Starting phenix.real_space_refine on Wed Mar 4 15:55:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b9i_15932/03_2026/8b9i_15932.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9i_15932/03_2026/8b9i_15932.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8b9i_15932/03_2026/8b9i_15932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9i_15932/03_2026/8b9i_15932.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b9i_15932/03_2026/8b9i_15932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9i_15932/03_2026/8b9i_15932.map" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 7861 atoms to isotropic. 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: 8 Type Number sf(0) Gaussians Al 1 5.89 5 P 13 5.49 5 Mg 1 5.21 5 S 48 5.16 5 C 5043 2.51 5 N 1381 2.21 5 O 1535 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8026 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 7784 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 984, 7781 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 49, 'TRANS': 932} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Conformer: "B" Number of residues, atoms: 984, 7781 Classifications: {'peptide': 984} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 49, 'TRANS': 932} Chain breaks: 2 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 bond proxies already assigned to first conformer: 7927 Chain: "C" Number of atoms: 204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 204 Classifications: {'RNA': 11} Modifications used: {'rna3p_pyr': 10} Link IDs: {'rna3p': 10} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "A" Number of atoms: 37 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 37 Unusual residues: {' MG': 1, 'ADP': 1, 'ALF': 1} Classifications: {'undetermined': 3, 'water': 4} Link IDs: {None: 6} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 3.44, per 1000 atoms: 0.43 Number of scatterers: 8026 At special positions: 0 Unit cell: (83.022, 96.174, 104.394, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 48 16.00 P 13 15.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1535 8.00 N 1381 7.00 C 5043 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: 0.55 Conformation dependent library (CDL) restraints added in 699.9 milliseconds 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1880 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 7 sheets defined 52.3% alpha, 12.8% beta 0 base pairs and 3 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 146 through 155 Processing helix chain 'A' and resid 166 through 182 removed outlier: 4.193A pdb=" N LYS A 171 " --> pdb=" O ILE A 167 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N GLU A 172 " --> pdb=" O GLU A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 242 Processing helix chain 'A' and resid 268 through 282 Processing helix chain 'A' and resid 288 through 292 removed outlier: 3.880A pdb=" N ASN A 291 " --> pdb=" O ASN A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 371 Processing helix chain 'A' and resid 371 through 382 Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.765A pdb=" N ALA A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET A 389 " --> pdb=" O PRO A 385 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 384 through 389' Processing helix chain 'A' and resid 389 through 400 Processing helix chain 'A' and resid 412 through 428 removed outlier: 4.589A pdb=" N ALA A 418 " --> pdb=" O THR A 414 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N GLN A 419 " --> pdb=" O THR A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 433 Processing helix chain 'A' and resid 442 through 457 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 495 through 497 No H-bonds generated for 'chain 'A' and resid 495 through 497' Processing helix chain 'A' and resid 509 through 512 removed outlier: 3.746A pdb=" N ARG A 512 " --> pdb=" O ILE A 509 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 512' Processing helix chain 'A' and resid 513 through 530 Processing helix chain 'A' and resid 543 through 551 Processing helix chain 'A' and resid 570 through 579 Processing helix chain 'A' and resid 583 through 591 removed outlier: 4.104A pdb=" N ARG A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG A 590 " --> pdb=" O SER A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 630 Processing helix chain 'A' and resid 636 through 650 Processing helix chain 'A' and resid 662 through 676 removed outlier: 3.582A pdb=" N THR A 676 " --> pdb=" O PHE A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 681 removed outlier: 4.096A pdb=" N ASP A 681 " --> pdb=" O ASN A 677 " (cutoff:3.500A) Processing helix chain 'A' and resid 695 through 700 Processing helix chain 'A' and resid 701 through 703 No H-bonds generated for 'chain 'A' and resid 701 through 703' Processing helix chain 'A' and resid 745 through 748 Processing helix chain 'A' and resid 758 through 767 Processing helix chain 'A' and resid 782 through 789 Processing helix chain 'A' and resid 795 through 799 Processing helix chain 'A' and resid 802 through 813 Processing helix chain 'A' and resid 816 through 823 Processing helix chain 'A' and resid 829 through 843 Processing helix chain 'A' and resid 853 through 861 Processing helix chain 'A' and resid 865 through 879 Processing helix chain 'A' and resid 880 through 892 Processing helix chain 'A' and resid 908 through 914 Processing helix chain 'A' and resid 920 through 939 Processing helix chain 'A' and resid 939 through 951 Processing helix chain 'A' and resid 953 through 975 Processing helix chain 'A' and resid 977 through 981 Processing helix chain 'A' and resid 994 through 1008 removed outlier: 3.722A pdb=" N CYS A1005 " --> pdb=" O LEU A1001 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LEU A1006 " --> pdb=" O ALA A1002 " (cutoff:3.500A) Processing helix chain 'A' and resid 1024 through 1026 No H-bonds generated for 'chain 'A' and resid 1024 through 1026' Processing helix chain 'A' and resid 1070 through 1077 Processing helix chain 'A' and resid 1101 through 1110 Processing helix chain 'A' and resid 1110 through 1125 removed outlier: 4.042A pdb=" N ALA A1114 " --> pdb=" O ALA A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1126 through 1129 removed outlier: 3.906A pdb=" N ILE A1129 " --> pdb=" O PRO A1126 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1126 through 1129' Processing helix chain 'A' and resid 1133 through 1148 Processing helix chain 'A' and resid 1149 through 1153 removed outlier: 4.474A pdb=" N GLY A1152 " --> pdb=" O LYS A1149 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 188 through 192 removed outlier: 3.702A pdb=" N ARG A 213 " --> pdb=" O VAL A 208 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 263 through 264 removed outlier: 5.895A pdb=" N TYR A 263 " --> pdb=" O ASP A1099 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 336 Processing sheet with id=AA4, first strand: chain 'A' and resid 472 through 474 removed outlier: 6.743A pdb=" N GLY A 466 " --> pdb=" O PHE A 484 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N THR A 486 " --> pdb=" O GLY A 466 " (cutoff:3.500A) removed outlier: 7.790A pdb=" N SER A 468 " --> pdb=" O THR A 486 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N ASN A 435 " --> pdb=" O HIS A 503 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 505 " --> pdb=" O ASN A 435 " (cutoff:3.500A) removed outlier: 5.989A pdb=" N TYR A 437 " --> pdb=" O ILE A 505 " (cutoff:3.500A) removed outlier: 7.278A pdb=" N ASP A 507 " --> pdb=" O TYR A 437 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR A 439 " --> pdb=" O ASP A 507 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY A 407 " --> pdb=" O SER A 539 " (cutoff:3.500A) removed outlier: 8.231A pdb=" N LEU A 557 " --> pdb=" O VAL A 402 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE A 404 " --> pdb=" O LEU A 557 " (cutoff:3.500A) removed outlier: 7.283A pdb=" N VAL A 559 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.655A pdb=" N ARG A 406 " --> pdb=" O VAL A 559 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 566 through 569 removed outlier: 6.133A pdb=" N GLN A 567 " --> pdb=" O CYS A 777 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N THR A 779 " --> pdb=" O GLN A 567 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N PHE A 569 " --> pdb=" O THR A 779 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 730 " --> pdb=" O PHE A 776 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N PHE A 778 " --> pdb=" O VAL A 730 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL A 732 " --> pdb=" O PHE A 778 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ALA A 655 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE A 656 " --> pdb=" O ILE A 714 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N SER A 716 " --> pdb=" O ILE A 656 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL A 658 " --> pdb=" O SER A 716 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 737 through 744 Processing sheet with id=AA7, first strand: chain 'A' and resid 1054 through 1057 removed outlier: 3.671A pdb=" N GLU A1054 " --> pdb=" O LYS A1064 " (cutoff:3.500A) removed outlier: 5.202A pdb=" N VAL A1061 " --> pdb=" O ALA A1028 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LYS A1020 " --> pdb=" O LYS A1016 " (cutoff:3.500A) 392 hydrogen bonds defined for protein. 1122 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 3 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.42: 3326 1.42 - 1.62: 4786 1.62 - 1.83: 78 1.83 - 2.03: 0 2.03 - 2.23: 1 Bond restraints: 8191 Sorted by residual: bond pdb=" C GLY A 346 " pdb=" N LEU A 348 " ideal model delta sigma weight residual 1.329 2.234 -0.905 1.40e-02 5.10e+03 4.17e+03 bond pdb=" F3 ALF A1203 " pdb="AL ALF A1203 " ideal model delta sigma weight residual 1.685 1.782 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" F2 ALF A1203 " pdb="AL ALF A1203 " ideal model delta sigma weight residual 1.685 1.781 -0.096 2.00e-02 2.50e+03 2.33e+01 bond pdb=" F1 ALF A1203 " pdb="AL ALF A1203 " ideal model delta sigma weight residual 1.684 1.779 -0.095 2.00e-02 2.50e+03 2.28e+01 bond pdb=" F4 ALF A1203 " pdb="AL ALF A1203 " ideal model delta sigma weight residual 1.686 1.779 -0.093 2.00e-02 2.50e+03 2.18e+01 ... (remaining 8186 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.15: 11139 14.15 - 28.31: 4 28.31 - 42.46: 0 42.46 - 56.62: 0 56.62 - 70.77: 2 Bond angle restraints: 11145 Sorted by residual: angle pdb=" F1 ALF A1203 " pdb="AL ALF A1203 " pdb=" F2 ALF A1203 " ideal model delta sigma weight residual 108.68 179.45 -70.77 3.00e+00 1.11e-01 5.57e+02 angle pdb=" F3 ALF A1203 " pdb="AL ALF A1203 " pdb=" F4 ALF A1203 " ideal model delta sigma weight residual 109.63 179.86 -70.23 3.00e+00 1.11e-01 5.48e+02 angle pdb=" CA PRO A 560 " pdb=" N PRO A 560 " pdb=" CD PRO A 560 " ideal model delta sigma weight residual 112.00 98.49 13.51 1.40e+00 5.10e-01 9.32e+01 angle pdb=" CA GLY A 346 " pdb=" C GLY A 346 " pdb=" N LEU A 348 " ideal model delta sigma weight residual 115.32 103.41 11.91 1.42e+00 4.96e-01 7.03e+01 angle pdb=" C GLY A 346 " pdb=" N LEU A 348 " pdb=" CA LEU A 348 " ideal model delta sigma weight residual 121.70 135.74 -14.04 1.80e+00 3.09e-01 6.08e+01 ... (remaining 11140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.51: 4768 33.51 - 67.02: 252 67.02 - 100.52: 26 100.52 - 134.03: 1 134.03 - 167.54: 3 Dihedral angle restraints: 5050 sinusoidal: 2164 harmonic: 2886 Sorted by residual: dihedral pdb=" O4' U C 6 " pdb=" C1' U C 6 " pdb=" N1 U C 6 " pdb=" C2 U C 6 " ideal model delta sinusoidal sigma weight residual -160.00 7.54 -167.54 1 1.50e+01 4.44e-03 8.43e+01 dihedral pdb=" C5' ADP A1201 " pdb=" O5' ADP A1201 " pdb=" PA ADP A1201 " pdb=" O2A ADP A1201 " ideal model delta sinusoidal sigma weight residual 300.00 144.92 155.08 1 2.00e+01 2.50e-03 4.58e+01 dihedral pdb=" O2A ADP A1201 " pdb=" O3A ADP A1201 " pdb=" PA ADP A1201 " pdb=" PB ADP A1201 " ideal model delta sinusoidal sigma weight residual -60.00 90.48 -150.48 1 2.00e+01 2.50e-03 4.49e+01 ... (remaining 5047 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 994 0.050 - 0.100: 226 0.100 - 0.150: 62 0.150 - 0.200: 3 0.200 - 0.251: 2 Chirality restraints: 1287 Sorted by residual: chirality pdb=" CB ILE A 719 " pdb=" CA ILE A 719 " pdb=" CG1 ILE A 719 " pdb=" CG2 ILE A 719 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU A 201 " pdb=" CB LEU A 201 " pdb=" CD1 LEU A 201 " pdb=" CD2 LEU A 201 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CA ILE A 343 " pdb=" N ILE A 343 " pdb=" C ILE A 343 " pdb=" CB ILE A 343 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.89e-01 ... (remaining 1284 not shown) Planarity restraints: 1401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 346 " -0.113 2.00e-02 2.50e+03 1.97e-01 3.90e+02 pdb=" C GLY A 346 " 0.337 2.00e-02 2.50e+03 pdb=" O GLY A 346 " -0.159 2.00e-02 2.50e+03 pdb=" N LEU A 348 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 559 " 0.068 5.00e-02 4.00e+02 9.48e-02 1.44e+01 pdb=" N PRO A 560 " -0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 560 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO A 560 " 0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN A 342 " 0.014 2.00e-02 2.50e+03 2.81e-02 7.92e+00 pdb=" C ASN A 342 " -0.049 2.00e-02 2.50e+03 pdb=" O ASN A 342 " 0.019 2.00e-02 2.50e+03 pdb=" N ILE A 343 " 0.016 2.00e-02 2.50e+03 ... (remaining 1398 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 68 2.55 - 3.14: 6179 3.14 - 3.73: 13209 3.73 - 4.31: 18362 4.31 - 4.90: 29800 Nonbonded interactions: 67618 Sorted by model distance: nonbonded pdb="MG MG A1202 " pdb=" O HOH A1302 " model vdw 1.963 2.170 nonbonded pdb=" F2 ALF A1203 " pdb=" O HOH A1301 " model vdw 2.099 2.990 nonbonded pdb=" F2 ALF A1203 " pdb=" O HOH A1302 " model vdw 2.146 2.990 nonbonded pdb=" OE1 GLN A 576 " pdb=" OG1 THR A 623 " model vdw 2.187 3.040 nonbonded pdb=" O3B ADP A1201 " pdb=" O HOH A1301 " model vdw 2.196 3.040 ... (remaining 67613 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 11.350 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.030 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:6.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 : 0.011 0.905 8191 Z= 0.742 Angle : 1.242 70.773 11145 Z= 0.516 Chirality : 0.046 0.251 1287 Planarity : 0.008 0.197 1401 Dihedral : 19.476 167.540 3170 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 2.31 % Allowed : 30.40 % Favored : 67.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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 are not related in a simple way. whole: 0.95 (0.28), residues: 977 helix: 1.73 (0.24), residues: 457 sheet: -0.38 (0.42), residues: 161 loop : -0.21 (0.36), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 624 TYR 0.012 0.001 TYR A 890 PHE 0.016 0.002 PHE A 878 TRP 0.010 0.001 TRP A 663 HIS 0.004 0.001 HIS A 746 Details of bonding type rmsd covalent geometry : bond 0.01100 ( 8191) covalent geometry : angle 1.24246 (11145) hydrogen bonds : bond 0.13279 ( 392) hydrogen bonds : angle 5.29879 ( 1122) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1954 Ramachandran restraints generated. 977 Oldfield, 0 Emsley, 977 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 294 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8110 (pp) outliers start: 20 outliers final: 9 residues processed: 150 average time/residue: 0.5902 time to fit residues: 93.4803 Evaluate side-chains 78 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 363 SER Chi-restraints excluded: chain A residue 527 VAL Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 929 SER Chi-restraints excluded: chain A residue 1058 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 6.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN A 332 GLN A 339 HIS A 510 HIS A 567 GLN A 621 GLN A 911 GLN A 973 GLN A1032 HIS A1037 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.090900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.068351 restraints weight = 22340.291| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.28 r_work: 0.2854 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2874 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2874 r_free = 0.2874 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2874 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.2045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.091 8191 Z= 0.134 Angle : 0.695 11.922 11145 Z= 0.341 Chirality : 0.045 0.202 1287 Planarity : 0.006 0.055 1401 Dihedral : 12.600 161.960 1254 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.27 % Favored : 96.63 % Rotamer: Outliers : 4.86 % Allowed : 28.79 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % 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 are not related in a simple way. whole: 0.95 (0.28), residues: 979 helix: 1.83 (0.24), residues: 457 sheet: -0.26 (0.39), residues: 179 loop : -0.45 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 844 TYR 0.008 0.001 TYR A 619 PHE 0.014 0.001 PHE A 667 TRP 0.025 0.002 TRP A 335 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 8191) covalent geometry : angle 0.69487 (11145) hydrogen bonds : bond 0.03647 ( 392) hydrogen bonds : angle 4.60293 ( 1122) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 79 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8961 (mp) REVERT: A 297 ASP cc_start: 0.6074 (OUTLIER) cc_final: 0.5142 (p0) REVERT: A 389 MET cc_start: 0.8976 (OUTLIER) cc_final: 0.8668 (tpp) REVERT: A 585 GLU cc_start: 0.9400 (pm20) cc_final: 0.8982 (tp30) REVERT: A 896 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7212 (mm-30) REVERT: A 954 MET cc_start: 0.8992 (OUTLIER) cc_final: 0.8762 (mmt) outliers start: 42 outliers final: 14 residues processed: 114 average time/residue: 0.5853 time to fit residues: 70.6501 Evaluate side-chains 85 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 67 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 627 MET Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1067 SER Chi-restraints excluded: chain A residue 1148 VAL Chi-restraints excluded: chain A residue 1150 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 34 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 46 optimal weight: 0.5980 chunk 73 optimal weight: 0.0570 chunk 38 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 39 optimal weight: 6.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 746 HIS A 911 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.066544 restraints weight = 26057.198| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 4.61 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3013 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3013 r_free = 0.3013 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3012 r_free = 0.3012 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3012 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 8191 Z= 0.131 Angle : 0.663 9.729 11145 Z= 0.326 Chirality : 0.044 0.176 1287 Planarity : 0.005 0.052 1401 Dihedral : 12.146 156.439 1250 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.17 % Favored : 96.73 % Rotamer: Outliers : 3.24 % Allowed : 29.13 % Favored : 67.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % 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 are not related in a simple way. whole: 1.03 (0.28), residues: 979 helix: 1.95 (0.24), residues: 457 sheet: -0.22 (0.39), residues: 179 loop : -0.49 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 844 TYR 0.024 0.001 TYR A1009 PHE 0.014 0.001 PHE A 667 TRP 0.016 0.001 TRP A 335 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8191) covalent geometry : angle 0.66287 (11145) hydrogen bonds : bond 0.03436 ( 392) hydrogen bonds : angle 4.44662 ( 1122) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9236 (OUTLIER) cc_final: 0.9018 (mp) REVERT: A 297 ASP cc_start: 0.6159 (OUTLIER) cc_final: 0.5278 (p0) REVERT: A 358 MET cc_start: 0.9075 (mtp) cc_final: 0.8791 (mmp) REVERT: A 585 GLU cc_start: 0.9421 (pm20) cc_final: 0.9047 (tp30) REVERT: A 896 GLU cc_start: 0.7667 (mm-30) cc_final: 0.7121 (mm-30) REVERT: A 954 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.8382 (mmt) REVERT: A 1018 LYS cc_start: 0.9100 (mttt) cc_final: 0.8745 (mmmm) outliers start: 28 outliers final: 10 residues processed: 100 average time/residue: 0.4958 time to fit residues: 53.2307 Evaluate side-chains 82 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 69 time to evaluate : 0.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 444 ILE Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 911 GLN Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 19 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 911 GLN A1097 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.086020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.062281 restraints weight = 34659.930| |-----------------------------------------------------------------------------| r_work (start): 0.2930 rms_B_bonded: 5.20 r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8191 Z= 0.185 Angle : 0.664 9.412 11145 Z= 0.329 Chirality : 0.045 0.173 1287 Planarity : 0.005 0.049 1401 Dihedral : 11.903 160.796 1242 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 4.05 % Allowed : 27.86 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % 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 are not related in a simple way. whole: 1.05 (0.28), residues: 979 helix: 1.92 (0.24), residues: 459 sheet: -0.18 (0.40), residues: 174 loop : -0.45 (0.36), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 443 TYR 0.018 0.001 TYR A1009 PHE 0.014 0.001 PHE A 667 TRP 0.015 0.001 TRP A 335 HIS 0.009 0.001 HIS A 910 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8191) covalent geometry : angle 0.66351 (11145) hydrogen bonds : bond 0.03788 ( 392) hydrogen bonds : angle 4.47053 ( 1122) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 63 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9239 (OUTLIER) cc_final: 0.9022 (mp) REVERT: A 219 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7029 (mp0) REVERT: A 297 ASP cc_start: 0.6241 (OUTLIER) cc_final: 0.5386 (p0) REVERT: A 358 MET cc_start: 0.9159 (mtp) cc_final: 0.8853 (mmp) REVERT: A 585 GLU cc_start: 0.9441 (pm20) cc_final: 0.9026 (tp30) REVERT: A 634 ASP cc_start: 0.8204 (t0) cc_final: 0.7928 (p0) REVERT: A 896 GLU cc_start: 0.7898 (mm-30) cc_final: 0.7358 (mm-30) REVERT: A 942 MET cc_start: 0.8866 (mpp) cc_final: 0.8488 (pmm) REVERT: A 954 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8435 (mmt) REVERT: A 1018 LYS cc_start: 0.9127 (mttt) cc_final: 0.8825 (mmmm) outliers start: 34 outliers final: 10 residues processed: 91 average time/residue: 0.4806 time to fit residues: 47.0314 Evaluate side-chains 72 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 449 VAL Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 12 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 78 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.087418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.064486 restraints weight = 25799.306| |-----------------------------------------------------------------------------| r_work (start): 0.2977 rms_B_bonded: 4.61 r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2979 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2979 r_free = 0.2979 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8191 Z= 0.134 Angle : 0.634 10.509 11145 Z= 0.312 Chirality : 0.043 0.166 1287 Planarity : 0.005 0.045 1401 Dihedral : 11.665 155.438 1240 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 3.12 % Allowed : 27.98 % Favored : 68.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % 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 are not related in a simple way. whole: 1.08 (0.28), residues: 979 helix: 1.97 (0.24), residues: 458 sheet: -0.12 (0.41), residues: 164 loop : -0.47 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 844 TYR 0.008 0.001 TYR A1009 PHE 0.018 0.001 PHE A 155 TRP 0.012 0.001 TRP A 335 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8191) covalent geometry : angle 0.63356 (11145) hydrogen bonds : bond 0.03367 ( 392) hydrogen bonds : angle 4.37637 ( 1122) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9217 (OUTLIER) cc_final: 0.8956 (mp) REVERT: A 179 GLN cc_start: 0.9388 (OUTLIER) cc_final: 0.8898 (tm-30) REVERT: A 297 ASP cc_start: 0.6337 (OUTLIER) cc_final: 0.5550 (p0) REVERT: A 358 MET cc_start: 0.9147 (mtp) cc_final: 0.8823 (mmp) REVERT: A 585 GLU cc_start: 0.9434 (pm20) cc_final: 0.9023 (tp30) REVERT: A 634 ASP cc_start: 0.8117 (t0) cc_final: 0.7908 (p0) REVERT: A 896 GLU cc_start: 0.7876 (mm-30) cc_final: 0.7316 (mm-30) REVERT: A 942 MET cc_start: 0.8850 (mpp) cc_final: 0.8541 (pmm) REVERT: A 954 MET cc_start: 0.8658 (OUTLIER) cc_final: 0.8397 (mmt) REVERT: A 1009 TYR cc_start: 0.9005 (t80) cc_final: 0.8493 (t80) REVERT: A 1018 LYS cc_start: 0.9123 (mttt) cc_final: 0.8806 (mmmm) outliers start: 26 outliers final: 11 residues processed: 84 average time/residue: 0.5531 time to fit residues: 49.4493 Evaluate side-chains 75 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 179 GLN Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 792 ASN Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1001 LEU Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 5 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 45 optimal weight: 5.9990 chunk 62 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 664 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.085849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.062299 restraints weight = 32177.506| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 5.07 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2934 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2934 r_free = 0.2934 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2934 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8191 Z= 0.168 Angle : 0.653 10.577 11145 Z= 0.320 Chirality : 0.044 0.195 1287 Planarity : 0.005 0.056 1401 Dihedral : 11.636 158.394 1240 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 3.24 % Allowed : 28.79 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % 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 are not related in a simple way. whole: 1.14 (0.28), residues: 979 helix: 2.02 (0.25), residues: 460 sheet: -0.19 (0.42), residues: 154 loop : -0.40 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 184 TYR 0.008 0.001 TYR A1009 PHE 0.017 0.001 PHE A 155 TRP 0.011 0.001 TRP A 335 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 8191) covalent geometry : angle 0.65291 (11145) hydrogen bonds : bond 0.03597 ( 392) hydrogen bonds : angle 4.39426 ( 1122) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9233 (OUTLIER) cc_final: 0.9021 (mp) REVERT: A 297 ASP cc_start: 0.6269 (OUTLIER) cc_final: 0.5514 (p0) REVERT: A 358 MET cc_start: 0.9184 (mtp) cc_final: 0.8846 (mmp) REVERT: A 585 GLU cc_start: 0.9455 (pm20) cc_final: 0.9029 (tp30) REVERT: A 792 ASN cc_start: 0.9169 (p0) cc_final: 0.8743 (p0) REVERT: A 896 GLU cc_start: 0.7971 (mm-30) cc_final: 0.7461 (mm-30) REVERT: A 942 MET cc_start: 0.8921 (mpp) cc_final: 0.8618 (pmm) REVERT: A 954 MET cc_start: 0.8698 (OUTLIER) cc_final: 0.8432 (mmt) REVERT: A 1009 TYR cc_start: 0.9028 (t80) cc_final: 0.8542 (t80) REVERT: A 1018 LYS cc_start: 0.9172 (mttt) cc_final: 0.8849 (mmmm) outliers start: 27 outliers final: 10 residues processed: 81 average time/residue: 0.5128 time to fit residues: 44.2798 Evaluate side-chains 69 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 821 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1076 LEU Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 87 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 3 optimal weight: 0.2980 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 60 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.087149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.063735 restraints weight = 31803.195| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 5.03 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8191 Z= 0.124 Angle : 0.643 11.767 11145 Z= 0.312 Chirality : 0.044 0.283 1287 Planarity : 0.004 0.042 1401 Dihedral : 11.547 153.821 1240 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 2.43 % Allowed : 29.60 % Favored : 67.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % 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 are not related in a simple way. whole: 1.16 (0.28), residues: 979 helix: 2.03 (0.24), residues: 459 sheet: -0.08 (0.41), residues: 164 loop : -0.43 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 184 TYR 0.006 0.001 TYR A 619 PHE 0.013 0.001 PHE A 667 TRP 0.010 0.001 TRP A 335 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8191) covalent geometry : angle 0.64309 (11145) hydrogen bonds : bond 0.03317 ( 392) hydrogen bonds : angle 4.31333 ( 1122) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 64 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9224 (OUTLIER) cc_final: 0.8992 (mp) REVERT: A 297 ASP cc_start: 0.6246 (OUTLIER) cc_final: 0.5540 (p0) REVERT: A 358 MET cc_start: 0.9166 (mtp) cc_final: 0.8828 (mmp) REVERT: A 585 GLU cc_start: 0.9458 (pm20) cc_final: 0.9011 (tp30) REVERT: A 792 ASN cc_start: 0.9169 (p0) cc_final: 0.8778 (p0) REVERT: A 896 GLU cc_start: 0.7977 (mm-30) cc_final: 0.7495 (mm-30) REVERT: A 942 MET cc_start: 0.8899 (mpp) cc_final: 0.8588 (pmm) REVERT: A 954 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8417 (mmt) REVERT: A 998 ASP cc_start: 0.8367 (OUTLIER) cc_final: 0.7766 (p0) REVERT: A 1009 TYR cc_start: 0.8993 (t80) cc_final: 0.8522 (t80) REVERT: A 1018 LYS cc_start: 0.9140 (mttt) cc_final: 0.8801 (mmmm) outliers start: 20 outliers final: 9 residues processed: 80 average time/residue: 0.5133 time to fit residues: 44.0118 Evaluate side-chains 74 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 14 optimal weight: 8.9990 chunk 16 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 97 optimal weight: 0.9990 chunk 15 optimal weight: 0.2980 chunk 39 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 94 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.086099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.064997 restraints weight = 19105.782| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 3.96 r_work: 0.2846 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2844 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2844 r_free = 0.2844 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2844 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8191 Z= 0.123 Angle : 0.653 12.255 11145 Z= 0.314 Chirality : 0.044 0.273 1287 Planarity : 0.004 0.041 1401 Dihedral : 11.485 151.612 1240 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 2.20 % Allowed : 29.94 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % 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 are not related in a simple way. whole: 1.17 (0.28), residues: 979 helix: 2.01 (0.24), residues: 459 sheet: -0.04 (0.42), residues: 164 loop : -0.41 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 367 TYR 0.005 0.001 TYR A 685 PHE 0.012 0.001 PHE A 667 TRP 0.010 0.001 TRP A 335 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 8191) covalent geometry : angle 0.65292 (11145) hydrogen bonds : bond 0.03322 ( 392) hydrogen bonds : angle 4.29837 ( 1122) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 LEU cc_start: 0.8728 (tp) cc_final: 0.8448 (tt) REVERT: A 297 ASP cc_start: 0.6121 (OUTLIER) cc_final: 0.5453 (p0) REVERT: A 358 MET cc_start: 0.9351 (mtp) cc_final: 0.8924 (mmp) REVERT: A 585 GLU cc_start: 0.9437 (pm20) cc_final: 0.8979 (tp30) REVERT: A 792 ASN cc_start: 0.9289 (p0) cc_final: 0.8909 (p0) REVERT: A 796 GLU cc_start: 0.8351 (tt0) cc_final: 0.8144 (pt0) REVERT: A 896 GLU cc_start: 0.8124 (mm-30) cc_final: 0.7644 (mm-30) REVERT: A 942 MET cc_start: 0.8834 (mpp) cc_final: 0.8520 (pmm) REVERT: A 954 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8537 (mmt) REVERT: A 998 ASP cc_start: 0.8188 (OUTLIER) cc_final: 0.7656 (p0) REVERT: A 1009 TYR cc_start: 0.9268 (t80) cc_final: 0.8864 (t80) REVERT: A 1018 LYS cc_start: 0.9147 (mttt) cc_final: 0.8853 (mmmm) outliers start: 18 outliers final: 9 residues processed: 75 average time/residue: 0.5664 time to fit residues: 45.3461 Evaluate side-chains 71 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 51 optimal weight: 5.9990 chunk 55 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 86 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.086936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.064406 restraints weight = 25656.256| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 4.58 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8191 Z= 0.132 Angle : 0.665 12.821 11145 Z= 0.322 Chirality : 0.044 0.264 1287 Planarity : 0.004 0.041 1401 Dihedral : 11.477 151.713 1240 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.89 % Favored : 96.01 % Rotamer: Outliers : 1.85 % Allowed : 29.94 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % 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 are not related in a simple way. whole: 1.16 (0.28), residues: 979 helix: 1.97 (0.24), residues: 459 sheet: -0.12 (0.42), residues: 154 loop : -0.30 (0.35), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 367 TYR 0.006 0.001 TYR A 890 PHE 0.012 0.001 PHE A 667 TRP 0.010 0.001 TRP A 335 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8191) covalent geometry : angle 0.66527 (11145) hydrogen bonds : bond 0.03321 ( 392) hydrogen bonds : angle 4.35716 ( 1122) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6189 (OUTLIER) cc_final: 0.5501 (p0) REVERT: A 358 MET cc_start: 0.9192 (mtp) cc_final: 0.8835 (mmp) REVERT: A 585 GLU cc_start: 0.9451 (pm20) cc_final: 0.8996 (tp30) REVERT: A 792 ASN cc_start: 0.9179 (p0) cc_final: 0.8790 (p0) REVERT: A 896 GLU cc_start: 0.8028 (mm-30) cc_final: 0.7517 (mm-30) REVERT: A 942 MET cc_start: 0.8900 (mpp) cc_final: 0.8581 (pmm) REVERT: A 954 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.8357 (mmt) REVERT: A 998 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7768 (p0) REVERT: A 1009 TYR cc_start: 0.9015 (t80) cc_final: 0.8596 (t80) REVERT: A 1018 LYS cc_start: 0.9156 (mttt) cc_final: 0.8814 (mmmm) outliers start: 15 outliers final: 10 residues processed: 70 average time/residue: 0.5901 time to fit residues: 43.7169 Evaluate side-chains 74 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 629 MET Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 61 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.086338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.063035 restraints weight = 32171.541| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 5.08 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2960 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2960 r_free = 0.2960 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2960 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8191 Z= 0.143 Angle : 0.674 13.210 11145 Z= 0.325 Chirality : 0.044 0.265 1287 Planarity : 0.004 0.041 1401 Dihedral : 11.465 152.538 1240 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 1.97 % Allowed : 29.83 % Favored : 68.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % 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 are not related in a simple way. whole: 1.12 (0.28), residues: 979 helix: 1.94 (0.24), residues: 460 sheet: -0.12 (0.42), residues: 154 loop : -0.36 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 367 TYR 0.007 0.001 TYR A 890 PHE 0.012 0.001 PHE A 667 TRP 0.010 0.001 TRP A 335 HIS 0.003 0.001 HIS A 746 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 8191) covalent geometry : angle 0.67425 (11145) hydrogen bonds : bond 0.03379 ( 392) hydrogen bonds : angle 4.35328 ( 1122) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6243 (OUTLIER) cc_final: 0.5587 (p0) REVERT: A 358 MET cc_start: 0.9203 (mtp) cc_final: 0.8838 (mmp) REVERT: A 585 GLU cc_start: 0.9481 (pm20) cc_final: 0.9007 (tp30) REVERT: A 792 ASN cc_start: 0.9168 (p0) cc_final: 0.8783 (p0) REVERT: A 896 GLU cc_start: 0.8016 (mm-30) cc_final: 0.7484 (mm-30) REVERT: A 942 MET cc_start: 0.8910 (mpp) cc_final: 0.8595 (pmm) REVERT: A 954 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8430 (mmt) REVERT: A 998 ASP cc_start: 0.8294 (OUTLIER) cc_final: 0.7728 (p0) REVERT: A 1009 TYR cc_start: 0.9028 (t80) cc_final: 0.8628 (t80) REVERT: A 1018 LYS cc_start: 0.9166 (mttt) cc_final: 0.8826 (mmmm) outliers start: 16 outliers final: 9 residues processed: 72 average time/residue: 0.5618 time to fit residues: 43.2051 Evaluate side-chains 72 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 389 MET Chi-restraints excluded: chain A residue 581 VAL Chi-restraints excluded: chain A residue 729 ILE Chi-restraints excluded: chain A residue 762 LEU Chi-restraints excluded: chain A residue 871 MET Chi-restraints excluded: chain A residue 954 MET Chi-restraints excluded: chain A residue 998 ASP Chi-restraints excluded: chain A residue 1004 LEU Chi-restraints excluded: chain A residue 1148 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 8.9990 chunk 78 optimal weight: 4.9990 chunk 92 optimal weight: 0.0670 chunk 4 optimal weight: 6.9990 chunk 93 optimal weight: 5.9990 chunk 89 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 98 optimal weight: 7.9990 chunk 22 optimal weight: 0.1980 chunk 75 optimal weight: 0.7980 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.087829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.064288 restraints weight = 34912.081| |-----------------------------------------------------------------------------| r_work (start): 0.2988 rms_B_bonded: 5.35 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8191 Z= 0.123 Angle : 0.672 13.283 11145 Z= 0.324 Chirality : 0.044 0.281 1287 Planarity : 0.004 0.041 1401 Dihedral : 11.423 149.041 1240 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 1.85 % Allowed : 30.06 % Favored : 68.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.11 % 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 are not related in a simple way. whole: 1.07 (0.28), residues: 979 helix: 1.89 (0.24), residues: 459 sheet: -0.03 (0.41), residues: 164 loop : -0.43 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 367 TYR 0.005 0.001 TYR A 619 PHE 0.012 0.001 PHE A 667 TRP 0.010 0.001 TRP A 335 HIS 0.004 0.001 HIS A 746 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8191) covalent geometry : angle 0.67182 (11145) hydrogen bonds : bond 0.03239 ( 392) hydrogen bonds : angle 4.33229 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2403.10 seconds wall clock time: 41 minutes 43.30 seconds (2503.30 seconds total)