Starting phenix.real_space_refine on Thu Aug 6 10:00:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8b9i_15932/08_2026/8b9i_15932.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b9i_15932/08_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8b9i_15932/08_2026/8b9i_15932.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8b9i_15932/08_2026/8b9i_15932.cif" model { file = "/net/cci-nas-00/data/ceres_data/8b9i_15932/08_2026/8b9i_15932.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b9i_15932/08_2026/8b9i_15932.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8b9i_15932/08_2026/8b9i_15932.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b9i_15932/08_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-2.2rc3-6140/lib/python3.11/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: {'RNAv2': 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: 14 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: 3.26, per 1000 atoms: 0.41 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: 0.71 Conformation dependent library (CDL) restraints added in 547.7 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: 1.51 Time building geometry restraints manager: 0.94 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 - 31.02: 4694 31.02 - 62.03: 287 62.03 - 93.05: 26 93.05 - 124.07: 1 124.07 - 155.08: 2 Dihedral angle restraints: 5010 sinusoidal: 2124 harmonic: 2886 Sorted by residual: dihedral pdb=" O5' U C 6 " pdb=" C5' U C 6 " pdb=" C4' U C 6 " pdb=" C3' U C 6 " ideal model delta sinusoidal sigma weight residual -180.00 -125.58 -54.42 3 6.40e+00 2.44e-02 5.10e+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 5007 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 982 0.050 - 0.100: 228 0.100 - 0.150: 62 0.150 - 0.200: 6 0.200 - 0.251: 9 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=" P U C 3 " pdb=" OP1 U C 3 " pdb=" OP2 U C 3 " pdb=" O5' U C 3 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" P C C 2 " pdb=" OP1 C C 2 " pdb=" OP2 C C 2 " pdb=" O5' C C 2 " both_signs ideal model delta sigma weight residual True 2.17 -2.41 -0.24 2.00e-01 2.50e+01 1.45e+00 ... (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: 1.270 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.020 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 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 : 1.248 70.773 11145 Z= 0.516 Chirality : 0.050 0.251 1287 Planarity : 0.008 0.197 1401 Dihedral : 18.882 155.085 3130 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/Z covalent geometry : bond 0.01100 / 0.74 ( 8191) covalent geometry : angle 1.24847 / 0.52 (11145) hydrogen bonds : bond 0.13279 / 8.56 ( 392) hydrogen bonds : angle 5.29879 / 3.68 ( 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 : 0.341 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: 0.5056 time to fit residues: 80.1663 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... 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 = 0.3470 r_free = 0.3470 target = 0.090829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.068171 restraints weight = 22285.212| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 4.27 r_work: 0.2852 rms_B_bonded: 4.90 restraints_weight: 0.5000 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2870 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2870 r_free = 0.2870 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 = 0.2870 r_free = 0.2870 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2870 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.090 8191 Z= 0.135 Angle : 0.722 11.560 11145 Z= 0.345 Chirality : 0.049 0.582 1287 Planarity : 0.006 0.055 1401 Dihedral : 9.449 135.125 1214 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 4.74 % Allowed : 28.90 % 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: 0.96 (0.28), residues: 979 helix: 1.85 (0.24), residues: 457 sheet: -0.27 (0.39), residues: 179 loop : -0.44 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 844 TYR 0.008 0.001 TYR A 619 PHE 0.014 0.001 PHE A 667 TRP 0.023 0.001 TRP A 335 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 ( 8191) covalent geometry : angle 0.72227 / 0.35 (11145) hydrogen bonds : bond 0.03717 / 2.54 ( 392) hydrogen bonds : angle 4.60844 / 3.22 ( 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 118 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 77 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: 0.9191 (OUTLIER) cc_final: 0.8968 (mp) REVERT: A 229 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.9030 (mtpp) REVERT: A 297 ASP cc_start: 0.6071 (OUTLIER) cc_final: 0.5146 (p0) REVERT: A 389 MET cc_start: 0.8970 (OUTLIER) cc_final: 0.8665 (tpp) REVERT: A 585 GLU cc_start: 0.9400 (pm20) cc_final: 0.8981 (tp30) REVERT: A 954 MET cc_start: 0.8991 (OUTLIER) cc_final: 0.8731 (mmt) outliers start: 41 outliers final: 13 residues processed: 111 average time/residue: 0.4949 time to fit residues: 58.6859 Evaluate side-chains 84 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 66 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 229 LYS 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: 4.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 5.9990 chunk 73 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 72 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3451 r_free = 0.3451 target = 0.089090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.066107 restraints weight = 26118.986| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 4.58 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 8191 Z= 0.136 Angle : 0.692 10.209 11145 Z= 0.331 Chirality : 0.048 0.582 1287 Planarity : 0.005 0.053 1401 Dihedral : 8.709 135.179 1208 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.58 % Favored : 96.32 % Rotamer: Outliers : 3.35 % Allowed : 28.90 % Favored : 67.75 % 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: 1.04 (0.28), residues: 979 helix: 1.94 (0.24), residues: 457 sheet: -0.20 (0.39), residues: 179 loop : -0.47 (0.36), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 844 TYR 0.011 0.001 TYR A1009 PHE 0.014 0.001 PHE A 667 TRP 0.015 0.001 TRP A 335 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 8191) covalent geometry : angle 0.69188 / 0.33 (11145) hydrogen bonds : bond 0.03504 / 2.41 ( 392) hydrogen bonds : angle 4.42793 / 3.09 ( 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 105 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 76 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9214 (OUTLIER) cc_final: 0.8996 (mp) REVERT: A 219 GLU cc_start: 0.7288 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: A 229 LYS cc_start: 0.9370 (OUTLIER) cc_final: 0.9047 (mtpp) REVERT: A 297 ASP cc_start: 0.6135 (OUTLIER) cc_final: 0.5261 (p0) REVERT: A 358 MET cc_start: 0.9083 (mtp) cc_final: 0.8847 (mmp) REVERT: A 585 GLU cc_start: 0.9429 (pm20) cc_final: 0.9045 (tp30) REVERT: A 954 MET cc_start: 0.8663 (OUTLIER) cc_final: 0.8357 (mmt) REVERT: A 1009 TYR cc_start: 0.8809 (t80) cc_final: 0.8566 (t80) REVERT: A 1018 LYS cc_start: 0.9070 (mttt) cc_final: 0.8769 (mmmm) outliers start: 29 outliers final: 12 residues processed: 99 average time/residue: 0.4804 time to fit residues: 50.8615 Evaluate side-chains 83 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 ASN Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 229 LYS Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 297 ASP Chi-restraints excluded: chain A residue 415 THR 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: 6.9990 chunk 25 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 61 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 64 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 ASN A 440 GLN A 911 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.060714 restraints weight = 34897.207| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 5.18 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2897 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2897 r_free = 0.2897 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2897 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.2990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 8191 Z= 0.243 Angle : 0.721 8.928 11145 Z= 0.349 Chirality : 0.050 0.535 1287 Planarity : 0.005 0.049 1401 Dihedral : 8.388 132.093 1202 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.60 % Rotamer: Outliers : 4.16 % Allowed : 27.75 % 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: 1.01 (0.28), residues: 979 helix: 1.89 (0.24), residues: 458 sheet: -0.20 (0.42), residues: 154 loop : -0.45 (0.35), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 844 TYR 0.016 0.001 TYR A1009 PHE 0.014 0.002 PHE A 667 TRP 0.016 0.001 TRP A 335 HIS 0.005 0.001 HIS A 910 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.24 ( 8191) covalent geometry : angle 0.72078 / 0.35 (11145) hydrogen bonds : bond 0.04056 / 2.85 ( 392) hydrogen bonds : angle 4.53566 / 3.16 ( 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 96 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 61 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9226 (OUTLIER) cc_final: 0.8970 (mp) REVERT: A 179 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.8896 (tm-30) REVERT: A 219 GLU cc_start: 0.7443 (OUTLIER) cc_final: 0.7181 (mp0) REVERT: A 297 ASP cc_start: 0.6246 (OUTLIER) cc_final: 0.5395 (p0) REVERT: A 358 MET cc_start: 0.9179 (mtp) cc_final: 0.8916 (mmp) REVERT: A 585 GLU cc_start: 0.9446 (pm20) cc_final: 0.9012 (tp30) REVERT: A 634 ASP cc_start: 0.8231 (t0) cc_final: 0.7972 (p0) REVERT: A 942 MET cc_start: 0.8886 (mpp) cc_final: 0.8527 (pmm) REVERT: A 954 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8477 (mmt) REVERT: A 1009 TYR cc_start: 0.8957 (t80) cc_final: 0.8726 (t80) REVERT: A 1018 LYS cc_start: 0.9115 (mttt) cc_final: 0.8828 (mmmm) REVERT: A 1080 ARG cc_start: 0.7946 (mmt180) cc_final: 0.7629 (mmt180) outliers start: 35 outliers final: 11 residues processed: 91 average time/residue: 0.4528 time to fit residues: 44.1955 Evaluate side-chains 74 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 179 GLN 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 415 THR Chi-restraints excluded: chain A residue 449 VAL 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: 3.9990 chunk 89 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 28 optimal weight: 4.9990 chunk 66 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1097 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.086562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.063651 restraints weight = 25863.069| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 4.59 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.3218 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= 0.140 Angle : 0.663 10.430 11145 Z= 0.318 Chirality : 0.047 0.519 1287 Planarity : 0.005 0.049 1401 Dihedral : 8.097 124.287 1200 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 3.35 % Allowed : 28.21 % Favored : 68.44 % 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: 1.96 (0.24), residues: 460 sheet: -0.19 (0.39), residues: 174 loop : -0.44 (0.36), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 844 TYR 0.008 0.001 TYR A1009 PHE 0.016 0.001 PHE A 155 TRP 0.012 0.001 TRP A 335 HIS 0.003 0.001 HIS A 691 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 8191) covalent geometry : angle 0.66328 / 0.32 (11145) hydrogen bonds : bond 0.03434 / 2.39 ( 392) hydrogen bonds : angle 4.37759 / 3.06 ( 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 89 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 61 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9213 (OUTLIER) cc_final: 0.8994 (mp) REVERT: A 297 ASP cc_start: 0.6371 (OUTLIER) cc_final: 0.5578 (p0) REVERT: A 358 MET cc_start: 0.9152 (mtp) cc_final: 0.8833 (mmp) REVERT: A 585 GLU cc_start: 0.9424 (pm20) cc_final: 0.8995 (tp30) REVERT: A 634 ASP cc_start: 0.8164 (t0) cc_final: 0.7922 (p0) REVERT: A 797 MET cc_start: 0.9078 (ttm) cc_final: 0.8870 (tpt) REVERT: A 896 GLU cc_start: 0.7829 (mm-30) cc_final: 0.7256 (mm-30) REVERT: A 942 MET cc_start: 0.8872 (mpp) cc_final: 0.8563 (pmm) REVERT: A 954 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8403 (mmt) REVERT: A 1009 TYR cc_start: 0.8946 (t80) cc_final: 0.8642 (t80) REVERT: A 1018 LYS cc_start: 0.9099 (mttt) cc_final: 0.8785 (mmmm) outliers start: 28 outliers final: 12 residues processed: 84 average time/residue: 0.5090 time to fit residues: 45.9525 Evaluate side-chains 74 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 ILE 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 415 THR 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 1076 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: 4.9990 chunk 66 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 46 optimal weight: 0.9980 chunk 33 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 212 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.085756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.062405 restraints weight = 32195.799| |-----------------------------------------------------------------------------| r_work (start): 0.2939 rms_B_bonded: 5.02 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2938 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2938 r_free = 0.2938 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2938 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.3385 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= 0.156 Angle : 0.665 10.508 11145 Z= 0.318 Chirality : 0.047 0.545 1287 Planarity : 0.005 0.053 1401 Dihedral : 7.892 121.263 1200 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 3.01 % Allowed : 28.44 % Favored : 68.55 % 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: 1.13 (0.28), residues: 979 helix: 2.00 (0.24), residues: 460 sheet: -0.19 (0.42), residues: 154 loop : -0.38 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 184 TYR 0.009 0.001 TYR A1009 PHE 0.018 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/Z covalent geometry : bond 0.00367 / 0.16 ( 8191) covalent geometry : angle 0.66545 / 0.32 (11145) hydrogen bonds : bond 0.03555 / 2.48 ( 392) hydrogen bonds : angle 4.35222 / 3.04 ( 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 83 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 58 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.9004 (mp) REVERT: A 297 ASP cc_start: 0.6327 (OUTLIER) cc_final: 0.5554 (p0) REVERT: A 358 MET cc_start: 0.9168 (mtp) cc_final: 0.8842 (mmp) REVERT: A 585 GLU cc_start: 0.9454 (pm20) cc_final: 0.9007 (tp30) REVERT: A 627 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8462 (tmm) REVERT: A 634 ASP cc_start: 0.8187 (t0) cc_final: 0.7963 (p0) REVERT: A 896 GLU cc_start: 0.7906 (mm-30) cc_final: 0.7389 (mm-30) REVERT: A 942 MET cc_start: 0.8928 (mpp) cc_final: 0.8619 (pmm) REVERT: A 954 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8418 (mmt) REVERT: A 1009 TYR cc_start: 0.8982 (t80) cc_final: 0.8574 (t80) REVERT: A 1018 LYS cc_start: 0.9149 (mttt) cc_final: 0.8831 (mmmm) outliers start: 25 outliers final: 11 residues processed: 79 average time/residue: 0.4892 time to fit residues: 41.6625 Evaluate side-chains 72 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.407 ------------------------------------------------------------------------------- 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 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 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 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: 0.8980 chunk 83 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 91 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 44 optimal weight: 8.9990 chunk 1 optimal weight: 0.0470 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.087215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.063984 restraints weight = 31765.246| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 4.99 r_work (final): 0.2981 ------------------------------------------------------------------------------- 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 = 0.28 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 = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2979 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.3561 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= 0.123 Angle : 0.655 11.539 11145 Z= 0.310 Chirality : 0.047 0.539 1287 Planarity : 0.004 0.043 1401 Dihedral : 7.776 117.147 1200 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.68 % Favored : 96.22 % Rotamer: Outliers : 2.66 % Allowed : 29.13 % 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: 1.14 (0.28), residues: 979 helix: 2.02 (0.24), residues: 460 sheet: -0.09 (0.41), residues: 164 loop : -0.46 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 367 TYR 0.006 0.001 TYR A1009 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/Z covalent geometry : bond 0.00292 / 0.12 ( 8191) covalent geometry : angle 0.65502 / 0.31 (11145) hydrogen bonds : bond 0.03289 / 2.29 ( 392) hydrogen bonds : angle 4.25047 / 2.97 ( 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 85 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 63 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9245 (OUTLIER) cc_final: 0.9037 (mp) REVERT: A 233 LEU cc_start: 0.8825 (tp) cc_final: 0.8568 (tt) REVERT: A 297 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.5582 (p0) REVERT: A 358 MET cc_start: 0.9130 (mtp) cc_final: 0.8821 (mmp) REVERT: A 585 GLU cc_start: 0.9454 (pm20) cc_final: 0.9018 (tp30) REVERT: A 627 MET cc_start: 0.9151 (OUTLIER) cc_final: 0.8502 (tmm) REVERT: A 717 THR cc_start: 0.9063 (m) cc_final: 0.8630 (p) REVERT: A 792 ASN cc_start: 0.9161 (p0) cc_final: 0.8762 (p0) REVERT: A 896 GLU cc_start: 0.7871 (mm-30) cc_final: 0.7340 (mm-30) REVERT: A 942 MET cc_start: 0.8916 (mpp) cc_final: 0.8609 (pmm) REVERT: A 954 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8350 (mmt) REVERT: A 998 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.7840 (p0) REVERT: A 1018 LYS cc_start: 0.9153 (mttt) cc_final: 0.8829 (mmmm) outliers start: 22 outliers final: 9 residues processed: 80 average time/residue: 0.5370 time to fit residues: 46.1602 Evaluate side-chains 74 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 871 MET 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 97 optimal weight: 0.2980 chunk 15 optimal weight: 7.9990 chunk 39 optimal weight: 0.7980 chunk 37 optimal weight: 0.7980 chunk 94 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.086770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.065301 restraints weight = 19112.539| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 4.02 r_work: 0.2842 rms_B_bonded: 4.66 restraints_weight: 0.5000 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2840 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2840 r_free = 0.2840 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 = 0.2840 r_free = 0.2840 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (9 function evaluations) r_final: 0.2840 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.3695 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= 0.121 Angle : 0.661 11.870 11145 Z= 0.313 Chirality : 0.047 0.549 1287 Planarity : 0.004 0.043 1401 Dihedral : 7.715 115.851 1200 Min Nonbonded Distance : 2.012 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 2.20 % Allowed : 29.83 % 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: 1.18 (0.28), residues: 979 helix: 2.03 (0.24), residues: 460 sheet: -0.06 (0.41), residues: 164 loop : -0.42 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 367 TYR 0.006 0.001 TYR A 187 PHE 0.014 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/Z covalent geometry : bond 0.00288 / 0.12 ( 8191) covalent geometry : angle 0.66129 / 0.31 (11145) hydrogen bonds : bond 0.03253 / 2.27 ( 392) hydrogen bonds : angle 4.18311 / 2.92 ( 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 78 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 ILE cc_start: 0.9115 (OUTLIER) cc_final: 0.8888 (mp) REVERT: A 233 LEU cc_start: 0.8729 (tp) cc_final: 0.8478 (tt) REVERT: A 297 ASP cc_start: 0.6054 (OUTLIER) cc_final: 0.5384 (p0) REVERT: A 358 MET cc_start: 0.9362 (mtp) cc_final: 0.8940 (mmp) REVERT: A 585 GLU cc_start: 0.9465 (pm20) cc_final: 0.8991 (tp30) REVERT: A 627 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8527 (tmm) REVERT: A 792 ASN cc_start: 0.9292 (p0) cc_final: 0.8898 (p0) REVERT: A 896 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7417 (mm-30) REVERT: A 942 MET cc_start: 0.8848 (mpp) cc_final: 0.8534 (pmm) REVERT: A 954 MET cc_start: 0.8854 (OUTLIER) cc_final: 0.8543 (mmt) REVERT: A 998 ASP cc_start: 0.8285 (OUTLIER) cc_final: 0.7643 (p0) REVERT: A 1009 TYR cc_start: 0.9257 (t80) cc_final: 0.8740 (t80) REVERT: A 1018 LYS cc_start: 0.9146 (mttt) cc_final: 0.8853 (mmmm) REVERT: A 1080 ARG cc_start: 0.7401 (mtt-85) cc_final: 0.6722 (mtt-85) outliers start: 18 outliers final: 9 residues processed: 73 average time/residue: 0.5209 time to fit residues: 40.9255 Evaluate side-chains 71 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 57 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 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 871 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 51 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 10 optimal weight: 3.9990 chunk 90 optimal weight: 0.9990 chunk 31 optimal weight: 0.2980 chunk 86 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.087520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.064532 restraints weight = 25736.856| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 4.65 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2950 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2950 r_free = 0.2950 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2950 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3731 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= 0.148 Angle : 0.680 12.690 11145 Z= 0.322 Chirality : 0.048 0.557 1287 Planarity : 0.004 0.043 1401 Dihedral : 7.697 118.036 1200 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.11 % 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: 1.20 (0.28), residues: 979 helix: 2.03 (0.24), residues: 460 sheet: -0.11 (0.43), residues: 154 loop : -0.33 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 367 TYR 0.008 0.001 TYR A 890 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/Z covalent geometry : bond 0.00353 / 0.15 ( 8191) covalent geometry : angle 0.68043 / 0.32 (11145) hydrogen bonds : bond 0.03427 / 2.39 ( 392) hydrogen bonds : angle 4.23737 / 2.95 ( 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 77 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 57 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6174 (OUTLIER) cc_final: 0.5517 (p0) REVERT: A 358 MET cc_start: 0.9248 (mtp) cc_final: 0.8861 (mmp) REVERT: A 585 GLU cc_start: 0.9475 (pm20) cc_final: 0.8982 (tp30) REVERT: A 627 MET cc_start: 0.9132 (OUTLIER) cc_final: 0.8401 (tmm) REVERT: A 792 ASN cc_start: 0.9196 (p0) cc_final: 0.8791 (p0) REVERT: A 896 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7365 (mm-30) REVERT: A 942 MET cc_start: 0.8919 (mpp) cc_final: 0.8600 (pmm) REVERT: A 954 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8414 (mmt) REVERT: A 998 ASP cc_start: 0.8356 (OUTLIER) cc_final: 0.7768 (p0) REVERT: A 1009 TYR cc_start: 0.9025 (t80) cc_final: 0.8404 (t80) REVERT: A 1018 LYS cc_start: 0.9153 (mttt) cc_final: 0.8822 (mmmm) REVERT: A 1080 ARG cc_start: 0.7511 (mtt-85) cc_final: 0.6884 (mtt-85) outliers start: 20 outliers final: 9 residues processed: 72 average time/residue: 0.4748 time to fit residues: 36.6497 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 : 0.223 ------------------------------------------------------------------------------- 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 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 871 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 61 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 85 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 58 optimal weight: 7.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.086910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.063466 restraints weight = 32097.449| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 5.13 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8191 Z= 0.136 Angle : 0.687 13.249 11145 Z= 0.326 Chirality : 0.048 0.548 1287 Planarity : 0.004 0.043 1401 Dihedral : 7.698 118.110 1200 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.06 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: 1.10 (0.28), residues: 979 helix: 1.92 (0.24), residues: 460 sheet: -0.11 (0.43), residues: 154 loop : -0.38 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 367 TYR 0.006 0.001 TYR A 890 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/Z covalent geometry : bond 0.00329 / 0.14 ( 8191) covalent geometry : angle 0.68748 / 0.33 (11145) hydrogen bonds : bond 0.03344 / 2.31 ( 392) hydrogen bonds : angle 4.29214 / 3.03 ( 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 71 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 ASP cc_start: 0.6105 (OUTLIER) cc_final: 0.5454 (p0) REVERT: A 358 MET cc_start: 0.9223 (mtp) cc_final: 0.8857 (mmp) REVERT: A 585 GLU cc_start: 0.9489 (pm20) cc_final: 0.8999 (tp30) REVERT: A 627 MET cc_start: 0.9147 (OUTLIER) cc_final: 0.8424 (tmm) REVERT: A 792 ASN cc_start: 0.9197 (p0) cc_final: 0.8794 (p0) REVERT: A 896 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7303 (mm-30) REVERT: A 942 MET cc_start: 0.8922 (mpp) cc_final: 0.8603 (pmm) REVERT: A 954 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8404 (mmt) REVERT: A 998 ASP cc_start: 0.8350 (OUTLIER) cc_final: 0.7744 (p0) REVERT: A 1009 TYR cc_start: 0.9021 (t80) cc_final: 0.8429 (t80) REVERT: A 1018 LYS cc_start: 0.9156 (mttt) cc_final: 0.8816 (mmmm) REVERT: A 1080 ARG cc_start: 0.7507 (mtt-85) cc_final: 0.6890 (mtt-85) outliers start: 15 outliers final: 9 residues processed: 67 average time/residue: 0.5810 time to fit residues: 41.6587 Evaluate side-chains 70 residues out of total 866 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.240 ------------------------------------------------------------------------------- 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 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 871 MET 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 88 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 89 optimal weight: 0.9980 chunk 25 optimal weight: 0.7980 chunk 12 optimal weight: 0.3980 chunk 98 optimal weight: 6.9990 chunk 22 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.087624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.064138 restraints weight = 34974.193| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 5.32 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.29 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8191 Z= 0.129 Angle : 0.682 13.349 11145 Z= 0.323 Chirality : 0.048 0.546 1287 Planarity : 0.004 0.043 1401 Dihedral : 7.680 117.983 1200 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.78 % Favored : 96.11 % Rotamer: Outliers : 1.73 % Allowed : 30.17 % 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: 1.08 (0.28), residues: 979 helix: 1.89 (0.24), residues: 460 sheet: -0.06 (0.43), residues: 154 loop : -0.39 (0.35), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 367 TYR 0.006 0.001 TYR A 890 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/Z covalent geometry : bond 0.00311 / 0.13 ( 8191) covalent geometry : angle 0.68244 / 0.32 (11145) hydrogen bonds : bond 0.03292 / 2.27 ( 392) hydrogen bonds : angle 4.26470 / 3.01 ( 1122) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2321.44 seconds wall clock time: 40 minutes 25.05 seconds (2425.05 seconds total)