Starting phenix.real_space_refine on Sat Oct 11 05:39:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sfq_40448/10_2025/8sfq_40448.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sfq_40448/10_2025/8sfq_40448.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/cci-nas-00/data/ceres_data/8sfq_40448/10_2025/8sfq_40448.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sfq_40448/10_2025/8sfq_40448.map" model { file = "/net/cci-nas-00/data/ceres_data/8sfq_40448/10_2025/8sfq_40448.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sfq_40448/10_2025/8sfq_40448.cif" } resolution = 3.5 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= -0.001 sd= 0.031 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 91 5.49 5 S 23 5.16 5 C 7395 2.51 5 N 2050 2.21 5 O 2486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12045 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 10138 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1240, 10138 Classifications: {'peptide': 1240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 46, 'TRANS': 1193} Chain breaks: 2 Chain: "B" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 826 Classifications: {'RNA': 39} Modifications used: {'5*END': 1, 'rna2p_pur': 3, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 16} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain: "C" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 696 Classifications: {'DNA': 34} Link IDs: {'rna3p': 33} Chain: "D" Number of atoms: 385 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 385 Classifications: {'DNA': 19} Link IDs: {'rna3p': 18} Time building chain proxies: 3.09, per 1000 atoms: 0.26 Number of scatterers: 12045 At special positions: 0 Unit cell: (89.964, 99.96, 137.445, 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 23 16.00 P 91 15.00 O 2486 8.00 N 2050 7.00 C 7395 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: 0.87 Conformation dependent library (CDL) restraints added in 494.3 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2368 Finding SS restraints... Secondary structure from input PDB file: 59 helices and 9 sheets defined 55.9% alpha, 10.7% beta 40 base pairs and 62 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 removed outlier: 3.660A pdb=" N PHE A 7 " --> pdb=" O PHE A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 33 Processing helix chain 'A' and resid 35 through 67 Proline residue: A 52 - end of helix removed outlier: 3.917A pdb=" N ILE A 57 " --> pdb=" O ILE A 53 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN A 67 " --> pdb=" O ASP A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 86 removed outlier: 3.787A pdb=" N GLU A 86 " --> pdb=" O SER A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 112 removed outlier: 4.093A pdb=" N TYR A 109 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N PHE A 110 " --> pdb=" O ILE A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 130 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 142 through 147 removed outlier: 4.094A pdb=" N LEU A 146 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 178 Processing helix chain 'A' and resid 188 through 196 Processing helix chain 'A' and resid 196 through 215 removed outlier: 4.050A pdb=" N LYS A 200 " --> pdb=" O ASP A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.625A pdb=" N HIS A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 241 removed outlier: 3.837A pdb=" N PHE A 241 " --> pdb=" O ILE A 237 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 248 Processing helix chain 'A' and resid 251 through 264 Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 289 through 298 removed outlier: 3.521A pdb=" N SER A 297 " --> pdb=" O HIS A 293 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 344 removed outlier: 3.502A pdb=" N ASN A 344 " --> pdb=" O LEU A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 344 through 356 removed outlier: 3.567A pdb=" N THR A 348 " --> pdb=" O ASN A 344 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N GLU A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU A 356 " --> pdb=" O LEU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 359 No H-bonds generated for 'chain 'A' and resid 357 through 359' Processing helix chain 'A' and resid 360 through 363 Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 383 through 396 Processing helix chain 'A' and resid 404 through 416 removed outlier: 3.934A pdb=" N HIS A 415 " --> pdb=" O ARG A 411 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLU A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 428 Processing helix chain 'A' and resid 429 through 452 Processing helix chain 'A' and resid 460 through 482 removed outlier: 3.568A pdb=" N LYS A 464 " --> pdb=" O LYS A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 493 through 508 Processing helix chain 'A' and resid 509 through 522 Processing helix chain 'A' and resid 548 through 553 Processing helix chain 'A' and resid 570 through 574 removed outlier: 4.167A pdb=" N GLY A 573 " --> pdb=" O LYS A 570 " (cutoff:3.500A) Processing helix chain 'A' and resid 600 through 610 Proline residue: A 606 - end of helix Processing helix chain 'A' and resid 612 through 622 removed outlier: 3.902A pdb=" N THR A 621 " --> pdb=" O ALA A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 647 removed outlier: 3.738A pdb=" N ASN A 646 " --> pdb=" O ILE A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 664 removed outlier: 3.583A pdb=" N ALA A 660 " --> pdb=" O GLN A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 687 Processing helix chain 'A' and resid 700 through 704 Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 727 through 738 removed outlier: 3.578A pdb=" N ILE A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 759 through 769 removed outlier: 3.514A pdb=" N PHE A 769 " --> pdb=" O TRP A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 770 through 776 Processing helix chain 'A' and resid 861 through 865 Processing helix chain 'A' and resid 887 through 899 Processing helix chain 'A' and resid 939 through 957 removed outlier: 3.663A pdb=" N LYS A 943 " --> pdb=" O ASP A 939 " (cutoff:3.500A) Processing helix chain 'A' and resid 964 through 987 removed outlier: 3.662A pdb=" N GLN A 974 " --> pdb=" O GLY A 970 " (cutoff:3.500A) Processing helix chain 'A' and resid 996 through 1007 Processing helix chain 'A' and resid 1014 through 1025 removed outlier: 3.831A pdb=" N CYS A1025 " --> pdb=" O ASP A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1088 removed outlier: 3.609A pdb=" N THR A1087 " --> pdb=" O VAL A1084 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE A1088 " --> pdb=" O TRP A1085 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1084 through 1088' Processing helix chain 'A' and resid 1090 through 1100 removed outlier: 3.639A pdb=" N GLY A1100 " --> pdb=" O HIS A1096 " (cutoff:3.500A) Processing helix chain 'A' and resid 1177 through 1190 Processing helix chain 'A' and resid 1199 through 1205 removed outlier: 3.508A pdb=" N GLU A1205 " --> pdb=" O PRO A1201 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1223 removed outlier: 3.620A pdb=" N ILE A1212 " --> pdb=" O ASP A1208 " (cutoff:3.500A) Processing helix chain 'A' and resid 1250 through 1254 removed outlier: 3.521A pdb=" N PHE A1253 " --> pdb=" O ASP A1250 " (cutoff:3.500A) Processing helix chain 'A' and resid 1261 through 1283 removed outlier: 3.626A pdb=" N GLU A1283 " --> pdb=" O ASN A1279 " (cutoff:3.500A) Processing helix chain 'A' and resid 1294 through 1307 Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.651A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N PHE A 869 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N TYR A 563 " --> pdb=" O ILE A 745 " (cutoff:3.500A) removed outlier: 11.301A pdb=" N ALA A 554 " --> pdb=" O TYR A 595 " (cutoff:3.500A) removed outlier: 8.429A pdb=" N TYR A 595 " --> pdb=" O ALA A 554 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU A 556 " --> pdb=" O MET A 593 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 531 through 533 removed outlier: 4.651A pdb=" N LEU A 787 " --> pdb=" O LEU A 533 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 365 through 366 Processing sheet with id=AA4, first strand: chain 'A' and resid 626 through 628 Processing sheet with id=AA5, first strand: chain 'A' and resid 926 through 931 removed outlier: 6.852A pdb=" N VAL A 919 " --> pdb=" O LEU A 927 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N GLN A 929 " --> pdb=" O ILE A 917 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 917 " --> pdb=" O GLN A 929 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N SER A 931 " --> pdb=" O ILE A 915 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N ILE A 915 " --> pdb=" O SER A 931 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N GLU A 993 " --> pdb=" O ILE A 907 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ARG A 909 " --> pdb=" O GLU A 993 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1101 through 1107 removed outlier: 6.651A pdb=" N PHE A1101 " --> pdb=" O LYS A1118 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N LYS A1118 " --> pdb=" O PHE A1101 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N PHE A1103 " --> pdb=" O HIS A1116 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP A1112 " --> pdb=" O ASP A1107 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 1145 through 1147 Processing sheet with id=AA8, first strand: chain 'A' and resid 1159 through 1162 Processing sheet with id=AA9, first strand: chain 'A' and resid 1226 through 1229 523 hydrogen bonds defined for protein. 1479 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 96 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 62 stacking parallelities Total time for adding SS restraints: 3.24 Time building geometry restraints manager: 1.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3172 1.34 - 1.46: 3308 1.46 - 1.58: 5799 1.58 - 1.70: 183 1.70 - 1.83: 38 Bond restraints: 12500 Sorted by residual: bond pdb=" CB ARG A 392 " pdb=" CG ARG A 392 " ideal model delta sigma weight residual 1.520 1.444 0.076 3.00e-02 1.11e+03 6.38e+00 bond pdb=" CB PRO A 453 " pdb=" CG PRO A 453 " ideal model delta sigma weight residual 1.492 1.613 -0.121 5.00e-02 4.00e+02 5.85e+00 bond pdb=" CB PHE A 683 " pdb=" CG PHE A 683 " ideal model delta sigma weight residual 1.502 1.554 -0.052 2.30e-02 1.89e+03 5.06e+00 bond pdb=" CB GLU A 422 " pdb=" CG GLU A 422 " ideal model delta sigma weight residual 1.520 1.582 -0.062 3.00e-02 1.11e+03 4.28e+00 bond pdb=" CA ASP A 184 " pdb=" CB ASP A 184 " ideal model delta sigma weight residual 1.531 1.562 -0.031 1.51e-02 4.39e+03 4.17e+00 ... (remaining 12495 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.19: 17165 5.19 - 10.39: 109 10.39 - 15.58: 18 15.58 - 20.77: 3 20.77 - 25.97: 1 Bond angle restraints: 17296 Sorted by residual: angle pdb=" CA PRO A 453 " pdb=" N PRO A 453 " pdb=" CD PRO A 453 " ideal model delta sigma weight residual 112.00 99.18 12.82 1.40e+00 5.10e-01 8.38e+01 angle pdb=" O3' DG D 6 " pdb=" P DA D 7 " pdb=" OP1 DA D 7 " ideal model delta sigma weight residual 108.00 133.97 -25.97 3.00e+00 1.11e-01 7.49e+01 angle pdb=" O3' DT C 27 " pdb=" P DA C 28 " pdb=" OP1 DA C 28 " ideal model delta sigma weight residual 108.00 125.19 -17.19 3.00e+00 1.11e-01 3.28e+01 angle pdb=" OP1 DA D 7 " pdb=" P DA D 7 " pdb=" OP2 DA D 7 " ideal model delta sigma weight residual 120.00 103.52 16.48 3.00e+00 1.11e-01 3.02e+01 angle pdb=" CA ASP A 184 " pdb=" CB ASP A 184 " pdb=" CG ASP A 184 " ideal model delta sigma weight residual 112.60 117.64 -5.04 1.00e+00 1.00e+00 2.54e+01 ... (remaining 17291 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.95: 6900 32.95 - 65.90: 497 65.90 - 98.85: 38 98.85 - 131.80: 0 131.80 - 164.75: 4 Dihedral angle restraints: 7439 sinusoidal: 3781 harmonic: 3658 Sorted by residual: dihedral pdb=" O4' C B 11 " pdb=" C1' C B 11 " pdb=" N1 C B 11 " pdb=" C2 C B 11 " ideal model delta sinusoidal sigma weight residual 200.00 51.52 148.48 1 1.50e+01 4.44e-03 7.90e+01 dihedral pdb=" O4' U B 12 " pdb=" C1' U B 12 " pdb=" N1 U B 12 " pdb=" C2 U B 12 " ideal model delta sinusoidal sigma weight residual 200.00 68.02 131.98 1 1.50e+01 4.44e-03 7.12e+01 dihedral pdb=" CA ALA A1067 " pdb=" C ALA A1067 " pdb=" N PRO A1068 " pdb=" CA PRO A1068 " ideal model delta harmonic sigma weight residual -180.00 -158.57 -21.43 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 7436 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.149: 1878 0.149 - 0.299: 35 0.299 - 0.448: 14 0.448 - 0.597: 2 0.597 - 0.747: 1 Chirality restraints: 1930 Sorted by residual: chirality pdb=" P DA D 7 " pdb=" OP1 DA D 7 " pdb=" OP2 DA D 7 " pdb=" O5' DA D 7 " both_signs ideal model delta sigma weight residual True 2.35 -3.09 -0.75 2.00e-01 2.50e+01 1.39e+01 chirality pdb=" P DA C 28 " pdb=" OP1 DA C 28 " pdb=" OP2 DA C 28 " pdb=" O5' DA C 28 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.55 2.00e-01 2.50e+01 7.60e+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 -2.86 -0.52 2.00e-01 2.50e+01 6.67e+00 ... (remaining 1927 not shown) Planarity restraints: 1895 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 452 " 0.087 5.00e-02 4.00e+02 1.22e-01 2.38e+01 pdb=" N PRO A 453 " -0.210 5.00e-02 4.00e+02 pdb=" CA PRO A 453 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO A 453 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 365 " -0.017 2.00e-02 2.50e+03 2.76e-02 1.34e+01 pdb=" CG PHE A 365 " 0.058 2.00e-02 2.50e+03 pdb=" CD1 PHE A 365 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 PHE A 365 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE A 365 " -0.014 2.00e-02 2.50e+03 pdb=" CE2 PHE A 365 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 365 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A1236 " 0.016 2.00e-02 2.50e+03 2.46e-02 1.22e+01 pdb=" CG TYR A1236 " -0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR A1236 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TYR A1236 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A1236 " -0.008 2.00e-02 2.50e+03 pdb=" CE2 TYR A1236 " 0.014 2.00e-02 2.50e+03 pdb=" CZ TYR A1236 " 0.013 2.00e-02 2.50e+03 pdb=" OH TYR A1236 " -0.011 2.00e-02 2.50e+03 ... (remaining 1892 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1596 2.76 - 3.29: 11600 3.29 - 3.83: 22227 3.83 - 4.36: 25046 4.36 - 4.90: 40352 Nonbonded interactions: 100821 Sorted by model distance: nonbonded pdb=" NH1 ARG A 392 " pdb=" OG SER A 425 " model vdw 2.220 3.120 nonbonded pdb=" OG SER A 236 " pdb=" OE1 GLU A 238 " model vdw 2.259 3.040 nonbonded pdb=" OG1 THR A 88 " pdb=" OE1 GLU A 90 " model vdw 2.268 3.040 nonbonded pdb=" O LYS A 429 " pdb=" OG SER A 432 " model vdw 2.281 3.040 nonbonded pdb=" O HIS A1280 " pdb=" OG SER A1284 " model vdw 2.287 3.040 ... (remaining 100816 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=0.00 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: 2.550 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.580 Find NCS groups from input model: 0.050 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 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 : 0.005 0.121 12500 Z= 0.220 Angle : 1.108 25.966 17296 Z= 0.523 Chirality : 0.066 0.747 1930 Planarity : 0.006 0.122 1895 Dihedral : 20.081 164.749 5071 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 0.72 % Allowed : 18.77 % Favored : 80.51 % 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: 0.23 (0.23), residues: 1234 helix: 0.23 (0.20), residues: 612 sheet: -0.01 (0.45), residues: 143 loop : 0.38 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 912 TYR 0.057 0.003 TYR A1236 PHE 0.058 0.003 PHE A 365 TRP 0.018 0.002 TRP A 483 HIS 0.005 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00520 (12500) covalent geometry : angle 1.10801 (17296) hydrogen bonds : bond 0.15025 ( 610) hydrogen bonds : angle 6.15449 ( 1667) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1001 SER cc_start: 0.9511 (m) cc_final: 0.9222 (p) REVERT: A 1155 ILE cc_start: 0.9403 (OUTLIER) cc_final: 0.9187 (tp) outliers start: 8 outliers final: 3 residues processed: 92 average time/residue: 0.1407 time to fit residues: 18.2451 Evaluate side-chains 64 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 60 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 1026 LEU Chi-restraints excluded: chain A residue 1155 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 415 HIS ** A 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 620 GLN ** A 878 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 883 ASN ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.040174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2568 r_free = 0.2568 target = 0.029194 restraints weight = 78449.352| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2610 r_free = 0.2610 target = 0.030486 restraints weight = 38654.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2635 r_free = 0.2635 target = 0.031308 restraints weight = 25004.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.031885 restraints weight = 19066.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.032275 restraints weight = 15876.195| |-----------------------------------------------------------------------------| r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 12500 Z= 0.256 Angle : 0.659 13.651 17296 Z= 0.349 Chirality : 0.042 0.157 1930 Planarity : 0.004 0.046 1895 Dihedral : 19.531 178.838 2529 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.80 % Allowed : 15.88 % Favored : 81.32 % 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: 1.34 (0.24), residues: 1234 helix: 1.41 (0.21), residues: 616 sheet: -0.16 (0.44), residues: 144 loop : 0.76 (0.30), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 392 TYR 0.018 0.002 TYR A 764 PHE 0.017 0.001 PHE A1249 TRP 0.011 0.001 TRP A1258 HIS 0.005 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00535 (12500) covalent geometry : angle 0.65909 (17296) hydrogen bonds : bond 0.04725 ( 610) hydrogen bonds : angle 4.62602 ( 1667) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 67 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9757 (mtpt) cc_final: 0.9421 (ptpp) REVERT: A 593 MET cc_start: 0.9233 (tmm) cc_final: 0.8883 (tmm) REVERT: A 908 ASP cc_start: 0.7870 (t0) cc_final: 0.7440 (t0) REVERT: A 1012 TYR cc_start: 0.8433 (m-80) cc_final: 0.8162 (m-80) outliers start: 31 outliers final: 14 residues processed: 92 average time/residue: 0.1015 time to fit residues: 14.3738 Evaluate side-chains 64 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 415 HIS Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 959 SER Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 124 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 chunk 75 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 28 optimal weight: 9.9990 chunk 50 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 10 optimal weight: 10.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 878 ASN ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1296 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.039919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.029026 restraints weight = 79243.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.030294 restraints weight = 39416.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.031137 restraints weight = 25663.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.031615 restraints weight = 19420.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2661 r_free = 0.2661 target = 0.032005 restraints weight = 16416.905| |-----------------------------------------------------------------------------| r_work (final): 0.2650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12500 Z= 0.231 Angle : 0.619 14.373 17296 Z= 0.326 Chirality : 0.041 0.145 1930 Planarity : 0.003 0.039 1895 Dihedral : 19.459 175.735 2521 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.34 % Allowed : 16.52 % Favored : 80.14 % 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: 1.61 (0.25), residues: 1234 helix: 1.70 (0.21), residues: 617 sheet: -0.14 (0.44), residues: 144 loop : 0.81 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1121 TYR 0.018 0.002 TYR A 61 PHE 0.017 0.001 PHE A1249 TRP 0.011 0.001 TRP A1258 HIS 0.007 0.001 HIS A 415 Details of bonding type rmsd covalent geometry : bond 0.00484 (12500) covalent geometry : angle 0.61940 (17296) hydrogen bonds : bond 0.04306 ( 610) hydrogen bonds : angle 4.39305 ( 1667) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 54 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9758 (mtpt) cc_final: 0.9440 (ptpp) REVERT: A 452 GLN cc_start: 0.9371 (tm-30) cc_final: 0.9151 (tm-30) REVERT: A 471 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9210 (tp) REVERT: A 908 ASP cc_start: 0.7858 (t0) cc_final: 0.7332 (t0) REVERT: A 1012 TYR cc_start: 0.8501 (m-80) cc_final: 0.8116 (m-80) REVERT: A 1099 GLU cc_start: 0.9509 (OUTLIER) cc_final: 0.9216 (pt0) REVERT: A 1127 ARG cc_start: 0.8848 (OUTLIER) cc_final: 0.8349 (mtt-85) REVERT: A 1133 MET cc_start: 0.8956 (mmp) cc_final: 0.8665 (mmp) outliers start: 37 outliers final: 19 residues processed: 85 average time/residue: 0.1067 time to fit residues: 14.0058 Evaluate side-chains 73 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 51 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 433 GLU Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 786 GLU Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1099 GLU Chi-restraints excluded: chain A residue 1127 ARG Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 55 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 97 optimal weight: 0.9990 chunk 9 optimal weight: 8.9990 chunk 79 optimal weight: 0.8980 chunk 26 optimal weight: 10.0000 chunk 107 optimal weight: 8.9990 chunk 124 optimal weight: 10.0000 chunk 99 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 415 HIS ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.040228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.029397 restraints weight = 79018.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.030707 restraints weight = 38685.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.031562 restraints weight = 25055.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.032120 restraints weight = 18937.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2679 r_free = 0.2679 target = 0.032435 restraints weight = 15766.161| |-----------------------------------------------------------------------------| r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8780 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 12500 Z= 0.169 Angle : 0.575 13.496 17296 Z= 0.301 Chirality : 0.039 0.147 1930 Planarity : 0.003 0.037 1895 Dihedral : 19.383 174.191 2521 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 3.61 % Allowed : 16.79 % Favored : 79.60 % 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: 1.89 (0.25), residues: 1234 helix: 1.92 (0.21), residues: 617 sheet: 0.13 (0.46), residues: 132 loop : 0.89 (0.30), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1121 TYR 0.016 0.001 TYR A 61 PHE 0.015 0.001 PHE A1249 TRP 0.010 0.001 TRP A1258 HIS 0.003 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00362 (12500) covalent geometry : angle 0.57501 (17296) hydrogen bonds : bond 0.03886 ( 610) hydrogen bonds : angle 4.12372 ( 1667) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 54 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9752 (mtpt) cc_final: 0.9447 (ptpp) REVERT: A 452 GLN cc_start: 0.9348 (tm-30) cc_final: 0.9086 (tm-30) REVERT: A 593 MET cc_start: 0.9309 (tmm) cc_final: 0.8969 (tmm) REVERT: A 908 ASP cc_start: 0.7869 (t0) cc_final: 0.7336 (t0) REVERT: A 949 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8918 (ptpp) REVERT: A 1012 TYR cc_start: 0.8476 (m-80) cc_final: 0.7998 (m-80) REVERT: A 1055 MET cc_start: 0.8979 (tmm) cc_final: 0.8631 (tmm) REVERT: A 1127 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8312 (mtt-85) REVERT: A 1133 MET cc_start: 0.9063 (mmp) cc_final: 0.8696 (mmp) outliers start: 40 outliers final: 16 residues processed: 86 average time/residue: 0.1132 time to fit residues: 14.6334 Evaluate side-chains 68 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 622 HIS Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1127 ARG Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 34 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 111 optimal weight: 0.3980 chunk 81 optimal weight: 9.9990 chunk 119 optimal weight: 0.7980 chunk 126 optimal weight: 7.9990 chunk 44 optimal weight: 50.0000 chunk 69 optimal weight: 5.9990 chunk 13 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 48 optimal weight: 30.0000 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 ASN ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.040005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2576 r_free = 0.2576 target = 0.029176 restraints weight = 79488.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.030476 restraints weight = 38985.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.031332 restraints weight = 25077.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.031867 restraints weight = 18881.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2677 r_free = 0.2677 target = 0.032238 restraints weight = 15799.886| |-----------------------------------------------------------------------------| r_work (final): 0.2663 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12500 Z= 0.170 Angle : 0.573 10.575 17296 Z= 0.300 Chirality : 0.039 0.150 1930 Planarity : 0.003 0.037 1895 Dihedral : 19.338 174.009 2521 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.89 % Allowed : 17.42 % Favored : 79.69 % 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: 2.01 (0.25), residues: 1234 helix: 2.01 (0.21), residues: 618 sheet: 0.20 (0.46), residues: 130 loop : 0.96 (0.30), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 912 TYR 0.015 0.001 TYR A 61 PHE 0.014 0.001 PHE A1249 TRP 0.010 0.001 TRP A1258 HIS 0.003 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00364 (12500) covalent geometry : angle 0.57288 (17296) hydrogen bonds : bond 0.03829 ( 610) hydrogen bonds : angle 4.03812 ( 1667) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 54 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 LYS cc_start: 0.9751 (mtpt) cc_final: 0.9433 (mtmm) REVERT: A 908 ASP cc_start: 0.7982 (t0) cc_final: 0.7421 (t0) REVERT: A 1012 TYR cc_start: 0.8526 (m-80) cc_final: 0.8023 (m-80) REVERT: A 1127 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8312 (mtt-85) REVERT: A 1133 MET cc_start: 0.9090 (mmp) cc_final: 0.8709 (mmp) outliers start: 32 outliers final: 22 residues processed: 77 average time/residue: 0.1089 time to fit residues: 12.8963 Evaluate side-chains 73 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1127 ARG Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 60 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 96 optimal weight: 1.9990 chunk 49 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 56 optimal weight: 4.9990 chunk 104 optimal weight: 9.9990 chunk 16 optimal weight: 7.9990 chunk 52 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 452 GLN A1206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.038785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.028073 restraints weight = 81469.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.029321 restraints weight = 40225.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.030158 restraints weight = 26077.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2624 r_free = 0.2624 target = 0.030660 restraints weight = 19763.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.031031 restraints weight = 16618.909| |-----------------------------------------------------------------------------| r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 12500 Z= 0.274 Angle : 0.634 11.154 17296 Z= 0.336 Chirality : 0.041 0.150 1930 Planarity : 0.003 0.035 1895 Dihedral : 19.469 174.477 2521 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.25 % Allowed : 17.78 % Favored : 78.97 % 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: 1.88 (0.25), residues: 1234 helix: 1.91 (0.21), residues: 619 sheet: 0.20 (0.46), residues: 132 loop : 0.87 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 411 TYR 0.020 0.002 TYR A 61 PHE 0.017 0.002 PHE A1249 TRP 0.010 0.001 TRP A1258 HIS 0.005 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00570 (12500) covalent geometry : angle 0.63368 (17296) hydrogen bonds : bond 0.04528 ( 610) hydrogen bonds : angle 4.22623 ( 1667) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 47 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 537 MET cc_start: 0.9220 (mmt) cc_final: 0.8699 (mmt) REVERT: A 908 ASP cc_start: 0.8289 (t0) cc_final: 0.7730 (t0) REVERT: A 1012 TYR cc_start: 0.8579 (m-80) cc_final: 0.7821 (m-80) REVERT: A 1055 MET cc_start: 0.9096 (tmm) cc_final: 0.8769 (tmm) REVERT: A 1133 MET cc_start: 0.9066 (mmp) cc_final: 0.8610 (mmp) outliers start: 36 outliers final: 28 residues processed: 73 average time/residue: 0.0955 time to fit residues: 11.1042 Evaluate side-chains 74 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 46 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 44 ASN Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 148 THR Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 467 LEU Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 920 ILE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 975 VAL Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1127 ARG Chi-restraints excluded: chain A residue 1225 MET Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 24 optimal weight: 0.7980 chunk 112 optimal weight: 9.9990 chunk 6 optimal weight: 0.8980 chunk 41 optimal weight: 6.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 115 optimal weight: 9.9990 chunk 79 optimal weight: 0.0060 chunk 69 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 overall best weight: 0.6996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 HIS ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.040745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.029974 restraints weight = 77283.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2646 r_free = 0.2646 target = 0.031298 restraints weight = 37709.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.032172 restraints weight = 24310.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.032735 restraints weight = 18253.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.033122 restraints weight = 15194.329| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8750 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12500 Z= 0.114 Angle : 0.563 9.497 17296 Z= 0.290 Chirality : 0.039 0.147 1930 Planarity : 0.003 0.035 1895 Dihedral : 19.298 169.832 2521 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.90 % Allowed : 19.04 % Favored : 79.06 % 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: 2.21 (0.25), residues: 1234 helix: 2.17 (0.21), residues: 618 sheet: 0.29 (0.47), residues: 132 loop : 1.06 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 386 TYR 0.014 0.001 TYR A 764 PHE 0.012 0.001 PHE A1249 TRP 0.010 0.001 TRP A1258 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00250 (12500) covalent geometry : angle 0.56331 (17296) hydrogen bonds : bond 0.03552 ( 610) hydrogen bonds : angle 3.83398 ( 1667) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 60 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 593 MET cc_start: 0.9197 (tmm) cc_final: 0.8973 (tmm) REVERT: A 908 ASP cc_start: 0.7860 (t0) cc_final: 0.7390 (t0) REVERT: A 948 GLU cc_start: 0.9281 (tt0) cc_final: 0.8917 (tt0) REVERT: A 949 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8887 (pttp) REVERT: A 1003 ARG cc_start: 0.9289 (mmm-85) cc_final: 0.9062 (mmm160) REVERT: A 1012 TYR cc_start: 0.8508 (m-80) cc_final: 0.7628 (m-80) REVERT: A 1046 THR cc_start: 0.9348 (p) cc_final: 0.9143 (p) REVERT: A 1133 MET cc_start: 0.9044 (mmp) cc_final: 0.8682 (mmp) outliers start: 21 outliers final: 15 residues processed: 74 average time/residue: 0.0997 time to fit residues: 11.4461 Evaluate side-chains 71 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 726 ILE Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 7 optimal weight: 6.9990 chunk 118 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 32 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 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 = 0.2972 r_free = 0.2972 target = 0.039817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2577 r_free = 0.2577 target = 0.029057 restraints weight = 79161.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2618 r_free = 0.2618 target = 0.030331 restraints weight = 38958.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.031171 restraints weight = 25379.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.031733 restraints weight = 19232.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.032088 restraints weight = 15973.300| |-----------------------------------------------------------------------------| r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 12500 Z= 0.177 Angle : 0.586 11.721 17296 Z= 0.304 Chirality : 0.039 0.148 1930 Planarity : 0.003 0.036 1895 Dihedral : 19.306 172.789 2521 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.17 % Allowed : 18.86 % Favored : 78.97 % 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: 2.26 (0.25), residues: 1234 helix: 2.21 (0.21), residues: 618 sheet: 0.33 (0.47), residues: 132 loop : 1.08 (0.31), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 912 TYR 0.014 0.001 TYR A 61 PHE 0.013 0.001 PHE A1249 TRP 0.009 0.001 TRP A1258 HIS 0.003 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00378 (12500) covalent geometry : angle 0.58610 (17296) hydrogen bonds : bond 0.03822 ( 610) hydrogen bonds : angle 3.89573 ( 1667) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 52 time to evaluate : 0.453 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 908 ASP cc_start: 0.8135 (t0) cc_final: 0.7682 (t0) REVERT: A 930 ARG cc_start: 0.9283 (OUTLIER) cc_final: 0.9057 (mtm110) REVERT: A 949 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8895 (pttp) REVERT: A 1003 ARG cc_start: 0.9297 (mmm-85) cc_final: 0.9000 (mmm-85) REVERT: A 1012 TYR cc_start: 0.8560 (m-80) cc_final: 0.7585 (m-80) REVERT: A 1046 THR cc_start: 0.9277 (p) cc_final: 0.9060 (p) REVERT: A 1133 MET cc_start: 0.9070 (mmp) cc_final: 0.8654 (mmp) outliers start: 24 outliers final: 15 residues processed: 71 average time/residue: 0.1046 time to fit residues: 11.4848 Evaluate side-chains 67 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 50 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 930 ARG Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 110 optimal weight: 5.9990 chunk 124 optimal weight: 10.0000 chunk 122 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 45 optimal weight: 0.0050 chunk 0 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 109 optimal weight: 5.9990 chunk 46 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 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 = 0.2993 r_free = 0.2993 target = 0.040566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.029741 restraints weight = 78089.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.031054 restraints weight = 38083.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.031922 restraints weight = 24585.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.032477 restraints weight = 18510.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.032864 restraints weight = 15470.484| |-----------------------------------------------------------------------------| r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12500 Z= 0.126 Angle : 0.572 11.119 17296 Z= 0.293 Chirality : 0.038 0.147 1930 Planarity : 0.003 0.036 1895 Dihedral : 19.234 169.821 2521 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.90 % Allowed : 19.31 % Favored : 78.79 % 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: 2.30 (0.25), residues: 1234 helix: 2.24 (0.21), residues: 619 sheet: 0.32 (0.47), residues: 132 loop : 1.10 (0.31), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1172 TYR 0.015 0.001 TYR A 595 PHE 0.011 0.001 PHE A1249 TRP 0.010 0.001 TRP A1258 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00279 (12500) covalent geometry : angle 0.57195 (17296) hydrogen bonds : bond 0.03503 ( 610) hydrogen bonds : angle 3.78937 ( 1667) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 52 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7326 (tpt) cc_final: 0.6993 (tpt) REVERT: A 537 MET cc_start: 0.9192 (mmt) cc_final: 0.8663 (mmt) REVERT: A 908 ASP cc_start: 0.7977 (t0) cc_final: 0.7491 (t0) REVERT: A 930 ARG cc_start: 0.9274 (OUTLIER) cc_final: 0.9018 (mtm110) REVERT: A 948 GLU cc_start: 0.9277 (tt0) cc_final: 0.8905 (tt0) REVERT: A 949 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8886 (pttp) REVERT: A 1003 ARG cc_start: 0.9319 (mmm-85) cc_final: 0.9023 (mmm-85) REVERT: A 1012 TYR cc_start: 0.8479 (m-80) cc_final: 0.7478 (m-80) REVERT: A 1046 THR cc_start: 0.9322 (p) cc_final: 0.9120 (p) REVERT: A 1055 MET cc_start: 0.9039 (tmm) cc_final: 0.8717 (tmm) REVERT: A 1133 MET cc_start: 0.9010 (mmp) cc_final: 0.8649 (mmp) outliers start: 21 outliers final: 17 residues processed: 68 average time/residue: 0.1116 time to fit residues: 11.6252 Evaluate side-chains 70 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 51 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 363 HIS Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 930 ARG Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 108 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 14 optimal weight: 0.4980 chunk 87 optimal weight: 7.9990 chunk 45 optimal weight: 3.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 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 = 0.3002 r_free = 0.3002 target = 0.041312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2613 r_free = 0.2613 target = 0.030572 restraints weight = 78240.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.031865 restraints weight = 38295.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2683 r_free = 0.2683 target = 0.032754 restraints weight = 24823.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.033305 restraints weight = 18635.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.033714 restraints weight = 15557.260| |-----------------------------------------------------------------------------| r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12500 Z= 0.128 Angle : 0.569 10.441 17296 Z= 0.292 Chirality : 0.038 0.147 1930 Planarity : 0.003 0.035 1895 Dihedral : 19.151 170.648 2521 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 1.90 % Allowed : 19.22 % Favored : 78.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.32 (0.25), residues: 1234 helix: 2.28 (0.21), residues: 619 sheet: 0.31 (0.47), residues: 130 loop : 1.10 (0.31), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A1094 TYR 0.014 0.001 TYR A 764 PHE 0.010 0.001 PHE A1249 TRP 0.010 0.001 TRP A1258 HIS 0.004 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00283 (12500) covalent geometry : angle 0.56903 (17296) hydrogen bonds : bond 0.03492 ( 610) hydrogen bonds : angle 3.74981 ( 1667) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2468 Ramachandran restraints generated. 1234 Oldfield, 0 Emsley, 1234 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 53 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.7330 (tpt) cc_final: 0.7001 (tpt) REVERT: A 537 MET cc_start: 0.9186 (mmt) cc_final: 0.8651 (mmt) REVERT: A 908 ASP cc_start: 0.8044 (t0) cc_final: 0.7545 (t0) REVERT: A 930 ARG cc_start: 0.9292 (OUTLIER) cc_final: 0.9060 (mtm110) REVERT: A 948 GLU cc_start: 0.9277 (tt0) cc_final: 0.8911 (tt0) REVERT: A 949 LYS cc_start: 0.9159 (OUTLIER) cc_final: 0.8889 (pttp) REVERT: A 1003 ARG cc_start: 0.9325 (mmm-85) cc_final: 0.9034 (mmm-85) REVERT: A 1012 TYR cc_start: 0.8484 (m-80) cc_final: 0.7546 (m-80) REVERT: A 1046 THR cc_start: 0.9317 (p) cc_final: 0.9110 (p) REVERT: A 1055 MET cc_start: 0.9056 (tmm) cc_final: 0.8747 (tmm) REVERT: A 1133 MET cc_start: 0.8913 (mmp) cc_final: 0.8591 (mmp) REVERT: A 1235 ASP cc_start: 0.9431 (t0) cc_final: 0.8723 (m-30) outliers start: 21 outliers final: 16 residues processed: 69 average time/residue: 0.1069 time to fit residues: 11.2942 Evaluate side-chains 68 residues out of total 1108 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 GLN Chi-restraints excluded: chain A residue 65 CYS Chi-restraints excluded: chain A residue 149 VAL Chi-restraints excluded: chain A residue 151 THR Chi-restraints excluded: chain A residue 152 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 671 GLU Chi-restraints excluded: chain A residue 752 LYS Chi-restraints excluded: chain A residue 754 HIS Chi-restraints excluded: chain A residue 779 ILE Chi-restraints excluded: chain A residue 873 VAL Chi-restraints excluded: chain A residue 930 ARG Chi-restraints excluded: chain A residue 945 ASP Chi-restraints excluded: chain A residue 949 LYS Chi-restraints excluded: chain A residue 1084 VAL Chi-restraints excluded: chain A residue 1281 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 131 random chunks: chunk 78 optimal weight: 5.9990 chunk 129 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 97 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 64 optimal weight: 0.2980 chunk 118 optimal weight: 4.9990 chunk 40 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 overall best weight: 4.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 946 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 = 0.2945 r_free = 0.2945 target = 0.038886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2556 r_free = 0.2556 target = 0.028292 restraints weight = 82524.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.029535 restraints weight = 40951.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.030372 restraints weight = 26735.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.030911 restraints weight = 20197.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.031250 restraints weight = 16840.434| |-----------------------------------------------------------------------------| r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 12500 Z= 0.272 Angle : 0.650 11.306 17296 Z= 0.341 Chirality : 0.041 0.196 1930 Planarity : 0.003 0.036 1895 Dihedral : 19.313 172.052 2521 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 13.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.99 % Allowed : 19.22 % Favored : 78.79 % 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: 2.16 (0.25), residues: 1234 helix: 2.14 (0.21), residues: 620 sheet: 0.30 (0.47), residues: 132 loop : 1.01 (0.31), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1094 TYR 0.022 0.002 TYR A 61 PHE 0.016 0.002 PHE A 769 TRP 0.009 0.001 TRP A 483 HIS 0.005 0.001 HIS A 720 Details of bonding type rmsd covalent geometry : bond 0.00567 (12500) covalent geometry : angle 0.65044 (17296) hydrogen bonds : bond 0.04384 ( 610) hydrogen bonds : angle 4.07941 ( 1667) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1967.43 seconds wall clock time: 35 minutes 7.34 seconds (2107.34 seconds total)