.54 % Favored : 72.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.25), residues: 1140 helix: 1.09 (0.22), residues: 576 sheet: -0.30 (0.52), residues: 101 loop : -0.79 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 221 TYR 0.021 0.002 TYR A 155 PHE 0.024 0.002 PHE A1105 TRP 0.012 0.002 TRP A1074 HIS 0.005 0.001 HIS A 160 Details of bonding type rmsd covalent geometry : bond 0.00550 (12592) covalent geometry : angle 0.61443 (17635) hydrogen bonds : bond 0.04371 ( 567) hydrogen bonds : angle 4.24733 ( 1535) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 86 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7487 (mtpp) cc_final: 0.6826 (ptpp) REVERT: A 43 ILE cc_start: 0.8662 (OUTLIER) cc_final: 0.8360 (tt) REVERT: A 103 GLU cc_start: 0.7542 (OUTLIER) cc_final: 0.6940 (pt0) REVERT: A 145 SER cc_start: 0.8701 (OUTLIER) cc_final: 0.8276 (t) REVERT: A 209 LYS cc_start: 0.8934 (ttmm) cc_final: 0.8612 (tptp) REVERT: A 221 ARG cc_start: 0.7795 (ttm110) cc_final: 0.7504 (ttm110) REVERT: A 298 ASP cc_start: 0.7572 (m-30) cc_final: 0.7221 (m-30) REVERT: A 383 MET cc_start: 0.7895 (mtp) cc_final: 0.7492 (mtp) REVERT: A 390 LEU cc_start: 0.8630 (OUTLIER) cc_final: 0.8307 (mm) REVERT: A 404 THR cc_start: 0.8743 (OUTLIER) cc_final: 0.8392 (p) REVERT: A 479 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8387 (mp0) REVERT: A 702 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6038 (mm) REVERT: A 708 ILE cc_start: 0.8405 (pt) cc_final: 0.8185 (pp) REVERT: A 757 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8177 (mt-10) REVERT: A 762 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7236 (tt0) REVERT: A 976 ARG cc_start: 0.8015 (ptp90) cc_final: 0.7552 (ptp90) REVERT: A 1177 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.7917 (p0) REVERT: A 1261 GLN cc_start: 0.8889 (pt0) cc_final: 0.8650 (pt0) REVERT: A 1307 GLU cc_start: 0.6856 (tt0) cc_final: 0.6280 (pt0) outliers start: 38 outliers final: 17 residues processed: 116 average time/residue: 0.5008 time to fit residues: 63.8081 Evaluate side-chains 106 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 80 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 124 ASP Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1163 LEU Chi-restraints excluded: chain A residue 1177 ASN Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 85 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 69 optimal weight: 0.5980 chunk 102 optimal weight: 0.7980 chunk 80 optimal weight: 0.0020 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 255 ASN A1272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.138438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.097770 restraints weight = 21464.494| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.18 r_work: 0.3245 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.4689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 12592 Z= 0.138 Angle : 0.540 9.430 17635 Z= 0.286 Chirality : 0.036 0.169 2060 Planarity : 0.003 0.059 1751 Dihedral : 19.166 93.846 3122 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 3.07 % Allowed : 24.56 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.50 (0.25), residues: 1140 helix: 1.30 (0.22), residues: 578 sheet: -0.18 (0.53), residues: 99 loop : -0.74 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 221 TYR 0.013 0.001 TYR A 155 PHE 0.017 0.001 PHE A1105 TRP 0.007 0.001 TRP A1074 HIS 0.005 0.001 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00301 (12592) covalent geometry : angle 0.53987 (17635) hydrogen bonds : bond 0.03471 ( 567) hydrogen bonds : angle 4.07379 ( 1535) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 86 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: A 26 LYS cc_start: 0.7473 (mtpp) cc_final: 0.6778 (ptpp) REVERT: A 103 GLU cc_start: 0.7500 (OUTLIER) cc_final: 0.6916 (pt0) REVERT: A 145 SER cc_start: 0.8603 (OUTLIER) cc_final: 0.8216 (t) REVERT: A 209 LYS cc_start: 0.8912 (ttmm) cc_final: 0.8601 (tptp) REVERT: A 290 PHE cc_start: 0.8002 (m-80) cc_final: 0.7761 (m-80) REVERT: A 383 MET cc_start: 0.7777 (mtp) cc_final: 0.7515 (mtp) REVERT: A 404 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8234 (p) REVERT: A 479 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: A 708 ILE cc_start: 0.8409 (pt) cc_final: 0.8198 (pp) REVERT: A 757 GLU cc_start: 0.8324 (mm-30) cc_final: 0.8084 (mt-10) REVERT: A 762 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.7060 (tt0) REVERT: A 976 ARG cc_start: 0.7971 (ptp90) cc_final: 0.7509 (ptp90) REVERT: A 1089 MET cc_start: 0.8796 (ttm) cc_final: 0.8560 (ttm) REVERT: A 1170 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8431 (pt0) REVERT: A 1307 GLU cc_start: 0.6736 (tt0) cc_final: 0.6208 (pt0) outliers start: 30 outliers final: 14 residues processed: 108 average time/residue: 0.5581 time to fit residues: 65.8129 Evaluate side-chains 95 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 702 LEU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 28 optimal weight: 0.7980 chunk 60 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 98 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 74 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 0.7980 chunk 121 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 758 ASN A1272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.137808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.096878 restraints weight = 21658.221| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.20 r_work: 0.3234 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12592 Z= 0.161 Angle : 0.567 8.815 17635 Z= 0.299 Chirality : 0.037 0.210 2060 Planarity : 0.003 0.062 1751 Dihedral : 19.153 94.280 3122 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.46 % Allowed : 25.59 % Favored : 71.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.57 (0.25), residues: 1140 helix: 1.35 (0.22), residues: 577 sheet: -0.14 (0.53), residues: 99 loop : -0.70 (0.28), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 221 TYR 0.016 0.001 TYR A 155 PHE 0.019 0.002 PHE A1105 TRP 0.008 0.001 TRP A1074 HIS 0.007 0.001 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00355 (12592) covalent geometry : angle 0.56748 (17635) hydrogen bonds : bond 0.03629 ( 567) hydrogen bonds : angle 4.11094 ( 1535) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2280 Ramachandran restraints generated. 1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 21 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7467 (mp) REVERT: A 26 LYS cc_start: 0.7433 (mtpp) cc_final: 0.6729 (ptpp) REVERT: A 103 GLU cc_start: 0.7506 (OUTLIER) cc_final: 0.6950 (pt0) REVERT: A 145 SER cc_start: 0.8649 (OUTLIER) cc_final: 0.8248 (t) REVERT: A 209 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8608 (tptp) REVERT: A 290 PHE cc_start: 0.8043 (m-80) cc_final: 0.7772 (m-80) REVERT: A 383 MET cc_start: 0.7904 (mtp) cc_final: 0.7491 (mtp) REVERT: A 390 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8285 (mm) REVERT: A 404 THR cc_start: 0.8544 (OUTLIER) cc_final: 0.8232 (p) REVERT: A 479 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8445 (mp0) REVERT: A 504 ASN cc_start: 0.8159 (p0) cc_final: 0.7919 (t0) REVERT: A 757 GLU cc_start: 0.8354 (mm-30) cc_final: 0.8140 (mt-10) REVERT: A 762 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7078 (tt0) REVERT: A 976 ARG cc_start: 0.7948 (ptp90) cc_final: 0.7481 (ptp90) REVERT: A 1089 MET cc_start: 0.8780 (ttm) cc_final: 0.8537 (ttm) REVERT: A 1170 GLU cc_start: 0.8693 (mt-10) cc_final: 0.8426 (pt0) REVERT: A 1307 GLU cc_start: 0.6792 (tt0) cc_final: 0.6225 (pt0) outliers start: 24 outliers final: 14 residues processed: 94 average time/residue: 0.5570 time to fit residues: 57.0303 Evaluate side-chains 90 residues out of total 1030 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 145 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 479 GLU Chi-restraints excluded: chain A residue 750 VAL Chi-restraints excluded: chain A residue 762 GLU Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1088 SER Chi-restraints excluded: chain A residue 1135 ASP Chi-restraints excluded: chain A residue 1312 LEU Chi-restraints excluded: chain A residue 1338 SER Chi-restraints excluded: chain A residue 1342 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 73 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 92 optimal weight: 0.9980 chunk 122 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 110 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1272 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.136912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.095909 restraints weight = 21601.443| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.19 r_work: 0.3216 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12592 Z= 0.189 Angle : 0.583 9.031 17635 Z= 0.308 Chirality : 0.038 0.176 2060 Planarity : 0.004 0.067 1751 Dihedral : 19.214 94.416 3122 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 2.97 % Allowed : 25.18 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.48 (0.25), residues: 1140 helix: 1.24 (0.22), residues: 577 sheet: -0.22 (0.52), residues: 101 loop : -0.69 (0.28), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 221 TYR 0.016 0.001 TYR A 155 PHE 0.022 0.002 PHE A1105 TRP 0.009 0.001 TRP A1074 HIS 0.008 0.001 HIS A 698 Details of bonding type rmsd covalent geometry : bond 0.00422 (12592) covalent geometry : angle 0.58267 (17635) hydrogen bonds : bond 0.03847 ( 567) hydrogen bonds : angle 4.14870 ( 1535) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4448.45 seconds wall clock time: 76 minutes 34.55 seconds (4594.55 seconds total)